FCC ID: 2AHGG-MAURICE Protein Detection Instrument

page 1 User Guide for Maurice, Maurice C. and Maurice S. Copyright 2016 ProteinSimple. All rights reserved. ProteinSimple 3001 Orchard Parkway San Jose, CA 95134 Toll-free: (888) 607-9692 Tel: (408) 510-5500 Fax: (408) 510-5599 email: support@proteinsimple.com web: www.proteinsimple.com User Guide for Maurice, Maurice C. and Maurice S. P/N 046-295 Revision 1, February 2016 For research use only. Not for use in diagnostic procedures Patents and Trademarks ProteinSimple's Maurice and iCE technology is covered by issued and pending patents in the U.S. and other countries. For more information please see http://www.proteinsimple.com/Intellectual_Property.html. ProteinSimple and the ProteinSimple logo are trademarks or registered trademarks of ProteinSimple. Other marks appearing in these materials are marks of their respective owners. Table of Contents Chapter 1:

Lets Get Started. 1 Welcome . 2 Maurice Systems. 2 Chapter 2:

Getting Your Lab Ready . 3 Introduction . 4 Space Requirements . 4 Physical Specifications. 5 Electrical Requirements . 5 Environmental Requirements. 5 Software and Computer Requirements . 6 General Guidelines and Information. 6 Intended Use. 6 Lifting and Moving the System: Lift Maurice Correctly . 6 Chapter 3:

Maurice. 7 Maurice Systems. 8 External Components. 9 System Door . 9 Status Light . 10 Internal Components . 10 Cartridge Slot . 10 Sample and Reagent Platform . 12 Rear Panel . 14 System Labels . 14 Computer Workstation . 16 Chapter 4:

Compass for iCE Overview . 17 Launching Compass for iCE . 18 User Guide for Maurice, Maurice C. and Maurice S. page 1 Compass for iCE Overview . 18 Changing the Screen View . 19 Batch Screen . 19 Run Summary Screen . 20 Analysis Screen. 22 Screen Panes . 24 Title Bar . 24 Main Menu . 24 Instrument Status Bar . 24 Screen Tab . 25 View Bar. 25 Compass for iCE Status Bar. 25 Software Menus . 25 File Menu . 26 Edit Menu . 26 View Menu . 27 Instrument Menu . 27 Window Menu . 27 Help Menu . 28 Changing the Compass for iCE Main Window Layout . 28 Resizing the Main Compass for iCE Window . 28 Resizing the Screen Tab . 29 Resizing Screen Panes. 29 Changing the Location of Screen Panes. 30 Restoring the Main Window to the Default Layout . 32 Software Help. 32 Checking for and Installing New Versions of Compass for iCE . 32 Viewing Release Notes . 32 page 2 Viewing the Software Log. 33 Compass for iCE Version Information . 33 Directory and File Information. 34 File Types. 35 Chapter 5:

cIEF Batches. 37 Batch Screen Overview . 38 Batch Screen Panes . 38 Software Menus Active in the Batch Screen . 39 Opening a Batch . 41 Creating a New Batch . 42 Step 1 - Open a Template Batch. 42 Step 2 - Assign Your Samples. 43 Step 3 - Assign Your Method Parameters. 46 Step 4 - Set Up Your Injections. 49 Step 5 - Add Batch Notes (Optional). 51 Step 6 - Modify Default Analysis Parameters

(Optional). 52 Step 7 - Save Your Batch . 52 Viewing Replicate Injections . 53 Batch History . 54 Making Changes to a Batch . 55 Viewing and Editing Batches in Completed Runs . 56 Batch Reports. 57 Chapter 6:

CE-SDS Batches. 59 Batch Screen Overview . 60 Batch Screen Panes . 60 Software Menus Active in the Batch Screen . 61 Opening a Batch . 63 Creating a New Batch . 64 User Guide for Maurice, Maurice C. and Maurice S. Step 1 - Open a Template Batch. 64 Step 2 - Assign Your Samples. 65 Step 3 - Assign Your Method Parameters . 68 Step 4 - Set Up Your Injections. 70 Step 5 - Add Batch Notes (Optional). 73 Step 6 - Modify Default Analysis Parameters

(Optional). 73 Step 7 - Save Your Batch . 74 Viewing Replicate Injections . 75 Batch History . 76 Making Changes to a Batch . 77 Viewing and Editing Batches in Completed Runs . 78 Batch Reports . 79 Chapter 7:

Running cIEF Applications on Maurice and Maurice C. 81 Before You Throw the Switch . 82 Power Up . 82 Running cIEF Applications . 82 What Youll Need. 82 Step 1: Prep Your Markers, Samples and Reagents . 83 Step 2: Prep the Cartridge . 86 Step 3: Install the Cartridge. 88 Step 4: Load Samples and Reagents. 90 Step 5: Create a Batch . 91 Step 6: Start the Batch. 100 Post-batch Procedures. 102 Checking Your Data . 105 Step 1: Select Your Detection Mode . 105 Step 2: Check Your pI Markers . 105 page 3 Opening One Run File. 156 Opening Multiple Run Files. 156 Batch Injection Information . 157 Injection Flags . 158 Run Status Information . 159 Viewing the Focus Series (cIEF Only) . 161 Viewing the Separation (CE-SDS Only) . 162 Current and Voltage Plots. 163 Run History . 165 Viewing Multiple Events. 165 Copying History Info . 167 Viewing Run Errors. 167 Injection Reports . 168 Example Analysis and Injection Report: CE-SDS169 Example Analysis and Injection Report: cIEF. 172 Switching Between Open Run Files . 174 Closing Run Files . 175 Chapter 10:

Controlling Maurice, Maurice C. and Maurice S. 177 Instrument Control . 178 Starting a Run. 178 Cleaning . 178 Stopping a Run . 180 Status Modes . 181 Shutdown . 181 Instrument Software (Embedded) Updates . 181 Self Test . 183 Viewing and Changing System Properties . 184 Checking Cartridge Status . 185 Step 3: Checking Sample Peaks . 108 Step 4: Assigning Peak Names . 111 Chapter 8:

Running CE-SDS Applications on Maurice and Maurice S. 112 Before You Throw the Switch . 113 Power Up . 113 Running CE-SDS Applications . 113 What Youll Need . 113 Step 1: Prep Your Internal Standard, Samples and Reagents. 114 Internal Standard . 114 Step 2: Prep the Cartridge . 120 Step 3: Install the Cartridge. 122 Step 4: Load Samples and Reagents . 124 Step 5: Create a Batch. 125 Step 6: Start the Batch. 133 Post-batch Procedures. 135 Checking Your Data . 139 Step 1: Check Your Internal Standard . 139 Step 2: Set Your Molecular Weight (MW) Markers . 143 Step 3: Checking Sample Peaks . 147 Step 4: Assigning Peak Names . 150 Chapter 9:

Run Status. 151 Run Summary Screen Overview. 152 Run Summary Screen Panes . 152 Software Menus Active in the Run Summary Screen. 154 Opening Run Files . 156 User Guide for Maurice, Maurice C. and Maurice S. page 4 Viewing Log Files . 186 Runs Log . 186 System Logs. 187 Error Log . 189 Self Test Logs. 192 Command Log. 194 Chapter 11:

CE-SDS Data Analysis . 195 Analysis Screen Overview . 196 Analysis Screen Panes. 196 Software Menus Active in the Analysis Screen . 197 Opening Run Files . 199 Opening One Run File. 199 Opening Multiple Run Files. 199 How Run Data is Displayed . 201 Experiment Pane: Batch Injection Information .201 Graph Pane: Electropherogram Data . 201 Peaks Pane: Calculated Results. 202 Injections Pane: User-Specified Peak Names . 204 Viewing Run Data . 205 Switching Between Samples and Standards Data Views . 205 Selecting and Displaying Injection Data . 208 Switching Between Single and Multiple Views of Injections . 211 Hiding Injection Data . 213 Data Notifications and Warnings. 214 Checking Your Results . 215 Group Statistics . 216 Using Groups . 216 Viewing Sample Injection Groups . 217 User Guide for Maurice, Maurice C. and Maurice S. Viewing Statistics . 217 Hiding or Removing Injections in Group Analysis . 219 Copying Results Tables and Graphs. 220 Copying Results Tables . 220 Copying the Graph. 220 Saving the Graph as an Image File . 220 Exporting Run Files. 221 Exporting Results Tables. 221 Exporting Raw Sample Electropherogram Data . 221 Changing Sample Protein Identification . 222 Adding or Removing Sample Data. 222 Hiding Sample Data . 224 Changing Peak Names for Sample Data . 225 Changing the Electropherogram View. 226 Autoscaling the Electropherogram. 227 Customizing the Data Display . 227 Stacking Multiple Electropherograms . 233 Overlaying Multiple Electropherograms. 234 Zooming . 235 Selecting Data Viewing Options. 236 Adding and Removing Baseline Points . 240 Selecting the Graph X-axis Range . 241 Closing Run Files . 243 Analysis Settings Overview. 244 Advanced Analysis Settings . 246 Internal Standard Settings . 246 Advanced Analysis Settings Groups . 247 Creating a New Analysis Group . 247 Changing the Default Analysis Group. 248 page 5 Injection Reports . 278 Example Analysis and Injection Report. 280 Importing and Exporting Analysis Settings. 283 Importing Analysis Settings . 283 Exporting Analysis Settings. 283 Chapter 12:

cIEF Data Analysis. 285 Analysis Screen Overview . 286 Analysis Screen Panes . 286 Software Menus Active in the Analysis Screen . 287 Opening Run Files . 289 Opening One Run File. 289 Opening Multiple Run Files. 289 How Run Data is Displayed . 291 Experiment Pane: Batch Injection Information 291 Graph Pane: Electropherogram Data . 291 Peaks Pane: Calculated Results. 292 Injections Pane: User-Specified Peak Names. 293 Viewing Run Data . 295 Switching Between Samples and Markers Data Views. 295 Selecting and Displaying Injection Data . 298 Switching Between Single and Multiple Views of Injections. 301 Hiding Injection Data . 303 Data Notifications and Warnings. 304 Checking Your Results . 305 Group Statistics . 305 Using Groups . 306 Viewing Sample Injection Groups . 306 Viewing Statistics . 307 Modifying an Analysis Group . 249 Deleting an Analysis Group . 249 Applying Analysis Groups to Specific Run Data 250 Markers Analysis Settings . 252 Markers Settings . 253 Changing the Injection Used for the CE-SDS MW Markers . 253 Standards Analysis Settings Groups. 254 Creating a New Standards Group . 255 Changing the Default Standards Group . 258 Modifying a Standards Group. 258 Deleting a Standards Group . 258 Applying Standards Groups to Specific Run Data . 259 Peak Fit Analysis Settings . 261 Range Settings . 262 Baseline Settings . 263 Peak Find Settings . 263 Peak Fit Analysis Settings Groups . 264 Creating a New Peak Fit Group. 265 Changing the Default Peak Fit Group . 267 Modifying a Peak Fit Group . 267 Deleting a Peak Fit Group . 268 Applying Peak Fit Groups to Specific Run Data . 268 Peak Names Settings . 271 Peak Names Analysis Settings Groups. 271 Creating a Peak Names Group . 272 Modifying a Peak Names Group . 275 Deleting a Peak Names Group . 275 Applying Peak Names Groups to Run Data . 276 User Guide for Maurice, Maurice C. and Maurice S. page 6 Hiding or Removing Injections in Group Analysis . 309 Copying Results Tables and Graphs. 310 Copying Results Tables. 310 Copying the Graph. 310 Saving the Graph as an Image File. 310 Exporting Run Files . 311 Exporting Results Tables . 311 Exporting Raw Sample Electropherogram Data . 311 Changing Sample Protein Identification. 312 Adding or Removing Sample Data. 312 Hiding Sample Data . 314 Changing Peak Names for Sample Data . 315 Changing the Electropherogram View. 316 Autoscaling the Electropherogram . 317 Customizing the Data Display . 317 Stacking Multiple Electropherograms. 323 Overlaying Multiple Electropherograms . 324 Zooming. 325 Selecting Data Viewing Options . 326 Adding and Removing Baseline Points . 330 Selecting the Graph X-axis Range . 331 Closing Run Files. 333 Analysis Settings Overview. 334 Advanced Analysis Settings. 336 pI Markers Settings. 336 Advanced Analysis Settings Groups . 337 Creating a New Analysis Group . 337 Changing the Default Analysis Group. 338 Modifying an Analysis Group . 339 User Guide for Maurice, Maurice C. and Maurice S. Deleting an Analysis Group . 339 Applying Analysis Groups to Specific Run Data 340 Detection Settings . 343 Changing the Detection Method. 343 Changing the Detection Exposure . 344 Peak Fit Analysis Settings . 345 Range Settings . 346 Baseline Settings . 346 Peak Find Settings. 346 Peak Fit Analysis Settings Groups. 348 Creating a New Peak Fit Group. 348 Changing the Default Peak Fit Group . 350 Modifying a Peak Fit Group . 350 Deleting a Peak Fit Group . 351 Applying Peak Fit Groups to Specific Run Data 351 Peak Names Settings. 354 Peak Names Analysis Settings Groups. 354 Creating a Peak Names Group . 355 Modifying a Peak Names Group . 358 Deleting a Peak Names Group . 358 Applying Peak Names Groups to Run Data. 359 pI Markers Analysis Settings. 362 Markers Analysis Settings Groups . 362 Creating a New Markers Group . 363 Changing the Default Markers Group . 365 Modifying a Markers Group . 366 Deleting a Markers Group . 366 Applying Markers Groups to Specific Run Data 367 Injection Reports . 369 Example Analysis and Injection Report . 371 page 7 Importing and Exporting Analysis Settings . 374 Importing Analysis Settings . 374 Exporting Analysis Settings . 374 Password Policy Settings . 406 LDAP Settings . 407 Encryption Details. 407 Chapter 13:

Setting Your Preferences . 377 Customize Your Preferences . 378 Enabling Access Control . 379 Setting Data Export Options . 379 Selecting Custom Plot Colors for Graph Overlay . 380 Grouping Options . 382 Setting Up Maurice Systems to Send Tweets . 383 Chapter 14:

Compass Access Control and 21 CFR Part 11 Compliance . 389 Overview . 390 Enabling Access Control . 391 Logging In to Compass for iCE . 392 Locking and Unlocking the Application. 393 Resolving Log In Issues . 393 Saving Changes . 394 Signing Files . 395 Instrument Command Log . 395 Run File History . 398 Troubleshooting Problems and Suggested Solutions . 398 Authorization Server . 399 Server Administration . 400 Adding Non-admin Users . 400 Adding Admin Users . 404 Resetting User Passwords . 405 Audit Trail. 406 User Guide for Maurice, Maurice C. and Maurice S. Chapter 15:

Maintenance and Troubleshooting . 409 Cartridge Handling and Care . 410 cIEF Cartridge . 410 CE-SDS Cartridge. 411 Maintenance . 412 Daily . 412 Yearly . 413 Changing the Fuse . 413 Spare Parts. 414 Software Updates. 414 Instrument Software (Embedded) Updates . 415 Frequently Asked Questions: cIEF Applications . 415 Troubleshooting . 419 cIEF Application Troubleshooting . 419 CE-SDS Application Troubleshooting . 421 Chapter 16:

General Information . 423 Compliance. 424 Safety Guidelines. 425 Chemical Hazards . 425 Chemical Waste Hazards . 426 Waste Production and Disposal. 427 Safety Data Sheets . 427 Instrument Safety Labels . 428 Consumables and Reagents . 429 page 8 Maurice CE-SDS Consumables, Kits and Reagents. 429 Maurice cIEF Consumables, Kits and Reagents .431 Maurice Systems Consumables and Reagents .433 Customer Service and Technical Support . 433 Legal Notices . 435 Maurice Disclaimer of Warranty . 435 Compass Software and Authorization Server License Agreement. 435 User Guide for Maurice, Maurice C. and Maurice S. page 1 Chapter 1:

Lets Get Started Chapter Overview Welcome Maurice Systems User Guide for Maurice, Maurice C. and Maurice S. Welcome page 2 Welcome Congratulations on bringing Maurice into your lab! We welcome you as a new user and are excited to be a part of your work. This user guide will provide you with details on system hardware, operating the system, how to use Compass for iCE software, maintenance procedures and other useful information. To help you get the most from you new lab addition, we've added some attention phrases to guide you through the user guide:

NOTE IMPORTANT CAUTION Points out useful information. Indicates information necessary for proper operation of Maurice systems. Cautions you about potentially hazardous situations that could result in injury to you or damage to the system. Warns you that serious physical injury can result if the listed precautions arent followed.

!WARNING!

Maurice Systems Maurice, Maurice C. and Maurice S. systems give you identity, purity and heterogeneity data on your biolog-

ics, and get you to results faster with short development times and simple workflows!

They're fluent in cIEF and CE-SDS. They take cIEF up a notch, and CE-SDS is a breeze. You'll get pI and charge heterogeneity data in less than 10 minutes flat with the added bonus of same-time absorbance and native fluorescence for sensitivity down to 0.7 g/mL. Their size applications have the high res and wide molecular weight range you need and they're done in 35 minutes. They make it easy. Just pop in a ready-to-go cartridge, drop in your sample vials or a 96-well plate, and hit start they'll do the rest!

They're time-savers. Develop methods fast so you get to results even faster. Your cIEF and CE-SDS methods are done in a day. The icing? You can develop platform methods and use them for multiple molecules. No maintenance and clean-up needed between the two applications. They're dependable. Get reproducible results with tight CVs day in and day out. Your data is reliable no matter what across samples, users, instruments or labs. User Guide for Maurice, Maurice C. and Maurice S. page 3 Chapter 2:

Getting Your Lab Ready Chapter Overview General Guidelines and Information Introduction Space Requirements Physical Specifications Electrical Requirements Environmental Requirements Software and Computer Requirements User Guide for Maurice, Maurice C. and Maurice S. Introduction page 4 Introduction This chapter will help you prepare the lab for Maurice. Please have the space, electrical and environmental requirements ready prior to scheduling your installation. NOTE: Please wait for an authorized ProteinSimple Field Service Engineer to unpack and install Maurice for you. Dont try doing this yourself. Handling Maurice incorrectly could cause injury to yourself or dam-

age to the system. Space Requirements You need a lab bench or table that can support 100 lb (46 kg) and has enough space for both Maurice and his computer. There should be sufficient clearance for both heat ventilation and to provide access if Maurice needs service. IMPORTANT Maurice needs a stable surface and must remain level to work properly. The lab bench or table cant shift or wobble under heavy weight. Dont use anti-vibration tables either, since Maurice may not stay level while hes working. Dimension Width Depth Height Meters 1.5 0.8 0.5 Feet 5.0 2.5 1.5 Recommended space requirements for Maurice. User Guide for Maurice, Maurice C. and Maurice S. Physical Specifications page 5 Physical Specifications Description Maurices Dimensions (Door Closed) Maurices Dimensions (Door Open) Specification 0.44 m x 0.42 m x 0.61m (H x W x D) 1.46 x 1.38 x 2.0 (H x W x D) 0.44 m x 0.57 m x 0.61m (H x W x D) 1.46 x 2.43 x 2.0 (H x W x D) Maurices Weight 46 kg (100 lb) Computer Workstation Dimensions 0.41 m x 0.66 m x 0.76 m (H x W x D) 1.35' x 2.17' x 2.49' (H x W x D) For indoor use only. Use up to altitudes of 1524 meters (5000 feet). Table 2-1: Physical Specifications Electrical Requirements Maurice requires a dedicated, grounded circuit capable of delivering the appropriate current and voltage for your country. The power requirements for all three Maurice systems are 100 V- 240 V (AC), 50/60 Hz, 500 W. In addition to these requirements, Maurice needs the grounded circuits terminate at the receptacles, and receptacles must be located within 10 ft (3 m) of the instrument. Environmental Requirements Maurice likes a consistent temperature in the lab (not too hot not too cold). He works best when condi-

tions stay within these ranges:

Requirement Specification Operating temperature range 18 - 25 C (64 - 77 F) Operating humidity range 20-80% relative, non-condensing Table 2-2: Environmental requirements. User Guide for Maurice, Maurice C. and Maurice S. Software and Computer Requirements page 6 Software and Computer Requirements Maurice brings his own computer to the lab with Compass for iCE software pre-installed. Compass for iCE is used to run cIEF and CE-SDS applications on Maurice and analyze resulting data. Just in case you need it, a CD containing Compass for iCE software also comes in the box. If you don't want to analyze your data at Maurice's workstation in the lab, Compass for iCE software can also be installed on a separate workstation, such as your desktop computer. Your computer must meet the recommended requirements listed below to run Compass for iCE software and process data. Component Operating System Processor Memory Free Disk Space Ethernet Ports Recommended Windows 7 Core i5 6 GB 100 GB 2 - One is required to connect to Maurice, the other is used for network access USB Ports 2 - To connect the keyboard and mouse Table 2-3: Computer requirements. General Guidelines and Information Intended Use NOTE: Maurice is for research use only. Not for use in diagnostic procedures. Lifting and Moving the System: Lift Maurice Correctly IMPORTANT Take all the standard precautions when lifting or moving Maurice. Since Maurice systems weigh 46 kg (100 lb), you should not lift him by yourself. Two people should lift him onto the lab bench. User Guide for Maurice, Maurice C. and Maurice S. page 7 Chapter 3:

Maurice Chapter Overview Maurice Systems Computer Workstation External Components Internal Components Rear Panel User Guide for Maurice, Maurice C. and Maurice S. Maurice Systems page 8 Maurice Systems Maurice, Maurice C. and Maurice S. systems include the instrument, computer workstation, Compass for iCE software and cIEF or CE-SDS Cartridges. Maurice with Computer Workstation cIEF and CE-SDS Cartridges All systems have the same hardware components, computer and software, the only difference between them are the applications you can run:

Maurice: cIEF and CE-SDS applications Maurice C.: cIEF applications only Maurice S.: CE-SDS applications only You can run samples in 96-well plates or in up to 48 sample vials with integrated 0.2 mL inserts on all three systems. Maurice C. Maurice Maurice S. User Guide for Maurice, Maurice C. and Maurice S. External Components page 9 External Components Touch Plate to Open Door Status Light System Door

!WARNING!

You cant replace or service any parts on Maurice systems except for the power entry fuse. System Door Maurice's door gives you access to the inside of the instrument to load cartridges, reagents and samples. To open the door, first make sure the status light is a steady blue. Then just touch the metal touch plate on the top of the door to open it. Close it by pushing the door until you hear the latch engage. NOTE: Maurices door must be closed before starting a batch. User Guide for Maurice, Maurice C. and Maurice S. Internal Components page 10 Start-up (magenta): You've just turned on the power and Maurice is warming up. Status Light The LED on Maurices front panel tells you what hes doing. Heres what his different status lights mean:

Ready (steady blue): Maurice is powered on and ready to go. Opening Door (long blue flash followed by blue pulses): Maurices door is opening. Running (pulsing blue): Maurice is running a batch. Trying to Open Door While Running (red flash): Maurices door cant be opened when hes run-

ning. Error (steady red): Maurice has detected an error. To get more information on the error, check the Status pane in the Run Summary Screen in Compass for iCE. Internal Components Cartridge Slot The cartridge slot holds Maurices ready-to-go application cartridges. The cartridge it holds depends on the system:

Maurice: cIEF and CE-SDS Cartridges Maurice C.: cIEF Cartridges only Maurice S.: CE-SDS Cartridges only User Guide for Maurice, Maurice C. and Maurice S. Internal Components page 11 The lights on either side of the cartridge slot will be orange after Maurice disengages the cartridge when the door is opened at the end of a batch, and whenever the slot is empty. Cartridge Slot The lights change to blue once a cartridge is installed correctly. NOTE: You can find cartridge prep, installation and post-run procedures in Chapter 7, Running cIEF Appli-

cations on Maurice and Maurice C. and Chapter 8, Running CE-SDS Applications on Maurice and Mau-

rice S. User Guide for Maurice, Maurice C. and Maurice S. Internal Components page 12 Sample and Reagent Platform Maurices sample and reagent platform has two rows for batch reagents. These reagents are kept at room temperature. Row P (top): These reagents are loaded under pressure during the batch. Only use glass reagent vials with pressure caps in this row. Use blue pressure caps with cIEF reagents and orange pres-

sure caps with CE-SDS reagents. Row N (bottom): Only use reagent vials with clear screw caps in this row. The sample block holds either a 96-well plate or 48-vial metal insert and is temperature-controlled. You can set it to 4 C, 10 C, 15 C or turn the temperature control off in Compass for iCE software. Sample cooling turns on when the run starts, and takes a few minutes to reach the temperature setting. After a run, the sample block stays at the set temperature until you open Maurices door, then it shuts off until you start the next run. This prevents excess condensation. NOTE: Because Maurice holds the sample block temperature after a run until you open the door, samples are still viable for your next run and after overnight runs. User Guide for Maurice, Maurice C. and Maurice S. Internal Components page 13 96-well Plate Insert 48-vial Insert NOTES:

When youre using a 96-well plate, well A1 should be in the top left corner of the insert. You can only use V-bottom plates with the 96-well plate insert. Remove plate lids before inserting a 96-well plate into Maurice. You can find info on where to load reagents and samples for cIEF applications in Step 4: Load Samples and Reagents on page 90 and for CE-SDS applications in Step 4: Load Samples and Reagents on page 124. User Guide for Maurice, Maurice C. and Maurice S. Internal Components page 14 Rear Panel Located on Maurices rear panel is the power entry, power switch and network connector. Power Entry Fuse Power Switch Network Connector System Power - The main system power components consist of the power input, fuse and power switch

!WARNING!

Only use the power supply cord provided with Maurice. If the cord is damaged, please contact Pro-

teinSimple Technical Support.

!WARNING!

You can't replace or service any parts on Maurice except the power entry fuse.

!WARNING! SHOCK HAZARD Disconnect the power cord from Maurices power input to disconnect power to the instrument. Network connection - A 10/100/1000 Mbps Ethernet (RJ-45 connector) is used to connect Maurice to a computer or local network. NOTE: Serial numbers are used to identify individual instruments. System Labels A full system label is located on the rear panel. It includes the ProteinSimple location, system model, power requirements, serial number and certification markings. User Guide for Maurice, Maurice C. and Maurice S. Internal Components page 15 A serial number label is located on the Maurice systems front lower right side, on the silver system base. User Guide for Maurice, Maurice C. and Maurice S. Computer Workstation page 16 Computer Workstation The PC has two built-in Ethernet ports, one is used for Maurice and the other is available for your companys network. ProteinSimple configures one port to have a fixed IP for a local link connection to the instrument, the other is configurable by users and will typically use a DHCP for dynamic IP. User Guide for Maurice, Maurice C. and Maurice S. page 17 Chapter 4:

Compass for iCE Overview Software Menus Chapter Overview Launching Compass for iCE Compass for iCE Overview Changing the Compass for iCE Main Window Layout Checking for and Installing New Versions of Compass for iCE Compass for iCE Version Information Directory and File Information Viewing Release Notes Viewing the Software Log Software Help User Guide for Maurice, Maurice C. and Maurice S. page 18 Chapter 4: Compass for iCE Overview Launching Compass for iCE To open Compass for iCE, just double-click the icon on the computer desktop. Compass for iCE Overview Compass for iCE has three main screens:

Batch - Youll create and review your batch. Run Summary - Check out the status of your run. Analysis - Take a look at the data from your experiment. Each screen has these components:

Title bar Screen Tabs Main Menu Instrument Status Bar Screen Panes Status Bar User Guide for Maurice, Maurice C. and Maurice S. Compass for iCE Overview page 19 Changing the Screen View To toggle between the Batch, Run Summary and Analysis screens, just click the button in the screen tab located in the upper right corner of the main window. Batch Screen The Batch screen is used to create, view, and edit batches. You can assign samples to 96-well plate wells or vials, create and modify methods, customize your injection list and assign methods to each of your injec-

tions. User Guide for Maurice, Maurice C. and Maurice S. page 20 Chapter 4: Compass for iCE Overview Run Summary Screen The Run Summary screen is used to monitor status of a batch in progress, the CE-SDS separation or cIEF Focus series for each injection and the current and voltage plots for each injection. User Guide for Maurice, Maurice C. and Maurice S. Compass for iCE Overview page 21 User Guide for Maurice, Maurice C. and Maurice S. page 22 Chapter 4: Compass for iCE Overview Analysis Screen The Analysis screen is used to view data from your batch, including the graph view (electropherograms) and a table with your results. You can also analyze your data for completed runs. User Guide for Maurice, Maurice C. and Maurice S. Compass for iCE Overview page 23 User Guide for Maurice, Maurice C. and Maurice S. page 24 Chapter 4: Compass for iCE Overview Screen Panes Each of the Batch, Run Summary and Analysis screens have multiple panes that let you view the individual components of a batch, method or data file. Each pane has a labeled tab and a unique icon. We'll describe panes specific to each screen later in the individual screen sections. The active pane in a screen is blue. To view a pane, click in the pane or on its tab. The example below shows panes in the Batch screen, and the Graph pane is active:

Title Bar In the title bar you will see the batch file name and the icons that allow the main Compass for iCE window to be minimized, maximized or closed. Main Menu Access to various software, instrument and screen operations is available through the main menu. More details on menu commands can be found in Software Menus on page 25. Instrument Status Bar The instrument status bar is used to start batches and cleaning protocols, indicate system status and show run progress. More details on instrument control and status can be found in Chapter 10, Controlling Maurice, Maurice C. and Maurice S.. User Guide for Maurice, Maurice C. and Maurice S. Software Menus page 25 NOTE: You will only see the instrument status bar when Compass for iCE is connected to an instrument. There is no status bar on computer workstations that you're only using for data analysis. Screen Tab The screen tab lets you move between Batch, Run Summary or Analysis screens and is located in the upper right corner of the main window. Just click a button to view a screen. View Bar The view bar is only displayed in the Analysis screen as part of the main menu, and allows you to switch between viewing standards or sample data, data for a single injection or all injections in the batch, or grouped injection data. View bar options are in Viewing Run Data on page 295 for cIEF applications or page 205 for CE-SDS applications. Compass for iCE Status Bar The status bar is in the lower right corner of the main window. It displays active software processes and their progress. Software Menus Some of the items in the Compass for iCE main menu are available in specific screens only, and menu com-

mands change depending on which screen is active. You can find menus and commands available for each screen in the Chapter 5, cIEF Batches, Chapter 6, CE-SDS Batches, Chapter 9, Run Status, Chapter 12, cIEF Data Analysis and Chapter 11, CE-SDS Data Analysis. User Guide for Maurice, Maurice C. and Maurice S. page 26 Chapter 4: Compass for iCE Overview File Menu The File menu contains basic file commands. Edit Menu The Edit menu contains basic editing commands, analysis and preferences options. Specific details on pref-

erences are described in Chapter 13, Setting Your Preferences. User Guide for Maurice, Maurice C. and Maurice S. Software Menus page 27 View Menu The View menu is only available in the Analysis screen, and allows you to change how your data is displayed. For more info on view options check out Viewing Run Data on page 295 for cIEF applications or page 205 for CE-SDS applications, and Using Groups on page 306 for cIEF applications or page 216 for CE-SDS appli-

cations. Instrument Menu The Instrument menu is only available when the software is connected directly to your instrument. You can lean more about instrument control options in Chapter 10, Controlling Maurice, Maurice C. and Maurice S. Window Menu The Window menu lets you to switch between the Batch, Run Summary or Analysis screens, and restore screens to the default layout. Batch - Displays the Batch screen where you create, view, and edit batches. User Guide for Maurice, Maurice C. and Maurice S. page 28 Chapter 4: Compass for iCE Overview Run Summary - Displays the Run Summary screen which lets you view the status of a batch in prog-

ress. Analysis - Displays the Analysis screen that lets you view electropherograms and results and change analysis parameters Default Layout - Restores the individual panes in the current screen back to their default size and location. Help Menu The Help menu gives you access to Help, software updates, release notes and other software info. User Guide - Displays the User Guide for Maurice, Maurice C. and Maurice S. Check for Updates - Automatically checks to see if a new version of Compass for iCE is available. Release Notes - Displays the software release notes for the current and prior versions. Compass for iCE Log - Displays the software log file. About Compass for iCE - Displays the software version and build information. Changing the Compass for iCE Main Window Layout You can easily resize the main window and the individual panes in each screen. Screen panes can also be moved outside of the main window. Resizing the Main Compass for iCE Window To resize the main window, roll the mouse over a corner or border until the sizing arrow appears. Then just click and drag to resize. User Guide for Maurice, Maurice C. and Maurice S. Changing the Compass for iCE Main Window Layout page 29 Resizing the Screen Tab The screen tab can be sized to show all or just some of the screen buttons. To resize, roll the mouse over the left edge of the tab until the sizing arrow appears, then click and drag to resize. If a screen button is hidden, a double arrow will display in the tab. Just click to display and select the hidden screen. Resizing Screen Panes To resize a pane - Roll the mouse over the pane border until the sizing arrow appears. Then just click and drag to resize. To maximize a pane - Click the maximize button in the upper right corner or double-click the tab. The other panes in the screen will automatically minimize to pane bars in the task area along the win-

dow border. User Guide for Maurice, Maurice C. and Maurice S. page 30 Chapter 4: Compass for iCE Overview To restore all minimized panes - Click Restore on the minimized pane bar. To restore only one minimized pane - Click the pane icon on the minimized pane bar. To restore a maximized pane to its original size - Double-click the tab or right click the tab and click Restore. To restore all panes to their original sizes - Select Window in the main menu and click Default Layout. Changing the Location of Screen Panes Panes can be moved to different locations within a screen. To move a pane - Click on its tab and drag it to the new location. As the pane is moved, area guides will display to assist you in choosing a drop location. Area guides with a black arrow let you know that if the pane is dropped at that location, it will be resized and relocated as an individual pane in that area of the screen. Area guides with a folder let you know that if the pane is dropped at that location, it will be added as a new tab in an area with one or more pane tabs. User Guide for Maurice, Maurice C. and Maurice S. Changing the Compass for iCE Main Window Layout page 31 Area guides with a window let you know that if the pane is dropped at that location, it will be a separate window outside the Compass for iCE main window. This example shows the Analysis screen after moving the Graph pane:

To detach a pane from the main window - Click on its tab and drag it outside the main Compass for iCE window or right click the tab and click Detached. To move a detached pane back inside the main window - Right click the tab and deselect Detached. To restore all panes to their original locations - Select Window in the main menu and click Default Layout. User Guide for Maurice, Maurice C. and Maurice S. page 32 Chapter 4: Compass for iCE Overview Restoring the Main Window to the Default Layout To restore screen pane sizes and locations to the original Compass for iCE layout, select Window from the main menu and click Default Layout. Software Help Select Help and click User Guide to view Maurice Systems User Guide. Checking for and Installing New Versions of Compass for iCE The software can automatically check to see if a newer version of software is available. To do this:

1. Make sure the computer being used has an active internet connection. 2. Select Help and click Check for Updates. If an update is found, a screen will display with the new ver-

sion thats available. 3. Click Finish to start the download and install the update. 4. 5. Follow the on-screen instructions to complete the software installation. Reboot the computer before using the new version of software. Viewing Release Notes Select Help and click Release Notes to view a PDF with feature updates and bug fixes for new and past ver-

sions of Compass for iCE. We recommend you review these notes whenever a software update is installed. NOTE: You can contact ProteinSimple Technical Support to request the release notes for new versions of Compass for iCE before you install it. User Guide for Maurice, Maurice C. and Maurice S. Viewing the Software Log page 33 Viewing the Software Log Select Help and click Compass Log to view the software log file. Compass for iCE Version Information Select Help and click About Compass for iCE to view the software version and build number information. User Guide for Maurice, Maurice C. and Maurice S. page 34 Chapter 4: Compass for iCE Overview Directory and File Information The main Compass for iCE directory is located in the Program Files folder, and also contains PDF files of the User Guide for Maurice, Maurice C. and Maurice S. Batch and run files are located in the Documents folder in the User directory on your computer:

Batches Folder - Contains all batch files that youve saved. New Batches Folder - Contains Maurice batch template files. Runs Folder - Contains all batch data files. Data is automatically written to this folder. User Guide for Maurice, Maurice C. and Maurice S. Directory and File Information page 35 NOTE: When a Compass for iCE software update is performed, the template s in the New Batch folder are overwritten. If you have customized these batches, we recommend saving them in a unique subfolder prior to updating the software, then transferring them back to the New Batch folder after the update to avoid losing your customizations. File Types These file types are used by Compass for iCE:

Batch Files - Use a *.batch file extension. Run Files - Use a *.mbz file extension. The default file format for run files is Date_Time_BatchName. An example run file name would be 2016-01-28_18-50-53_CE-SDS.mbz. Analysis Settings Files - Exported analysis settings files use a *.settings file extension. User Guide for Maurice, Maurice C. and Maurice S. page 36 Chapter 4: Compass for iCE Overview User Guide for Maurice, Maurice C. and Maurice S. page 37 Chapter 5:

cIEF Batches Chapter Overview Batch Screen Overview Opening a Batch Creating a New Batch Making Changes to a Batch Viewing Replicate Injections Batch History Viewing and Editing Batches in Completed Runs Batch Reports User Guide for Maurice, Maurice C. and Maurice S. page 38 Chapter 5: cIEF Batches Batch Screen Overview You can use the Batch screen to create, view, and edit batches. To get to this screen, click the Batch screen tab:

Batch Screen Panes The Batch screen has five panes:

Layout - Displays a map of either the 96-well plate or 48-vial tray of batch sample locations. Injections - Lists the injections, sample ID, sample locations and methods that Maurice or Maurice C. will execute for each sample in the batch. History - Lists all batch file events from initial creation to the most current update. Notes - Lets you enter specific information about your batch. Methods - Lets you create methods and enter method parameters used in the batch. User Guide for Maurice, Maurice C. and Maurice S. Batch Screen Overview page 39 Software Menus Active in the Batch Screen These main menu items are active in the Batch screen:

Window Help File Edit Instrument (when the software is connected to Maurice or Maurice S.) File Menu These File menu options are active:

New Batch - Creates a new batch from a starter template. Open Batch - Opens an existing batch. Save/Save As - Saves the open batch. Batch Report - Exports a table of sample and method details for each injection in the batch as a PDF file. Exit - Closes Compass for iCE. User Guide for Maurice, Maurice C. and Maurice S. page 40 Edit Menu The following Edit menu options are active in the Batch screen:

Chapter 5: cIEF Batches Cut - Cuts the information currently selected. Copy - Copies the information currently selected. Paste - Pastes the copied information. NOTE: Cut, Copy and Paste work differently depending on the pane youre in. How and when you can use them is described throughout the chapter. Plate Layout - Lets you select between a 96-well plate or a 48-vial tray to run samples in. Default Analysis - Displays the default settings that will be used to analyze the data generated with your batch. Preferences - Lets you set and save your preferences for data export, graph colors, grouped data and Twitter settings. See Chapter 13, Setting Your Preferences for more information. User Guide for Maurice, Maurice C. and Maurice S. Opening a Batch page 41 Opening a Batch To open an existing batch:

1. Select File in the main menu and click Open Batch. 2. A list of the last five batches opened will display. Select one of those or click Browse to open the 3. Batches folder and select a different one. To make changes to the batch, see the steps in Creating a New Batch on page 42. When youre done, select File from the main menu and click Save. User Guide for Maurice, Maurice C. and Maurice S. page 42 Chapter 5: cIEF Batches Creating a New Batch To create a new batch, we recommend that you use one of the template methods and make any necessary modifications from there. Step 1 - Open a Template Batch 1. Select File in the main menu and click New Batch:

NOTE: If youre using a Maurice system, both cIEF and CE-SDS template batches are available in the menu. 2. Select Maurice cIEF. A batch using the default method will display. User Guide for Maurice, Maurice C. and Maurice S. Creating a New Batch page 43 Step 2 - Assign Your Samples The Layout pane shows the default locations of where batch reagent should be placed in your Maurice sys-

tems samples and reagents platform, and a map of either the 96-well plate or the 48-vial tray used for sam-

ples. The same reagent locations are used for every batch:

P1 - 0.5% Methyl Cellulose with blue pressure cap P2 - Fluorescence Calibration Standard with blue pressure cap P3 - Water vial with blue pressure cap P6 - Empty vial (air) with blue pressure cap N1 - Water vial with clear screw cap 1. To assign samples, select 48 vials or a 96-well plate depending on what youre running. Clicking on the vial/plate icon toggles between formats. 2. To select samples:

Add samples and select methods later: Use your mouse to highlight the well or vial positions your samples are located in, then click Add. For this example were using vials. User Guide for Maurice, Maurice C. and Maurice S. page 44 Chapter 5: cIEF Batches NOTE: The template batch automatically adds a sample in well or vial A1 by default, but if you dont have a sample in this position you can remove it after youve added new positions for your samples. Add samples with preassigned methods: Highlight the well or vial positions your samples are located in, then right-click and select a method. Either option of adding samples populates the Injections table:

User Guide for Maurice, Maurice C. and Maurice S. Creating a New Batch page 45 To remove samples, just highlight the ones you want to remove and click Remove. Theyll also be removed in the Injections table. You can also right-click well(s) or vial(s) in the Layout pane and click Remove Sample(s). 3. The sample platform is temperature controlled with a default setting of 10 C. To change the tempera-

ture or turn it off, click the down arrow next to the temperature and select an option. NOTE: The two reagent rows are kept at room temperature. User Guide for Maurice, Maurice C. and Maurice S. page 46 Chapter 5: cIEF Batches Step 3 - Assign Your Method Parameters NOTE: We recommend using the default method parameters. Please see the Maurice cIEF Method Devel-

opment Guide for more information on method optimization. The Methods pane lists all of the methods used in a batch. You can add and remove methods here and change method parameters. 1. In the Methods table, click the first cell in the Name column and enter a new method name if needed. 2. Click the first cell in the Separation column, then click the selection button [...] to set the pre-focusing and focusing time (in minutes) and voltage (V). To change time and voltage parameters: Just click in a cell under Time or Voltage and type the new value(s). To add a profile step: Click Add. A new row will be added in the table. Then just type in a load time (in minutes) and voltage value (in V). To remove a profile step: Select the row you want to remove and click Remove. User Guide for Maurice, Maurice C. and Maurice S. Creating a New Batch page 47 3. Click the first cell in the Detection column the selection button [...] to set your exposure times for absorption and fluorescence detection modes. To change the exposure time: Just click in a cell under Exposure and type the new value(s) in seconds. NOTES:

The first exposure is an instrument default setting and cant be changed. Fluorescence is the default detection for the remaining exposures and cant be changed. To add a profile step: Click Add. A new row will be added in the table. Then just type in an expo-

sure time (in seconds). To remove a profile step: Select the row you want to remove and click Remove. 4. Click the first cell in the Sample Load(s) column and set the load time in seconds. NOTE: We recommend using the default Sample Load time of 55 seconds. Please contact ProteinSimple Technical Support if you have questions on the Sample Load time to use for your application. User Guide for Maurice, Maurice C. and Maurice S. page 48 Chapter 5: cIEF Batches 5. Click the first cell in the pI Markers column to select pI markers. Add new markers or remove existing ones then click OK. NOTE: When you edit the pI markers in the method for a batch, Compass for iCE automatically creates a Markers group in the pI Markers Analysis settings for you. To add a pI marker: Click Add. A new row will be added in the table. Then just type in a pI and a position (in pixels). To remove a pI marker: Select the row you want to remove and click Remove. 6. Optional: Click the first cell in the Ampholytes column and enter the ampholytes youre using. User Guide for Maurice, Maurice C. and Maurice S. Creating a New Batch page 49 7. Optional: Click the first cell in the Additives column and enter any additives youre using. 8. You can now:

Click New in the upper right corner of the Methods pane to add a new one if you want to use dif-

ferent methods for different samples. Then just repeat the steps above for the new method. Make updates to the remaining methods by repeating the prior steps. Select a method and click Remove in the upper right corner of the Methods pane to delete it. Step 4 - Set Up Your Injections The Injection pane lists all sample injections for the batch. Any samples that were added in Step 2 - Assign Your Samples are automatically added to this list. Selecting an injection in the table also selects the sample the injection will be made from in the plate or vial map in the Layout pane and vice-versa. User Guide for Maurice, Maurice C. and Maurice S. page 50 Chapter 5: cIEF Batches 1. To add sample names, click the Sample ID cell for the injection and type a name. The sample name also displays when you hover the mouse over the sample in the plate or vial map:

2. Assign your methods to each injection. Just click the Method cell for the injection and select a method from the drop down menu. If you added your samples with pre-assigned methods and dont need to make any changes, skip to the next step. User Guide for Maurice, Maurice C. and Maurice S. Creating a New Batch page 51 Hovering over a method name displays the method parameters:

3. You can add or remove injections as needed using a few different options. If you dont need to make any changes here, just skip to the next step. To add sequential replicate injections: Highlight an injection and click Replicate. A new injec-

tion will be added under the row you selected To add injections at the end of the batch: Click on any sample position in the Layout pane or sample injection in the Injection table and click Add. A new injection using the same sample will be added to the end of the table. Assign the method if needed. To copy and paste injections: Right-click on an injection in the Injection table and select Copy. Click on the injection number above where you want to insert the copied injection, right click and select Paste. The copied injection will be inserted under the row you selected. Step 5 - Add Batch Notes (Optional) 1. Click on the Notes pane. 2. Click in the notes area and type any information you want to add about your batch. User Guide for Maurice, Maurice C. and Maurice S. page 52 Chapter 5: cIEF Batches Step 6 - Modify Default Analysis Parameters (Optional) You can preset the parameters used to analyze data generated with the batch. We recommend using the default parameters for cIEF applications, but if you need to modify parameters:

1. Select Edit from the main menu and click Default Analysis. The following screen will display:

2. Change the parameters you want to, then click OK. For detailed information on analysis parameters, please refer to Analysis Settings Overview on page 334. User Guide for Maurice, Maurice C. and Maurice S. Viewing Replicate Injections page 53 Step 7 - Save Your Batch 1. Once all of your sample, method and injection info is entered, select File > Save. Enter any comments on the batch if you want, then click Save. 2. Enter a name for your batch then click Save. Viewing Replicate Injections Injections with replicates have an arrow next to the injection number. You can expand or collapse the list of replicate injections by toggling the arrow:

To show all replicate injections in the batch, click the Expand All Injections button. User Guide for Maurice, Maurice C. and Maurice S. page 54 Chapter 5: cIEF Batches To hide all replicate injections in the batch, click the Collapse All Injections button. Batch History Clicking on the History pane shows the batch event history, starting with the date and time the batch was created through the most current event. Clicking on a row in the table displays the full event details in the box under the table. User Guide for Maurice, Maurice C. and Maurice S. Making Changes to a Batch page 55 Date: Date and time of the batch event. User Name: User that initiated the event. User names only display if youre using the Access Con-

trol feature to help satisfy the 21CFR Part 11 data security requirements. Go to Enabling Access Control on page 391 to learn how to set it up. Message: Description of the event that took place. Comment: Comments entered by the user when the batch was saved. You can copy the information in the History pane to use in other documents:

1. Click the History pane to make sure its active. 2. Click Edit in the main menu and select Copy. 3. Open a document and click Paste. Making Changes to a Batch 1. Select File in the main menu and click Open Batch. User Guide for Maurice, Maurice C. and Maurice S. page 56 Chapter 5: cIEF Batches 2. A list of the last five batches opened will display. Select one of these files or click Browse to open the Batch folder and select a different one. To open a batch used in a run file, click Browse. Go to the Run folder in the Compass for iCE direc-

tory and select the run file that uses the batch you want to edit. 3. To make changes to the batch, see the steps in Creating a New Batch on page 42. Then select File from the main menu and click Save or Save As. Viewing and Editing Batches in Completed Runs 1. Click the Analysis screen and open your run file(s). 2. After the run opens, click the Batch screen to view the batch used with the run. If you opened more than one run file, you can switch between viewing batches for each file. Just click the down arrow in the Run box and select the batch you want to view from the drop down list. 3. In completed run files, you can only make edits to the sample and method names in a batch, and these changes are saved to the run file only. Update sample and method names as needed. 4. Click the Analysis screen. Then select File from the main menu and click Save or Save As to save the new changes to the run file. User Guide for Maurice, Maurice C. and Maurice S. Batch Reports page 57 Batch Reports You can export a PDF file of sample and method details for each injection in the batch for completed run files. 1. Go to the Analysis or Run Summary screen, then click File > Open Run and select a run file (if you dont have one open already). 2. After the run opens, go to the Batch screen. 3. Select File from the main menu and click Batch Report. 4. The report name defaults to the run file name. If you want to change it, type in the Report Name box to make updates. 5. The Batch Report PDF is exported to the Runs folder in the Compass for iCE directory. Itll be in a folder with the report name used in the prior step. When the reports are done, the folder opens for you auto-

matically. User Guide for Maurice, Maurice C. and Maurice S. page 58 Chapter 5: cIEF Batches Heres an example Batch Report:

User Guide for Maurice, Maurice C. and Maurice S. page 59 Chapter 6:

CE-SDS Batches Chapter Overview Batch Screen Overview Opening a Batch Creating a New Batch Making Changes to a Batch Viewing Replicate Injections Batch History Viewing and Editing Batches in Completed Runs Batch Reports User Guide for Maurice, Maurice C. and Maurice S. page 60 Chapter 6: CE-SDS Batches Batch Screen Overview You can use the Batch screen to create, view, and edit batches. To get to this screen, click the Batch screen tab:

Batch Screen Panes The Batch screen has five panes:

Layout - Displays a map of either the 96-well plate or 48-vial tray of batch sample locations. Injections - Lists the injections, sample ID, sample locations and methods that Maurice or Maurice S. will execute for each sample in the batch. History - Lists all batch file events from initial creation to the most current update. Notes - Lets you enter specific information about your batch. Methods - Lets you create methods and enter method parameters used in the batch. User Guide for Maurice, Maurice C. and Maurice S. Batch Screen Overview page 61 Software Menus Active in the Batch Screen These main menu items are active in the Batch screen:

Window Help File Edit Instrument (when the software is connected to Maurice or Maurice S.) File Menu These File menu options are active:

New Batch - Creates a new batch from a starter template. Open Batch - Opens an existing batch. Save/Save As - Saves the open batch. Batch Report - Exports a table of sample and method details for each injection in the batch as a PDF file. This menu item is only active for batches in completed runs. Exit - Closes Compass for iCE. User Guide for Maurice, Maurice C. and Maurice S. page 62 Edit Menu The following Edit menu options are active in the Batch screen:

Chapter 6: CE-SDS Batches Cut - Cuts the information currently selected. Copy - Copies the information currently selected. Paste - Pastes the copied information. NOTE: Cut, Copy and Paste work differently depending on the pane youre in. How and when you can use them is described throughout the chapter. Plate Layout - Lets you select between a 96-well plate or a 48-vial tray to run samples in. Default Analysis - Displays the default settings that will be used to analyze the data generated with your batch. Preferences - Lets you set and save your preferences for data export, graph colors, grouped data and Twitter settings. See Chapter 13, Setting Your Preferences for more information. User Guide for Maurice, Maurice C. and Maurice S. Opening a Batch page 63 Opening a Batch To open an existing batch:

1. Select File in the main menu and click Open Batch. 2. A list of the last five batches opened will display. Select one of those or click Browse to open the 3. Batches folder and select a different one. To make changes to the batch, see the steps in Creating a New Batch on page 64. When youre done, select File from the main menu and click Save. User Guide for Maurice, Maurice C. and Maurice S. page 64 Chapter 6: CE-SDS Batches Creating a New Batch To create a new batch, we recommend that you use one of the template methods and make any necessary modifications from there. Step 1 - Open a Template Batch 1. Select File in the main menu and click New Batch:

NOTE: If youre using a Maurice system, both cIEF and CE-SDS template batches are available in the menu. 2. Select Maurice CE-SDS. A batch using the default method will display. User Guide for Maurice, Maurice C. and Maurice S. Creating a New Batch page 65 Step 2 - Assign Your Samples The Layout pane shows the default locations of where batch reagent should be placed in your Maurice sys-

tems samples and reagents platform, and a map of either the 96-well plate or the 48-vial tray used for sam-

ples. The same reagent locations are used for every batch:

P1 - Conditioning Solution 1 with orange pressure cap P2 - Conditioning Solution 2 with orange pressure cap P3 - DI water with orange pressure cap P4 - Separation Matrix with orange pressure cap P5 - Wash Solution vial with orange pressure cap P6 - Empty vial (air) with orange pressure cap N1 - Wash Solution vial with clear screw cap N2 - Wash Solution vial with clear screw cap N4 - Running Buffer - Bottom with clear screw cap 1. To assign samples, select a 96-well plate or 48 vials depending on what youre running. Clicking on the vial/plate icon toggles between formats. User Guide for Maurice, Maurice C. and Maurice S. page 66 Chapter 6: CE-SDS Batches 2. To select samples:

Add samples and select methods later: Use your mouse to highlight the well or vial positions your samples are located in, then click Add. For this example were using a 96-well plate. NOTE: The template batch automatically adds a sample in well or vial A1 by default, but if you dont have a sample in this position you can remove it after youve added new positions for your samples. Add samples with preassigned methods: Highlight the well or vial positions your samples are located in, then right-click and select a method. Either option of adding samples populates the Injections table:

User Guide for Maurice, Maurice C. and Maurice S. Creating a New Batch page 67 To remove samples, just highlight the ones you want to remove and click Remove. Theyll also be removed in the Injections table. You can also right-click well(s) or vial(s) in the Layout pane and click Remove Sample(s). 3. Compass for iCE can monitor the current during a separation for you, stop it if the current drops below the minimum value and reinject the sample for you automatically. Reinjections are enabled by default, but if you dont want to use this feature just click the reinject icon to toggle it off. NOTES:

If a sample was reinjected, the injection row will be flagged in the Injections pane in the Run Summary screen. See Injection Flags on page 158 for more info. A maximum of 10 reinjections are allowed per batch. User Guide for Maurice, Maurice C. and Maurice S. page 68 Chapter 6: CE-SDS Batches 4. The sample platform is temperature controlled with a default setting of 10 C. To change the tempera-

ture or turn it off, click the down arrow next to the temperature and select an option. NOTE: The two reagent rows are kept at room temperature. Step 3 - Assign Your Method Parameters NOTE: There are three default methods. We recommend using the default method parameters for the listed sample types. Please see the Maurice CE-SDS Application Guide for more information on method optimization. The Methods pane lists all of the methods used in a batch. You can add and remove methods here and change method parameters. 1. In the Methods table, click the first cell in the Name column and enter a new method name if needed. User Guide for Maurice, Maurice C. and Maurice S. Creating a New Batch page 69 2. Click the first cell in the Sample Load column, then click the selection button [...] to set your sample load profile time (in seconds) and voltage. To change time and voltage parameters: Just click in a cell under Time or Voltage and type the new value(s). To add a profile step: Click Add. A new row will be added in the table. Then just type in a load time (in seconds) and voltage value. To remove a profile step: Select the row you want to remove and click Remove. 3. Click the first cell in the Separation column the selection button [...] to set your separation profile parameters (in minutes) and voltage. NOTE: Run your reduced IgG samples and IgG Standard for 25 minutes and the CE-SDS MW Markers for 30 minutes. Run your non-reduced IgG samples and IgG Standard for 35 minutes. The default separation voltage for all sample types is 5750 volts. User Guide for Maurice, Maurice C. and Maurice S. page 70 Chapter 6: CE-SDS Batches To change time and voltage parameters: Just click in a cell under Time or Voltage and type the new value(s). To add a profile step: Click Add. A new row will be added in the table. Then just type in a load time (in seconds) and voltage value. To remove a profile step: Select the row you want to remove and click Remove. 4. You can now:

Click New in the upper right corner of the Methods pane to add a new one if you want to use dif-

ferent methods for different samples. Then just repeat the steps above for the new method. Make updates to the remaining methods by repeating the prior steps. Select a method and click Remove in the upper right corner of the Methods pane to delete it. Step 4 - Set Up Your Injections The Injection pane lists all sample injections for the batch. Any samples that were added in Step 2 - Assign Your Samples are automatically added to this list. Selecting an injection in the table also selects the sample the injection will be made from in the plate or vial map in the Layout pane and vice-versa. User Guide for Maurice, Maurice C. and Maurice S. Creating a New Batch page 71 1. To add sample names, click the Sample ID cell for the injection and type a name. The sample name also displays when you hover the mouse over the sample in the plate or vial map:

2. Assign your methods to each injection. Just click the Method cell for the injection and select a method from the drop down menu. If you added your samples with pre-assigned methods and dont need to make any changes, skip to the next step. User Guide for Maurice, Maurice C. and Maurice S. page 72 Chapter 6: CE-SDS Batches Hovering over a method name displays the method parameters:

3. You can add or remove injections as needed using a few different options. If you dont need to make any changes here, just skip to the next step. To add sequential replicate injections: Highlight an injection and click Replicate. A new injec-

tion will be added under the row you selected To add injections at the end of the batch: Click on any sample position in the Layout pane or sample injection in the Injection table and click Add. A new injection using the same sample will be added to the end of the table. Assign the method if needed. User Guide for Maurice, Maurice C. and Maurice S. Creating a New Batch page 73 To copy and paste injections: Right-click on an injection in the Injection table and select Copy. Click on the injection number above where you want to insert the copied injection, right click and select Paste. The copied injection will be inserted under the row you selected. Step 5 - Add Batch Notes (Optional) 1. Click on the Notes pane. 2. Click in the notes area and type any information you want to add about your batch. Step 6 - Modify Default Analysis Parameters (Optional) You can preset the parameters used to analyze data generated with the batch. We recommend using the default parameters for CE-SDS applications, but if you need to modify parameters:

User Guide for Maurice, Maurice C. and Maurice S. page 74 Chapter 6: CE-SDS Batches 1. Select Edit from the main menu and click Default Analysis. The following screen will display:

2. Change the parameters you want to, then click OK. For detailed information on analysis parameters, please refer to Analysis Settings Overview on page 244. Step 7 - Save Your Batch 1. Once all of your sample, method and injection info is entered, select File > Save. Enter any comments on the batch if you want, then click Save. User Guide for Maurice, Maurice C. and Maurice S. Viewing Replicate Injections page 75 2. Enter a name for your batch then click Save. Viewing Replicate Injections Injections with replicates have an arrow next to the injection number. You can expand or collapse the list of replicate injections by toggling the arrow:

To show all replicate injections in the batch, click the Expand All Injections button. User Guide for Maurice, Maurice C. and Maurice S. page 76 Chapter 6: CE-SDS Batches To hide all replicate injections in the batch, click the Collapse All Injections button. Batch History Clicking on the History pane shows the batch event history, starting with the date and time the batch was created through the most current event. Clicking on a row in the table displays the full event details in the box under the table. User Guide for Maurice, Maurice C. and Maurice S. Making Changes to a Batch page 77 Date: Date and time of the batch event. User Name: User that initiated the event. User names only display if youre using the Access Con-

trol feature to help satisfy the 21CFR Part 11 data security requirements. Go to Enabling Access Control on page 391 to learn how to set it up. Message: Description of the event that took place. Comment: Comments entered by the user when the batch was saved. You can copy the information in the History pane to use in other documents:

1. Click the History pane to make sure its active. 2. Click Edit in the main menu and select Copy. 3. Open a document and click Paste. Making Changes to a Batch 1. Select File in the main menu and click Open Batch. User Guide for Maurice, Maurice C. and Maurice S. page 78 Chapter 6: CE-SDS Batches 2. A list of the last five batches opened will display. Select one of these files or click Browse to open the Batch folder and select a different one. To open a batch used in a run file, click Browse. Go to the Run folder in the Compass for iCE direc-

tory and select the run file that uses the batch you want to edit. 3. To make changes to the batch, see the steps in Creating a New Batch on page 64. Then select File from the main menu and click Save or Save As. Viewing and Editing Batches in Completed Runs 1. Click the Analysis screen and open your run file(s). 2. After the run opens, click the Batch screen to view the batch used with the run. If you opened more than one run file, you can switch between viewing batches for each file. Just click the down arrow in the Run box and select the batch you want to view from the drop down list. 3. In completed run files, you can only make edits to the sample and method names in a batch, and these changes are saved to the run file only. Update sample and method names as needed. 4. Click the Analysis screen. Then select File from the main menu and click Save or Save As to save the new changes to the run file. User Guide for Maurice, Maurice C. and Maurice S. Batch Reports page 79 Batch Reports You can export a PDF file of sample and method details for each injection in the batch for completed run files. 1. Go to the Analysis or Run Summary screen, then click File > Open Run and select a run file (if you dont have one open already). 2. After the run opens, go to the Batch screen. 3. Select File from the main menu and click Batch Report. 4. The report name defaults to the run file name. If you want to change it, type in the Report Name box to make updates. 5. The Batch Report PDF is exported to the Runs folder in the Compass for iCE directory. Itll be in a folder with the report name used in the prior step. When the reports are done, the folder opens for you auto-

matically. User Guide for Maurice, Maurice C. and Maurice S. page 80 Chapter 6: CE-SDS Batches Heres an example Batch Report:

User Guide for Maurice, Maurice C. and Maurice S. page 81 Chapter 7:

Running cIEF Applications on Maurice and Maurice C. Chapter Overview Checking Your Data Before You Throw the Switch Power Up Running cIEF Applications Post-batch Procedures User Guide for Maurice, Maurice C. and Maurice S. Before You Throw the Switch page 82 Before You Throw the Switch Ensure that everyone using Maurice have:

Received instruction in general safety practices for laboratories. Received instruction in specific safety practices for Maurice. Received instruction on handling of biohazards (if biohazardous materials are to be used on Maurice). Read and understood all Product Inserts and related Safety Data Sheets (SDS). Turn on the computer connected to Maurice. Turn on Maurices main power switch. Power Up 1. 2. 3. Wait for Maurice to initialize. His indicator light will turn from magenta to blue when hes done. 4. Double-click the Compass for iCE software icon on the computer desktop to open the application. 5. Connect Maurice to Compass for iCE. Running cIEF Applications What Youll Need Maurice cIEF Cartridges Maurice cIEF Method Development Kit (optional) Maurice System Suitability Kit (optional) Maurice cIEF Fluorescence Calibration Standard Maurice cIEF pI Markers (3.38, 4.05, 5.85, 6.14, 7.05, 8.4, 9.99, or 10.17) Deionized (DI) water Glass reagent vials, 2 mL Clear screw caps for vials 0.5% Methyl Cellulose Solution 1% Methyl Cellulose Solution iCE Electrolyte Kit 96-well plate or vials with integrated inserts for samples User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 83 Blue pressure caps for vials P10, P20, P200, P1000 pipettes and tips Electrolyte pipette Vortexer Table-top centrifuge with plate adapter or vial adapter (12 mm, 2 mL vials) Step 1: Prep Your Markers, Samples and Reagents NOTES:

You can prepare your samples to run either in 96-well plates or vials. If you need to seal the 96-well plate during your run, we recommend the 4titude Pierceable Film (PN 4ti-

0566, 4titude). It can be used in both absorbance and native fluorescence modes. If youre currently using X-Pierce adhesive film (PN XP-100, Excel Scientific), we recommend using it for absorbance mode only. System Suitability Peptide Panel (Optional) NOTES:

Run the System Suitability Peptide Panel when you need to confirm performance on Maurice. The System Suitability Peptide Panel is lyophilized. Always reseal the foil bag containing the unopened tubes with desiccant to prevent moisture absorption. 1. Using scissors, carefully cut the top the package off leaving the sealing strip intact. 2. Take out the strip of tubes and cut one clear tube of lyophilized System Suitability Peptide Panel from the strip. Return the remaining tubes to the original package, reseal tightly and store at 2-8C. Pierce the foil on the tube with a clean pipette tip. 3. 4. Add 40 L of DI water to the tube. Gently resuspend by pipetting up and down to mix. 5. Add 160 L of the System Suitability Test Mix to the freshly reconstituted Peptide Panel. Gently mix by pipetting up and down. Transfer this solution to a 1.5 mL microcentrifuge tube. Vortex the tube 3 times, 5 seconds each. 6. 7. Centrifuge the tube at 10,000 xg for 3 minutes to sediment any particulates. User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 84 8. Carefully aspirate the top 160 L of the solution and pipette it into a sample vial with integrated insert or well of a 96-well plate. Youll want to insert the pipette tip all the way to the bottom of the insert or well when you dispense the solution to avoid introducing bubbles. NOTE: Make sure to check for and remove any bubbles at the bottom of the sample vial or well. 9. If you're using vials, close the sample vial with a clear screw cap. Clear screw cap Sample vial with integrated insert Samples 1. In a microcentrifuge tube, prepare your sample at a concentration of 1 mg/mL in a final volume of 40 L in DI water. In a separate tube, prepare IEF Separation Mix containing your chosen pI marker(s). 2. NOTE: Check out the Method Development Guide for suggested IEF Separation Mix recipes. Vortex the tube 3 times, 5 seconds each. 3. Add 160 L of IEF Separation Mix to the 40 L of your sample. 4. 5. Centrifuge the tube at 10,000 xg for 3 minutes to sediment any particulates 6. Carefully aspirate the top 160 L of the sample and pipette it into your sample vial with integrated insert or well of a 96-well plate by inserting the pipette tip all the way to the bottom to avoid introducing bub-

bles. Note: Make sure to check for and remove any bubbles at the bottom of the sample vial or well. User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 85 7. If you're using vials, close the sample vial with a clear screw cap. pI Markers 1. Open the vial of lyophilized pI marker by lifting the center tab and gently pulling it back to break the metal seal. Slowly remove the rubber stopper. 2. Add 210 L of DI water to the vial. 3. Put the rubber stopper back in the vial and vortex 3 times, 5 seconds each time to completely reconsti-

tute the lyophilized cake. Repeat this step for all pI markers you're using. 4. Aliquot 20 L of each reconstituted pI marker into separate tubes for storage. NOTES:

Keep your reconstituted pI markers on ice until you're ready to add them to your sample or IEF Separation Mix. If you'll use the pI markers within a month, store the aliquots at 2-8 C. Otherwise, store the aliquots at

-20 C. They'll be stable up to 6 months. 5. Use 2 L of each pI marker for every 200 L of sample. Reagents NOTE: Don't reuse reagents, vials or the clear screw caps. Always keep the blue pressure caps paired with their respective reagents. If you want to reuse pressure caps, first wash them thoroughly with DI water, soak overnight in DI water, rinse caps thoroughly with DI water again and air dry them before reusing. 1. Pipette 2 mL of 0.5% Methyl Cellulose into a glass reagent vial, label and close with a blue pressure cap. User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 86 Pressure cap Glass reagent vial 2. Pipette 500 L of Fluorescence Calibration Standard in a glass reagent vial, label and close with a blue pressure cap. Pipette 2 mL of DI water into a glass reagent vial, label and close with a blue pressure cap. 3. 4. Close an empty glass reagent vial with a blue pressure cap. 5. Pipette 2 mL of DI water into a glass reagent vial, label and close with a clear screw cap. Clear screw cap Glass reagent vial Step 2: Prep the Cartridge 1. Take the cIEF Cartridge out of its packaging. Save the packaging, youll need it later to store the car-

tridge. NOTE: When you remove the cartridge from its packaging, make sure the cartridge inlet doesnt come in contact with any surface. User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 87 2. 3. Put the cartridge on a flat surface with its electrolyte tanks facing up. Remove the stoppers from both electrolyte tanks. Optical Window Cartridge Inlet Anolyte Tank Catholyte Tank 4. Add 2 mL of Catholyte solution to the OH- electrolyte tank (white port). 5. Add 2 mL Anolyte solution to the H+ electrolyte tank (red port). NOTE: Make sure you dont overfill the electrolyte tanks. User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 88 6. Seal each tank with the rubber stoppers. Use the grey stopper for the OH- tank and the red one for the H+ tank. If excess liquid comes out of the tank, make sure to wipe it with a laboratory wipe. Step 3: Install the Cartridge 1. Open Maurices door by touching the metal plate on top of the door. NOTE: The indicator light on Maurices front panel will blink rapidly as the door disengages. 2. Swing the door open to access the cartridge slot and the reagents and samples platform. The lights on either side of the slot will be orange. User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 89 3. Double check to make sure youve got electrolytes loaded and the tanks are properly sealed with the 4. stoppers. Lift the cartridge and hold it vertically using the finger holds on either side, cartridge inlet down, with the cIEF label facing you. 5. Gently insert it into the slot. Youll feel the alignment groove on the cartridge align inside the slot when you insert it. User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 90 6. Continue to slide the cartridge into the slot until the locking mechanism engages. The lights on either side of the slot will change to blue once the cartridge is installed correctly. Step 4: Load Samples and Reagents 1. Place the reagent vials into their respective positions on the sample and reagents platform:

NOTES:

The two reagent rows in Maurices reagent and sample platform are kept at room temperature. Pressure caps are blue and have a raised, ringed surface. They should only be used in Reagent Row P. Use reagent vials with clear screw caps in Row N. P1 - 0.5% Methyl Cellulose with blue pressure cap P2 - Fluorescence Calibration Standard with blue pressure cap P3 - Water vial with blue pressure cap P6 - Empty vial (air) with blue pressure cap N1 - Water vial with clear screw cap User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 91 2. Depending on what you prepared your samples in, put your 96-well sample plate in the metal plate insert or your sample vials in the metal vial insert. NOTES:

If you need to seal the 96-well plate during your run, we recommend the 4titude Pierceable Film (PN 4ti-

0566, 4titude). It can be used in both absorbance and native fluorescence modes. If youre currently using X-Pierce adhesive film (PN XP-100, Excel Scientific), we recommend using it in absorbance mode only. Well A1 on the 96-well plate should be in the top left corner of the insert. 3. Close the instrument door. Maurice locks it automatically. Step 5: Create a Batch 1. 2. Launch Compass for iCE. Select the Batch tab. This is where youll enter sample/injection information, methods and batch parameters. User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 92 3. To create a batch, make sure Maurice is connected to Compass for iCE. If he isnt, select Instrument and click Connect. Then select your Maurice system and click Connect. To create a new batch:

On Maurice systems - in the main menu, select File > New Batch > Maurice cIEF. On Maurice C. systems - in the main menu, select File > New Batch To use an existing batch: In the main menu, select File > Open Batch. NOTE: If youre making changes to an existing batch, follow the steps in this section. Otherwise skip to Step 6: Start the Batch on page 100. User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 93 4. In the Layout pane, clicking on the vial/plate icon toggles between formats. Select 48 vials or a 96-well plate depending on what youre running. 5. Use your mouse to highlight the well positions for each of your samples, then click Add. This populates the Injections table:

User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 94 6. The sample platform is temperature controlled with a default setting of 10 C. To change the tempera-

ture or turn it off, click the down arrow next to the temperature and select an option. NOTE: The two reagent rows are kept at room temperature. 7. In the Methods pane:

NOTE: We recommend using the default method parameters. Please see the Maurice cIEF Method Devel-

opment Guide for more information on method optimization. a. Click the first cell in the Name column and enter a method name. User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 95 b. Click the first cell in the Separation column, then click the selection button [...] to set the pre-focus-

ing and focusing time (in minutes) and voltage. c. Click the first cell in the Detection column then click the selection button [...] to set your exposure times for absorption and fluorescence detection modes. d. Click the first cell in the Sample Load(s) column and set the load time in seconds. User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 96 e. Click the first cell in the pI Markers column to select pI markers. Add new markers or remove existing ones then click OK. f. Optional: Click the first cell in the Ampholytes column and enter the ampholytes youre using. g. Optional: Click the first cell in the Additives column and enter any additives youre using. User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 97 8. 9. You can now:

Make updates to the remaining methods by repeating the prior steps. Click New in the upper right corner of the Methods pane to add a new one if you want to use dif-

Select a method and click Remove in the upper right corner of the Methods pane to delete it. ferent methods for different samples. Then just repeat the steps above for the new method. In the Injections pane:

To add sample names: click the Sample ID cell for the injection and type a name. To assign methods for each injection: Click the Method cell for the injection and select a method from the drop down menu. To add sequential replicate injections: Highlight an injection and click Replicate. A new injec-

tion will be added under the row you selected User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 98 To add injections at the end of the batch: Click on any sample position in the Layout pane or sample injection in the Injection table and click Add. A new injection using the same sample will be added to the end of the table. Assign the method if needed. To copy and paste injections: Right-click on an injection in the Injection table and select Copy. Click on the injection number above where you want to insert the copied injection, right click and select Paste. The copied injection will be inserted under the row you selected. 10. Click on the Notes pane, then click in the notes area and type any information you want to add about your batch (optional). 11. You can preset the parameters used to analyze data generated with the batch (optional). We recom-

mend using the default parameters for cIEF applications, but if you want to modify parameters:

a. Select Edit from the main menu and click Default Analysis. The following screen will display:

User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 99 b. Change the parameters you want to, then click OK. For detailed information on analysis parameters, please refer to Analysis Settings Overview on page 244 12. Once all of your sample, method and injection info is entered, select File > Save. Enter any comments on the batch if you want, then click Save. 13. Enter a name for your batch then click Save. User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 100 Step 6: Start the Batch 1. Make sure Maurice is connected to Compass for iCE. If he isnt, select Instrument and click Connect. Then select your Maurice system and click Connect. 2. Click Start to start your batch. 3. The Start Run box shows you the number of injections and batches remaining on your cartridge. Make sure you still have enough injections left before you start the run. If not, prep a new cartridge. 4. Click in the Results File name box if you want to change the default run file name. Otherwise just leave it as is. If you dont want to save the file to the default Runs folder, click Browse to select a different location. Enter any run details youd like in the Comments box (optional). 5. 6. 7. Click Start to start the run. NOTE: The indicator light on Maurices front panel will pulse slowly while hes running the batch. User Guide for Maurice, Maurice C. and Maurice S. Running cIEF Applications page 101 To monitor the progress of your batch, click the Run Summary tab. See Chapter 9, Run Status for more details. To view results, analyze results or change analysis parameters on completed injections while the batch is still running, click the Analysis tab. See Chapter 12, cIEF Data Analysis for more details. User Guide for Maurice, Maurice C. and Maurice S. Post-batch Procedures page 102 When your batch is complete, you can view electropherograms for all injections in the Analysis tab, and all batch and injection details in the Run Summary tab. NOTE: If youd like Maurice to let you know when your run is done, you can set him up to tweet you. Go to Setting Up Maurice Systems to Send Tweets on page 383 for more info. Post-batch Procedures When the batch is done:

1. Open Maurices door. The lights on either side of the cartridge slot will be orange as Maurice will have already disengaged the cartridge. Remove your reagent vials and samples and discard. 2. 3. Gently pull out the cartridge making sure the cartridge inlet doesnt come into contact with any surface. User Guide for Maurice, Maurice C. and Maurice S. Post-batch Procedures page 103 If you're at 100 injections, the cartridge is at its limit. Put it back in its original packing and discard it per your institution's safety and waste disposal guidelines. NOTE: Disposal of cartridges, sample plates and vials depends on the samples you ran. If you arent sure what your sample origins are, we recommend you dispose of everything in biohazard waste. If you've still got injections left and the cartridge will be used again within 24 hours. You don't need to do anything. Just leave the cartridge in Maurice. If you've still got injections left and the cartridge wont be used within 24 hours. Clean and store the cartridge. Maurice has already cleaned the capillary for you, so here's all you need to do:

a. Put the cartridge on a flat surface with its electrolyte tanks facing up. b. Remove the stoppers from both the electrolyte tanks. c. Using an electrolyte pipette or low vacuum, aspirate the solutions from each tank. d. Fill each tank with 2 mL DI water, then aspirate it out. Repeat this rinse 3 times. NOTE: Make sure not to get any liquid on the cartridges optical window. User Guide for Maurice, Maurice C. and Maurice S. Post-batch Procedures page 104 e. Aspirate all the remaining liquid and make sure that the tanks are dry. f. Put the stoppers back on the tanks. g. Put the cartridge back in its protective packaging and store it at room temperature.

!WARNING! SHARPS HAZARD The capillary inlet of the cartridge may present a potential sharps hazard. Dispose of used cartridges according to your organizations health and safety regulations.

!WARNING! BIOHAZARD Cartridges, sample plates and vials should be handled by procedures recommended in the CDC/NIH manual: Biosafety in Microbiological and Biomedical Laboratories (BMBL). The manual is available from the U.S. Government Printing Office or online at http://

www.cdc.gov/biosafety/publications/bmbl5/. Depending on the samples used, the cartridges, plates and vials may constitute a chemi-

cal or a biohazard. Dispose of the cartridges, plates and vials in accordance with good lab-

User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 105 oratory practices and local, state/provincial, or national environmental and health regulations. Read and understand the Safety Data Sheets (SDSs) provided by the manufacturers of the chemicals in the waste content before you store, handle, or dispose of chemical waste. Checking Your Data Compass for iCE detects your sample protein and pI marker peaks and reports results automatically. But, we always recommend you review your data using the steps in this section as a good general practice to make sure your results are accurate. If you see a data warning in the Experiment pane, these steps will also help you identify and correct any issues. Step 1: Select Your Detection Mode 1. Go to the Analysis screen and open your run (if it isnt already open). 2. The data displays in absorbance mode by default. If you want to look at fluorescence data instead, select Edit from the main menu and click Analysis. In the Analysis window, select Detection in the left side-

bar, then click Fluorescence in the Detection page. Step 2: Check Your pI Markers To make sure your pI markers are identified correctly:

1. Go to the Analysis screen. 2. Click Markers in the View bar. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 106 3. Click the Single View icon in the View bar. 4. Click Injection 1 in the Experiment pane. 5. Check that your pI markers in the electropherogram have been correctly identified. Each marker peak will have a green vertical line running through it and be labeled Mkr. Theyre also identified with an M in the Peaks table. 6. If your pI markers arent identified correctly, heres how to manually correct them:

To set an unidentified peak as a pI marker: Right-click the peak in the electropherogram or Peaks table and select Force Standard. Compass will assign that peak as a pI marker, and correctly reassign the remaining pI marker peaks. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 107 A lock icon indicating the pI marker was set manually will display next to the peak in the Peaks table and a check mark will appear next to the injection in the Experiment pane to show a manual correction was made. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 108 NOTE: To remove pI marker peak assignments that were made manually, right click on the peak in the electropherogram or Peaks table and click Clear. To clear all the manual settings for the injection, click Clear All. If an incorrect peak is identified as a pI marker: Right-click the peak in the electropherogram or Peaks table and select Not a Marker. Compass should correctly reassign the remaining peaks as pI markers and update the Peaks table. An M with a red slash through it will appear next to the incorrectly assigned peak in the Peaks table and a check mark will appear next to the injection in the Experiment pane to show a manual correction was made. 7. Repeat the previous steps for the remaining pI marker peaks as needed in the current injection and for all other injections to make sure all your pI markers are identified correctly. Step 3: Checking Sample Peaks All detected peaks will be labeled automatically with the calculated protein pI. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 109 NOTE: The reported protein pI in Compass may vary slightly from predicted pIs based on sample, buffer, and method conditions. To make sure your sample proteins are identified correctly:

1. Click Samples in the View bar. 2. Click the Single View icon in the View bar. 3. Click Injection 1 in the Experiment pane. 4. If your sample peaks arent identified correctly, heres how to manually correct them:

If a peak is incorrectly identified as a sample peak: Right-click the peak in the electropherogram or Peaks table and select Remove Peak. Compass will no longer identify it as a sample peak in the electro-

pherogram and the peak data will be removed in the results table. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 110 A check mark will appear next to the injection in the Experiment pane to indicate a manual correction was made. To identify a peak as a sample peak: Right-click the peak in the electropherogram or Peaks table and select Add Peak. Compass will calculate and display the results for the peak in the results table and identify the peak in the electropherogram. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 111 A check mark will appear next to the injection in the Experiment pane to indicate a manual correction was made. NOTE: To remove sample peak assignments that were made manually and go back to the original peak data, right-click the peak in the electropherogram and select Clear. 5. Repeat the previous steps for the remaining injections to make sure all sample peaks are correctly iden-

tified. Step 4: Assigning Peak Names Compass can also optionally identify and automatically name sample peaks using user-specified peak name settings. For more information on how to do this, see Peak Names Settings on page 354. User Guide for Maurice, Maurice C. and Maurice S. page 112 Chapter 8:

Running CE-SDS Applications on Maurice and Maurice S. Chapter Overview Checking Your Data Before You Throw the Switch Power Up Running CE-SDS Applications Post-batch Procedures User Guide for Maurice, Maurice C. and Maurice S. Before You Throw the Switch page 113 Before You Throw the Switch Ensure that everyone using Maurice have:

Received instruction in general safety practices for laboratories. Received instruction in specific safety practices for Maurice. Received instruction on handling of biohazards (if biohazardous materials are to be used on Maurice). Read and understood all Product Inserts and related Safety Data Sheets (SDS). Turn on the computer connected to Maurice. Turn on Maurices main power switch. Power Up 1. 2. 3. Wait for Maurice to initialize. His indicator light will turn from magenta to blue when hes done. 4. Double-click the Compass for iCE software icon on the computer desktop to open the application. 5. Connect Maurice to Compass for iCE. Running CE-SDS Applications What Youll Need Maurice CE-SDS Size Application Kit which includes:

Separation Matrix Running Buffer (Top and Bottom) 1X Sample Buffer Maurice CE-SDS Cartridges Cartridge Cleaning Vials Wash Solution Conditioning Solutions (1 and 2) Glass reagent vials, 2 mL Clear screw caps for vials Orange pressure caps for vials 25X Internal Standard 96-well plates Maurice CE-SDS IgG Standard (optional) User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 114

-mercaptoethanol (ME, >98% = 14.2 M) for reducing conditions Iodoacetamide (IAM, 250 mM) for alkylation at non-reducing conditions Maurice CE-SDS MW Markers (optional) Deionized (DI) water Water bath or thermocycler Sample vials with integrated inserts for samples (optional) P10, P20, P200, P1000 and pipette tips Vortexer Table-top centrifuge with plate adapter or vial adapter (12 mm, 2 mL vials) Step 1: Prep Your Internal Standard, Samples and Reagents NOTE: You can prepare your samples to run either in 96-well plates or vials. Using 96-well plates is the default method. Internal Standard NOTES:

The Internal Standard is lyophilized. Always reseal the foil bag containing the unopened tubes with desic-

cant to prevent moisture absorption. Aliquot the reconstituted solution into appropriately sized vials and store at -80 C for long term storage. For short-term storage (< 1 week), the solution can be stored at 2-8 C 1. Open the vial of lyophilized 25X Internal Standard by lifting the center tab and gently pulling it back to 2. break the metal seal. Then slowly remove the rubber stopper. Reconstitute by adding 240 L of 1X Sample Buffer. Pipette up and down a few times to mix thoroughly. This results in a 25X Internal Standard solution. NOTE: Dont vortex the reconstituted Internal Standard during prep. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 115 Sample Prep Under Reducing Conditions Reduced IgG Sample 1. In a microcentrifuge tube, dilute your IgG sample with 1X Sample Buffer to a concentration of 1mg/mL in a final volume of 50 L. NOTE: Dilute at least 1:1 with 1X Sample Buffer. 2. Add 2 L of reconstituted 25X Internal Standard for every 50 L of sample volume. 3. Add 2.5 L of 14.2 M -mercaptoethanol to 50 L of sample. 4. Mix thoroughly. NOTE: Heating in the presence of SDS linearizes the protein and allows for SDS binding. The reducing agents break up inter- and intra-molecular disulfide bonds. 5. Centrifuge the tube and heat the mixture in a water bath or thermocycler at 70 C for 10 minutes. 6. 7. Put the tube on ice for 5 minutes. Vortex briefly and spin down. Reduced IgG Standard (Optional) NOTE: The IgG Standard is lyophilized. Always reseal the foil bag containing the unopened tubes with des-

iccant to prevent moisture absorption. 1. Using scissors, carefully cut the top of the foil package, leaving the sealing strip intact. 2. Take out the strip of tubes and carefully cut one pink tube of lyophilized IgG Standard from the strip. Put the unopened tubes back in the package, seal tightly and store at 2-8 C. Pierce the foil on the tube with a clean pipette tip. Reconstitute the IgG Standard with 50 L of 1X Sample Buffer. Gently resuspend by pipetting the solu-

tion up and down. Transfer the solution to a microcentrifuge tube. 3. 4. 5. Add 2 L of reconstituted 25X Internal Standard. 6. Add 2.5 L of 14.2 M -mercaptoethanol. 7. Mix thoroughly by vortex. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 116 8. Centrifuge the tube and heat mixture in a water bath or thermocycler at 70 C for 10 minutes. 9. 10. Vortex briefly and spin down. Put the tube on ice for 5 minutes. CE-SDS Molecular Weight (MW) Markers (Optional) NOTE: The CE-SDS MW Markers are lyophilized. Always reseal the foil bag containing the unopened tubes with desiccant to prevent moisture absorption. 1. Using scissors, carefully cut the top of the foil package leaving the sealing strip intact. 2. Take out the strip of tubes and carefully cut one green tube of lyophilized CE-SDS MW Markers from the strip. Put the unopened tubes back in the package, seal tightly and store at 2-8 C. Pierce the foil on the tube with a clean pipette tip. Reconstitute the CE-SDS MW Markers with 50 L of 1X Sample Buffer. Gently resuspend by pipetting the solution up and down. Transfer the solution to a microcentrifuge tube. 3. 4. 5. Add 2 L of reconstituted 25X Internal Standard. 6. Add 2.5 L of 14.2 M -mercaptoethanol. 7. Mix thoroughly. 8. Centrifuge the tube and heat the mixture in a water bath or thermocycler at 70 C for 10 minutes. 9. 10. Vortex briefly and spin down. Put the tube on ice for 5 minutes. Spin Samples, Standards and CE-SDS MW Markers If youre using a 96-well plate:

1. Transfer 50 L of each of your samples, IgG Standard and CE-SDS MW Markers to their designated wells in a 96-well plate. Pop any bubbles in the samples with a clean pipette tip. 2. Cover the plate with a lid and spin for 10 minutes at 1000 xg in a centrifuge with a plate adapter. 3. If youre using vials:

1. Transfer 50 L of each of your samples, IgG Standard and CE-SDS MW Markers to their designated sam-

ple vials with integrated inserts. 2. Close the vials with a clear screw cap. 3. Place the vials in a centrifuge using a vial adapter (12 mm, 2 mL vials) and spin for 10 minutes at 1000 xg. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 117 Clear screw cap Sample vial with integrated insert Sample Prep Under Non-reducing Conditions Alkylation Reagent NOTES:

We use a 250 mM solution of iodoacetamide (IAM) as an alkylating reagent. Prepare a fresh 250 mM solution of iodoacetamide in DI water before use. 1. Weigh out 46 mg of IAM directly into a 1.5 mL microcentrifuge tube. 2. Add 1 mL of DI water to the tube and mix thoroughly. Non-reduced IgG Sample 1. In a microcentrifuge tube, dilute your IgG sample with 1X Sample Buffer to a concentration of 1 mg/mL in a final volume of 50 L. NOTE: Dilute at least 1:1 with 1X Sample Buffer. 2. Add 2 L of reconstituted 25X Internal Standard for every 50 L of sample volume. 3. Add 2.5 L of 250 mM IAM. 4. Mix thoroughly. 5. Centrifuge the tube and heat the mixture in a water bath or thermocycler at 70 C for 10 minutes. 6. Put the tube on ice for 5 minutes. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 118 7. Vortex briefly and spin down. Non-reduced IgG Standard (Optional) NOTE: The IgG Standard is lyophilized. Always reseal the foil bag containing the unopened tubes with des-

iccant to prevent moisture absorption. 1. Using scissors, carefully cut the top of the foil package, leaving the sealing strip intact. 2. Take out the strip of tubes and carefully cut one pink tube of lyophilized IgG Standard from the strip. Put the unopened tubes back in the package, seal tightly and store at 2-8 C. Pierce the foil on the tube with a clean pipette tip. Reconstitute the IgG Standard with 50 L of 1X Sample Buffer. Gently resuspend by pipetting the solu-

tion up and down. Transfer the solution to a microcentrifuge tube. 3. 4. 5. Add 2 L of reconstituted 25X Internal Standard. 6. Add 2.5 L of 250 mM IAM. 7. Mix thoroughly by vortex. NOTE: Heating in the presence of SDS linearizes the protein and allows for SDS binding. The alkylating agents prevent disulfide-bond scrambling catalyzed by free sulfhydryl groups. This minimizes the appear-

ance of fragments under non-reducing conditions. 8. Centrifuge the tube and heat mixture in a water bath or thermocycler at 70 C for 10 minutes. 9. 10. Vortex briefly and spin down. Put the tube on ice for 5 minutes. Transfer 50 L of each of your samples and IgG Standard to their designated wells in a 96-well plate. Spin Samples and Standards If youre using a 96-well plate:

1. 2. Cover the plate with a lid and spin for 10 minutes at 1000 xg in a centrifuge with a plate adapter. 3. If youre using vials:

1. 2. Close the vials with a clear screw cap. Transfer 50 L of your samples and IgG Standard to their designated sample vials with integrated inserts. Pop any bubbles in the samples with a clean pipette tip. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 119 3. Place the vials in a centrifuge using vial adapter (12 mm, 2 mL vials) and spin for 10 minutes at 1000 xg. Reagents NOTE: Don't reuse reagents, vials or the clear screw caps. Always keep the orange pressure caps paired with their respective reagents. If you want to reuse pressure caps, first wash them thoroughly with DI water, soak overnight in DI water, rinse caps thoroughly with DI water again and air dry them before reus-

ing. 1. Pipette 1.5 mL of Conditioning Solution 1 into a glass reagent vial, label and close with an orange pres-

sure cap. Pressure cap Glass reagent vial 2. 3. 4. Pipette 1.5 mL of Conditioning Solution 2 into a glass reagent vial, label and close with an orange pres-

sure cap. Pipette 1.0 mL of Wash Solution into a glass reagent vial, label each and close with an orange pressure cap. Pipette 1.5 mL of Wash Solution into two glass reagent vials. Label each and close both with clear screw caps. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 120 Clear screw cap Glass reagent vial Pipette 1 mL of Separation Matrix into a glass reagent vial, label and close with an orange pressure cap. Pipette 1 mL of Running Buffer - Bottom into a glass reagent vial, label and close with a clear screw cap. Pipette 1.5 mL of DI water into a glass reagent vials, label and close with an orange pressure cap. 5. 6. 7. 8. Close an empty glass reagent vial with an orange pressure cap. Step 2: Prep the Cartridge 1. Take the CE-SDS Cartridge out of its packaging. Save the packaging, youll need it later to store the car-

tridge. NOTE: When you remove the cartridge from its packaging, make sure the cartridge inlet doesnt come in contact with any surface. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 121 2. Pull the cartridge insert out of the cartridge. Cartridge Insert Optical Window Cartridge Inlet 3. Slide the Top Running Buffer vial into the cartridge insert so that the metal pin on the side of the vial is facing out. Press the vial up until it is completely inside the cartridge insert. NOTE: The Top Running Buffer vial has metal pins on either side, so no specific orientation is necessary. 4. Slide the cartridge insert back into the cartridge. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 122 Step 3: Install the Cartridge 1. Open Maurices door by touching the metal plate on top of the door. NOTE: The indicator light on Maurices front panel will blink rapidly as the door disengages. 2. Swing the door open to access the cartridge slot and the reagents and samples platform. The lights on either side of the slot will be orange. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 123 3. Lift the cartridge and hold it vertically using the finger holds on either side, cartridge inlet down, with the CE-SDS label facing you. 4. Gently insert it into the slot. Youll feel the alignment groove on the cartridge align inside the slot when you insert it. 5. Continue to slide the cartridge into the slot until the locking mechanism engages. The lights on either side of the slot will change to blue once the cartridge is installed correctly. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 124 Step 4: Load Samples and Reagents 1. Place the reagent vials into their respective positions in the sample and reagents platform:

NOTES:

The two reagent rows in Maurices reagent and sample platform are kept at room temperature. Pressure caps are orange and have a raised, ringed surface. They should only be used in Reagent Row P. Use reagent vials with clear screw caps in Row N. P1 - Conditioning Solution 1 with orange pressure cap P2 - Conditioning Solution 2 with orange pressure cap P3 - DI water with orange pressure cap P4 - Separation Matrix with orange pressure cap P5 - Wash Solution vial with orange pressure cap P6 - Empty vial (air) with orange pressure cap N1 - Wash Solution vial with clear screw cap N2 - Wash Solution vial with clear screw cap N4 - Running Buffer - Bottom with clear screw cap User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 125 2. Depending on what you prepared your samples in, put your 96-well sample plate in the metal plate insert or your sample vials in the metal vial insert. NOTE: Well A1 on the 96-well plate should be in the top left corner of the insert. 3. Close the instrument door. Maurice locks it automatically. Step 5: Create a Batch 1. 2. Launch Compass for iCE. Select the Batch tab. This is where youll enter sample/injection information, methods and batch parameters. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 126 3. To create a batch, make sure Maurice is connected to Compass for iCE. If he isnt, select Instrument and click Connect. Then select your Maurice system and click Connect. To create a new batch:

On Maurice systems - in the main menu, select File > New Batch > Maurice CE-SDS. On Maurice S. systems - in the main menu, select File > New Batch. To use an existing batch: In the main menu, select File > Open Batch. NOTE: If youre making changes to an existing batch, follow the steps in this section. Otherwise skip to Step 6: Start the Batch on page 133. 4. In the Layout pane, clicking on the vial/plate icon toggles between formats. Select a 96-well plate or 48 vials depending on what youre running. 5. Use your mouse to highlight the well positions for each of your samples, then click Add. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 127 This populates the Injections table:

6. Compass for iCE can monitor the current during a separation for you, stop it if the current drops below the minimum value and reinject the sample for you automatically. Reinjections are enabled by default, but if you dont want to use this feature just click the reinject icon to toggle it off. NOTES:

If a sample was reinjected, the injection row will be flagged in the Injections pane in the Run Summary screen. See Injection Flags on page 158 for more info. A maximum of 10 reinjections are allowed per batch. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 128 7. The sample platform is temperature controlled with a default setting of 10 C. To change the tempera-

ture or turn it off, click the down arrow next to the temperature and select an option. NOTE: The two reagent rows are kept at room temperature. 8. In the Methods pane:

NOTE: There are three default methods. We recommend using the default method parameters for the listed samples. Please see the Maurice CE-SDS Application Guide for more information on method optimi-

zation. a. Click the first cell in the Name column and enter a new method name if needed. b. Click the first cell in the Sample Load column, then click then click the selection button [...] to set your load profile time (in seconds) and voltage. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 129 c. Click the first cell in the Separation column then click the selection button [...] to set your separation time (in minutes) and voltage. NOTE: Run your reduced IgG samples and IgG Standard for 25 minutes and the CE-SDS MW Markers for 30 minutes. Run your non-reduced IgG samples and IgG Standard for 35 minutes. The default separation voltage for all sample types is 5750 volts. 9. You can now:

Make updates to the remaining methods by repeating the prior steps. Click New in the upper right corner of the Methods pane to add a new one if you want to use dif-

Select a method and click Remove in the upper right corner of the Methods pane to delete it. ferent methods for different samples. Then just repeat the steps above for the new method. 10. In the Injections pane:

a. To add sample names: Click the Sample ID cell for the injection and type a name. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 130 b. To assign methods for each injection: Click the Method cell for the injection and select a method from the drop down menu. To add sequential replicate injections: Highlight an injection and click Replicate. A new injec-

tion will be added under the row you selected To add injections at the end of the batch: Click on any sample position in the Layout pane or sample injection in the Injection table and click Add. A new injection using the same sample will be added to the end of the table. Assign the method if needed. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 131 To copy and paste injections: Right-click on an injection in the Injection table and select Copy. Click on the injection number above where you want to insert the copied injection, right click and select Paste. The copied injection will be inserted under the row you selected. 11. Click on the Notes pane, then click in the notes area and type any information you want to add about your batch (optional). 12. You can preset the parameters used to analyze data generated with the batch (optional). We recom-

mend using the default parameters for CE-SDS applications, but if you want to modify parameters:

a. Select Edit from the main menu and click Default Analysis. The following screen will display:

User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 132 b. Change the parameters you want to, then click OK. For detailed information on analysis parameters, please refer to Analysis Settings Overview on page 244 13. Once all of your sample, method and injection info is entered, select File > Save. Enter any comments on the batch if you want, then click Save. 14. Enter a name for your batch then click Save. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 133 Step 6: Start the Batch 1. Make sure Maurice is connected to Compass for iCE. If he isnt, select Instrument and click Connect. Then select your Maurice system and click Connect. 2. Click Start to start your batch. 3. The Start Run box shows you the number of injections and batches remaining on your cartridge. Make sure you still have enough injections left before you start the run. If not, prep a new cartridge. 4. Click in the Results File name box if you want to change the default run file name. Otherwise just leave it as is. If you dont want to save the file to the default Runs folder, click Browse to select a different location. Enter any run details youd like in the Comments box (optional). 5. 6. 7. Click Start to start the run. NOTE: The indicator light on Maurices front panel will pulse slowly while hes running the batch. User Guide for Maurice, Maurice C. and Maurice S. Running CE-SDS Applications page 134 To monitor the progress of your batch, click the Run Summary tab. See Chapter 9, Run Status for more details. To view results, analyze results or change analysis parameters on completed injections while the batch is still running, click the Analysis tab. See Chapter 11, CE-SDS Data Analysis for more details. User Guide for Maurice, Maurice C. and Maurice S. Post-batch Procedures page 135 When your batch is complete, you can view electropherograms for all injections in the Analysis tab, and all batch and injection details in the Run Summary tab. NOTE: If youd like Maurice to let you know when your run is done, you can set him up to tweet you. Go to Setting Up Maurice Systems to Send Tweets on page 383 for more info. Post-batch Procedures When the batch is done:

1. Open Maurices door. The lights on either side of the cartridge slot will be orange as Maurice will have already disengaged the cartridge. Remove your reagent vials and samples and discard. 2. 3. Gently pull out the cartridge making sure the cartridge inlet doesnt come into contact with any surface. User Guide for Maurice, Maurice C. and Maurice S. Post-batch Procedures page 136 NOTE: If you see any separation matrix sticking to the capillary inlet, soak it in DI water for 5 minutes. Then wipe it using a lint-free laboratory wipe that's been moistened with DI water. 4. 5. Pull the cartridge insert out. Remove the Top Running Buffer vial and dispose of it according to your institution's safety and waste disposal guidelines. 6. Check the saturation sensor on the back of the cartridge insert. If it's red, you'll need to use a new car-

tridge insert for your next batch. If the saturation sensor isn't red, you can keep using the current car-

tridge insert with that cartridge. Saturation Sensor NOTE: Don't dispose of the cartridge insert unless the saturation sensor is red. User Guide for Maurice, Maurice C. and Maurice S. Post-batch Procedures page 137 If you're at 100 injections, the cartridge is at its limit. Put it in its original packing and discard it along with the cartridge insert and the Top Running Buffer vial per your institution's safety and waste disposal guidelines. Discard the cleaning vial you've used with that cartridge too. NOTE: Disposal of cartridges, sample plates and vials depends on the samples you ran. If you arent sure what your sample origins are, we recommend you dispose of everything in biohazard waste. If you've still got injections left and the cartridge will be used again within 2 hours. You can leave the cartridge in Maurice. When you're ready to run the next batch, just replace the Top Running Buffer vial with a fresh one. If you've still got injections left and the cartridge won't be used within 2 hours. Clean and store the cartridge:

a. Pipette 1.5 mL of DI water in a new glass reagent vial and close it with an orange pressure cap. Place this vial in P3. Insert a Cleaning Vial into the cartridge insert. b. c. Slide the cartridge insert back into the cartridge. d. e. Insert the cartridge in Maurice. In the Compass main menu, select Instrument and click Cartridge Cleanup. User Guide for Maurice, Maurice C. and Maurice S. Post-batch Procedures page 138 I f. Youll get the following message. Click OK. Itll only take six minutes. g. Once the cleanup procedure is done, remove the cartridge. h. Pull the insert from the cartridge. i. Remove the Cleaning Vial and push the empty insert back into the cartridge. NOTE: The cleaning vial is paired with the cartridge and can be used for a maximum of three Cartridge Cleanup cycles of that cartridge. Dispose of the cleaning vial when you dispose of the cartridge. Don't use it with other cartridges. j. Put the cartridge back in its protective packaging and store it at room temperature.

!WARNING! SHARPS HAZARD The capillary inlet of the cartridge may present a potential sharps hazard. Dispose of used cartridges according to your organizations health and safety regulations. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 139

!WARNING! BIOHAZARD Cartridges, sample plates and vials should be handled by procedures recommended in the CDC/NIH manual: Biosafety in Microbiological and Biomedical Laboratories (BMBL). The manual is available from the U.S. Government Printing Office or online at http://

www.cdc.gov/biosafety/publications/bmbl5/. Depending on the samples used, the cartridges, plates and vials may constitute a chemi-

cal or a biohazard. Dispose of the cartridges, plates and vials in accordance with good lab-

oratory practices and local, state/provincial, or national environmental and health regulations. Read and understand the Safety Data Sheets (SDSs) provided by the manu-

facturers of the chemicals in the waste content before you store, handle, or dispose of chemical waste. Checking Your Data Compass for iCE detects your sample proteins, CE-SDS MW Markers and Internal Standard peaks and reports results automatically. But, we always recommend you review your data using the steps in this section as a good general practice to make sure your results are accurate. If you see a data warning in the Experiment pane, these steps will also help you identify and correct any issues. Step 1: Check Your Internal Standard To make sure your Internal Standard is identified correctly:

1. Go to the Analysis screen and open your run (if it isnt already open). 2. Click Standards in the View bar. 3. Click the Single View icon in the View bar. 4. Click Injection 1 in the Experiment pane. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 140 5. Check that your Internal Standard in the electropherogram has been correctly identified. Itll be labeled Std 1 and will have a green vertical line running through it. The Internal Standard is also identified with an S in the Peaks table. 6. If your Internal Standard isnt identified correctly, heres how to manually correct it:

To set an unidentified peak as the Internal Standard: Right-click the peak in the electropherogram or Peaks table and select Force Standard. Compass will assign that peak as the Internal Standard. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 141 A lock icon indicating the Internal Standard was set manually will display next to the peak in the Peaks table and a check mark will appear next to the injection in the Experiment pane to show a manual cor-

rection was made. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 142 NOTE: To remove an Internal Standard peak assignment that was made manually, right click on the peak in the electropherogram or Peaks table and click Clear. To clear all the manual settings for the injection, click Clear All. If an incorrect peak is identified as the Internal Standard: Right-click the peak in the electrophero-

gram or Peaks table and select Not a Standard. An S with a red slash through it will appear next to the incorrectly assigned peak in the Peaks table and a check mark will appear next to the injection in the Experiment pane to show a manual correction was made. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 143 7. Repeat the previous steps for all other injections to make sure your Internal Standard is identified cor-

rectly. Step 2: Set Your Molecular Weight (MW) Markers NOTE: Youll only need to do this if you ran the CE-SDS MW Markers. If you didnt, you can skip to the next section. Compass reports the relative migration time (RMT) of your sample in the Peaks table. If you also want to know the relative molecular weight of your sample, you can run the CE-SDS MW Markers as one of your injections. You'll see these sizing markers when you run the CE-SDS MW Markers: 10, 20, 33, 55, 103, 178, and 240 kDa. To get MW data:

1. Click Samples in the View bar. 2. Select Edit from the main menu and click Analysis. In the Analysis window, select Markers in the left sidebar. Then click the Markers Injection drop down menu to select the injection you ran your CE-SDS MW Markers in. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 144 3. The default Maurice CE-SDS MW Markers molecular weights and relative migration time (RMT) values are already populated in the table. If youd like to use these values, skip to the next step. If youre using different markers, click in the MW and RMT cells to type new values, click a row and select Remove to delete, or click Add to add a new one. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 145 4. Click OK to close the Analysis window. Compass will automatically assign the molecular weights to your makers and label them Mkr. A MW (kDa) column will also now display in the Peaks table. NOTE: The Mkr 10 peak is also the Internal Standard in every sample. 5. It's always a good idea to verify that all your CE-SDS MW Markers are identified correctly. Heres how to manually correct them:

To set an unidentified peak as a MW Marker: Right-click the peak in the electropherogram or Peaks table and select Add Peak. Compass will assign that peak as a MW Marker, and correctly reassign the remaining marker peaks. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 146 A check mark will appear next to the injection in the Experiment pane to show a manual correction was made. NOTE: To remove MW Marker peak assignments that were made manually, right click on the peak in the electropherogram or Peaks table and click Clear. If an incorrect peak is identified as a MW Marker: Right-click the peak in the electropherogram or Peaks table and select Remove Peak. Compass should correctly reassign the remaining peaks as mark-

ers and update the Peaks table. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 147 A check mark will appear next to the injection in the Experiment pane to show a manual correction was made. Step 3: Checking Sample Peaks All detected peaks will be labeled automatically with the RMT (default) or apparent MW (if the CE-SDS MW Markers were run). To make sure your sample proteins are identified correctly:

1. Click Samples in the View bar. 2. Click the Single View icon in the View bar. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 148 3. Click Injection 1 in the Experiment pane. 4. If your sample peaks arent identified correctly, heres how to manually correct them:

If a peak is incorrectly identified as a sample peak: Right-click the peak in the electropherogram or Peaks table and select Remove Peak. Compass will no longer identify it as a sample peak in the electro-

pherogram and the peak data will be removed in the results table. A check mark will appear next to the injection in the Experiment pane to indicate a manual correction was made. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 149 To identify a peak as a sample peak: Right-click the peak in the electropherogram or Peaks table and select Add Peak. Compass will calculate and display the results for the peak in the results table and identify the peak in the electropherogram. A check mark will appear next to the injection in the Experiment pane to indicate a manual correction was made. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Data page 150 NOTE: To remove sample peak assignments that were made manually and go back to the original peak data, right-click the peak in the electropherogram and select Clear. 5. Repeat the previous steps for the remaining injections to make sure all sample peaks are correctly iden-

tified. Step 4: Assigning Peak Names Compass can also optionally identify and automatically name sample peaks using user-specified peak name settings. For more information on how to do this, see Peak Names Settings on page 354. User Guide for Maurice, Maurice C. and Maurice S.

page 151 Chapter 9:

Run Status Run Summary Screen Overview Batch Injection Information Run Status Information Viewing the Focus Series (cIEF Only) Viewing the Separation (CE-SDS Only) Chapter Overview Opening Run Files Current and Voltage Plots Closing Run Files Run History Viewing Run Errors Injection Reports Switching Between Open Run Files User Guide for Maurice, Maurice C. and Maurice S. page 152 Chapter 9: Run Status Run Summary Screen Overview You can use the Run Summary screen to monitor the stats of a batch in progress, see the CE-SDS separation or cIEF Focus series for your injections or the current and voltage plots for each injection. To get to this screen, click the Run Summary screen tab:

Run Summary Screen Panes The Run Summary screen has five panes:

Injections - Lists the sample IDs, sample locations and methods used for each injection in the run. It also shows the status of the current injection if a run is in progress. Status - Displays run file information and the current status of a run if ones in progress. History - Running history of all run file events from when the run was first started to the most current analysis update. Separation Plot (CE-SDS only)- Lets you view the raw protein separation in the capillary for each injection. Focus Series (cIEF only) - Lets you view the recorded focusing of proteins along the pH gradient in the capillary for each injection. IV Plot - Lets you view plots of the total current and voltage measured during the separation for each injection. User Guide for Maurice, Maurice C. and Maurice S. Run Summary Screen Overview page 153 User Guide for Maurice, Maurice C. and Maurice S. page 154 Chapter 9: Run Status Software Menus Active in the Run Summary Screen These main menu items are active in the Run Summary screen:

Window Help File Edit Instrument (when the software is connected to an instrument) User Guide for Maurice, Maurice C. and Maurice S. Run Summary Screen Overview page 155 File Menu These File menu options are active:

Open Run - Opens a run file. Add Run - Lets you open and view other run files besides the one thats already open. Close - Closes the run file currently being viewed. Close All - Closes all open run files. Save/Save As - If you made changes in the Analysis screen before you went to the Run Summary screen, this saves your changes to the run file. Injection Report - Exports the raw and analyzed data, IV plot, peaks table, sample and system info for individual injections as PDF files. You can also export the run history with all analysis events. Exit - Closes Compass for iCE. Edit Menu These Edit menu options are active:

Copy - Copies the information in the History pane so you can paste it into other documents. Preferences - Lets you set and save your preferences for data export, graph colors, grouped data and Twitter settings. See Chapter 13, Setting Your Preferences for more information. User Guide for Maurice, Maurice C. and Maurice S. page 156 Chapter 9: Run Status Opening Run Files You can open one run file or multiple files at the same time to compare information between runs. Opening One Run File 1. Select File in the main menu and click Open Run. 2. A list of the last 10 runs opened will display. Select one of these runs or click Browse to open the Runs folder and select a different file. Opening Multiple Run Files 1. To open the first run file, select File in the main menu and click Open Run. 2. A list of the last 10 runs opened will display. Select one of these runs or click Browse to open the Runs folder and select a different file. User Guide for Maurice, Maurice C. and Maurice S. Batch Injection Information page 157 3. To open another run file, select File in the main menu and click Add Run. 4. A list of runs will display. You can only open a run that uses the same application as the run thats already open (cIEF or CE-SDS), so the run files displayed are only for that application. Select one of these runs or click Browse to open the Runs folder and select a different file. Repeat the last two steps to open additional runs. 5. Batch Injection Information The Injections pane lists the system protocols (Setup and Cleanup) and injections performed during the run. User Guide for Maurice, Maurice C. and Maurice S. page 158 Chapter 9: Run Status Clicking on an injection displays its data in the Focus Series (cIEF) or Separation (CE-SDS) and IV Plot panes. Hovering over a method name displays the method parameters:

For runs in progress, the Status column displays:

Running for Setup, Conditioning (CE-SDS only) and Cleanup protocols that are in progress Loading or Separating for injections in progress. Once the separation starts, a status bar displays next to the injection so you know when the separation will be done. Hovering your mouse over the progress bar tells you the time left for the injection. Completed for Setup, Conditioning and Cleanup protocols and injections that are done. Injection Flags If Compass for iCE detects a potential injection issue, a flag icon will display next to the injection row in the Injections pane. Past cartridge injection limit notification - This means the injection is over the guaranteed number of injections for the cartridge. Roll your mouse over the icon to display details. User Guide for Maurice, Maurice C. and Maurice S. Run Status Information page 159 Reinjection notification (CE-SDS only) - This means the current during the separation dropped below the minimum value, so the separation was stopped and the sample was rein-

jected. The second injection always runs to completion even if the current drops again. Roll your mouse over the icon to display details. Run Status Information The Status pane shows info specific to each run file:

Cartridge serial number Run file name and path (directory location) Batch name and type Instrument and serial number Type of sample tray used Run start/complete date and time Type of cartridge User Guide for Maurice, Maurice C. and Maurice S. page 160 Chapter 9: Run Status Cartridge batch injection limit, injections/batches remaining and expiration date To go to the run file directory location - Double click the path hyperlink, or right-click and select Open Directory. To copy the path - Right-click on the path hyperlink and click Copy. The path can then be copied into documents. The path can also be copied into the Windows Explorer address bar to launch Com-

pass for iCE and open the run file automatically. User Guide for Maurice, Maurice C. and Maurice S. Viewing the Focus Series (cIEF Only) page 161 Viewing the Focus Series (cIEF Only) You can view your proteins focusing along the pH gradient in the capillary for each injection in the Focus Series pane. NOTE: The Focus Series plot displays in absorbance only, even if the fluorescence detection mode is selected in the Analysis settings. Select an injection in the Injections pane. 1. 2. Click the Focus Series pane. Itll display the final focusing plot:

User Guide for Maurice, Maurice C. and Maurice S. page 162 Chapter 9: Run Status 3. To view the focusing as it happened, drag the slider bar under the plot to the left or right. To view it frame by frame, click the left/right arrows. To zoom in on an area of the plot - Hold the mouse button down and draw a box around the area with the mouse. To zoom out - Click Zoom Out in the upper right corner of the pane. NOTE: Focus Series data for a run in progress wont be available until the injection is executing. Once it starts, the plot displays data up to the current point in time. Viewing the Separation (CE-SDS Only) You can view your protein separation in the capillary for each injection in the Separation pane. User Guide for Maurice, Maurice C. and Maurice S. Current and Voltage Plots page 163 Select an injection in the Injections pane. 1. 2. Click the Separation pane. Itll display a plot of the raw separation data. To zoom in on an area of the plot - Hold the mouse button down and draw a box around the area with the mouse. To zoom out - Click Zoom Out in the upper right corner of the pane. NOTE: Separation data for a run in progress wont be available until the injection is executing. Once it starts, the plot displays data up to the current point in time. Current and Voltage Plots To view plots of the total current and voltage measured during an injection:

1. Select an injection in the Injections pane. User Guide for Maurice, Maurice C. and Maurice S. page 164 Chapter 9: Run Status 2. Click the IV Plot pane. The blue Y-axis and plot shows the run voltage in volts (V), and the red Y-axis and plot shows the run current in microamps (A). The X-axis displays time in seconds. To zoom in on an area of the plot - Hold the mouse button down and draw a box around the area with the mouse. To zoom out - Click Zoom Out in the upper right corner of the pane. NOTE: IV Plots for a run in progress wont be available until the injection is executing. Once it starts, the plot displays in real time. User Guide for Maurice, Maurice C. and Maurice S. Run History page 165 Run History The History pane shows the run file event history, starting with the date and time the run was started through the most current analysis event. Clicking on a row in the table displays the full event details in the box under the table. Date: Date and time of the run event. User Name: User that initiated the event. User names only display if youre using the Access Con-

trol feature to help satisfy the 21CFR Part 11 data security requirements. Message: Description of the event that took place. Comment: Comments entered by the user when the batch was saved. Viewing Multiple Events Items in the table with multiple analysis events have an arrow next to the date and time. You can view or hide these details by toggling the arrow:

User Guide for Maurice, Maurice C. and Maurice S. page 166 Chapter 9: Run Status To view details for all items with multiple analysis events in the run, click the Expand All button. User Guide for Maurice, Maurice C. and Maurice S. Viewing Run Errors page 167 To hide all items with multiple analysis events, click the Collapse All button. Copying History Info You can copy the information in the History pane to use in other documents:

1. Click the History pane to make sure its active. 2. Click Edit in the main menu and select Copy. 3. Open a document and click Paste. Viewing Run Errors If an error is detected during the run it will display in the Status pane:

User Guide for Maurice, Maurice C. and Maurice S. page 168 Chapter 9: Run Status Injection Reports You can export PDF files of the raw and analyzed data, IV plot, peaks table, sample and system info for indi-

vidual or all injections in a run file. You can also export the run history with all analysis events. 1. Click File > Open Run and select a run file. 2. If you want reports for all injections, skip to the next step. Otherwise, select the injection in the Injection pane that you want a report for. Select File from the main menu in either screen and click Injection Report. In the Injection Reports window:

a. Choose either Selected injections or All injections. b. Select the Analysis log checkbox if you want a run history report with all analysis events. c. The report name defaults to the run file name. If you want to change it, type in the Report Name box to make updates. d. Click OK. 3. 4. User Guide for Maurice, Maurice C. and Maurice S. Injection Reports page 169 5. The Injection Report PDF(s) are exported to the Runs folder in the Compass for iCE directory. Theyll be in a folder with the report name used in the prior step. When the reports are done, the folder opens for you automatically. Example Analysis and Injection Report: CE-SDS User Guide for Maurice, Maurice C. and Maurice S. page 170 Chapter 9: Run Status User Guide for Maurice, Maurice C. and Maurice S. Injection Reports page 171 User Guide for Maurice, Maurice C. and Maurice S. page 172 Chapter 9: Run Status Example Analysis and Injection Report: cIEF User Guide for Maurice, Maurice C. and Maurice S. Injection Reports page 173 User Guide for Maurice, Maurice C. and Maurice S. page 174 Chapter 9: Run Status Switching Between Open Run Files If youve got more than one run file open, you can switch between viewing the run information in each. User Guide for Maurice, Maurice C. and Maurice S. Closing Run Files page 175 1. Click the down arrow in the Run box. 2. Select the run you want to view from the drop down list. Closing Run Files If youve got more than one run file open, you can close just one file or all the open files at the same time. To close the run file being viewed - Select File from the main menu and click Close. To close all open run files - Select File from the main menu and click Close All. User Guide for Maurice, Maurice C. and Maurice S. page 176 Chapter 9: Run Status User Guide for Maurice, Maurice C. and Maurice S. page 177 Chapter 10:

Controlling Maurice, Maurice C. and Maurice S. Instrument Control Stopping a Run Status Modes Instrument Software (Embedded) Updates Self Test Viewing and Changing System Properties Chapter Overview Checking Cartridge Status Viewing Log Files User Guide for Maurice, Maurice C. and Maurice S. page 178 Chapter 10: Controlling Maurice, Maurice C. and Maurice S. Instrument Control The Instrument menu lets you to control Maurice, Maurice C. and Maurice S. NOTE: Instrument menu options are only active when youve got a computer with Compass for iCE soft-

ware connected directly to your Maurice system. Starting a Run To start your run, click the Start button in the Batch screen. You can also start a run by selecting Instrument in the main menu and clicking Start. For more info on creating and starting batches check out Chapter 7, Running cIEF Applications on Maurice and Maurice C. or Chapter 8, Running CE-SDS Applications on Maurice and Maurice S. Cleaning Cartridge Cleanup (CE-SDS Cartridges Only) If you've still got injections left after your last run and you wont use the cartridge again within 2 hours, youll need to run a clean up and store it. Check out page 137 for the details on how to do that. Cartridge Purge Youll want to run the Cartridge Purge any time you have to stop a run manually or if the run stops because of an error. This runs the Cleanup step that normally happens at the end of a batch. It flushes the cartridge of any reagents and samples so its ready to go for the next run. 1. In the Batch screen, select File > Open Batch and click Browse. User Guide for Maurice, Maurice C. and Maurice S. Instrument Control page 179 2. Go to the New Batches folder and select either Maurice cIEF Cartridge Purge or Maurice CE-SDS Car-

tridge Purge, depending on what cartridge youre using. 3. After the purge batch loads, just click Start. The CE-SDS Cartridge purge takes about 25 minutes, and the cIEF one takes a little over 10 minutes. User Guide for Maurice, Maurice C. and Maurice S. page 180 Chapter 10: Controlling Maurice, Maurice C. and Maurice S. 4. Once the purge is done, if youll be starting a new run:

cIEF Cartridges: If you've still got injections left and the cartridge will be used again within 24 hours, you don't need to do anything. Just leave the cartridge in Maurice. CE-SDS Cartridges: If you've still got injections left and the cartridge will be used again within 2 hours, you'll just need to put in a new Top Running Buffer vial in the cartridge insert. If you wont be starting a new run:

CE-SDS Cartridges: Follow the steps in Post-batch Procedures on page 135. cIEF Cartridges: Follow the steps in Post-batch Procedures on page 102. Stopping a Run 1. Click Stop. 2. Click Yes in the pop-up window. User Guide for Maurice, Maurice C. and Maurice S. Status Modes page 181 3. When the run stops, run the Cartridge Purge on page 178. 4. Once the purge is done:

If youll be starting a new run:

cIEF Cartridges: If you've still got injections left and the cartridge will be used again within 24 hours, you don't need to do anything. Just leave the cartridge in Maurice. CE-SDS Cartridges: If you've still got injections left and the cartridge will be used again within 2 hours, you don't need to do anything other than prepare the cartridge for the next batch as described Step 2: Prep the Cartridge on page 120. If you wont be starting a new run:

CE-SDS Cartridges: Follow the steps in Post-batch Procedures on page 135. cIEF Cartridges: Follow the steps in Post-batch Procedures on page 102. Status Modes The instrument status bar displays status, buttons and progress bars depending on what Maurice, Maurice C. or Maurice S. are doing. Ready/Start button - The instrument is ready and a batch is loaded. Click Start to begin a run. Not Ready/Reset button - The instrument isnt ready and needs to reinitialize. Click Reset to start the initialization protocol. Running/Stop button - The instrument is running. The run name, time it started and when it will be done show in the run progress bar. Click Stop to stop the run. Cleaning/Stop button - The instrument is running a cleaning protocol. The time the cleaning proto-

col started and when it will be done show in the run progress bar. Error/Reset button - Theres an error. Go to the Status pane in the Run Summary screen to view details. When youve fixed the source of the error, click Reset. Shutdown Close Compass for iCE software. Maurice can stay on unless he wont be used for an extended period. Instrument Software (Embedded) Updates To check for embedded software updates:

User Guide for Maurice, Maurice C. and Maurice S. page 182 Chapter 10: Controlling Maurice, Maurice C. and Maurice S. If youre on the network:

1. Select Instrument > Update, then select Network. 2. The following screen displays. Click Update. If youre not on the network:

1. Call ProteinSimple Technical Support or your FAS for assistance on getting the latest update. 2. Copy the new embedded software file onto Maurices computer. 3. Select Instrument > Update, then select Local. 4. 5. Browse to the location of the embedded software file, select it and click OK. The following screen displays. Click Update. User Guide for Maurice, Maurice C. and Maurice S. Self Test page 183 Self Test Maurice, Maurice C. and Maurice S. can run a series of self tests for you to make sure theyre operating prop-

erly. 1. 2. To start the test, select Instrument > Self Test. The following screen displays. Click OK. The test takes approximately 11 minutes. NOTE: We recommend running the self test before you start a run. User Guide for Maurice, Maurice C. and Maurice S. page 184 Chapter 10: Controlling Maurice, Maurice C. and Maurice S. To view the results when the tests done, select Instrument > Properties and click Test Log. See Self Test Logs on page 192 for more info. System Name System Location Instrument Type Serial number Instrument software version (firmware) Viewing and Changing System Properties Selecting Instrument > Properties displays your system properties. They include:

Network name and address Date and time of the instrument clock Adapter block currently in use Number of hours on the Deuterium (UV) lamp Current sample chiller temperature User Guide for Maurice, Maurice C. and Maurice S. Checking Cartridge Status page 185 Insert image here. To change the system name or location: Click in the name or location boxes and enter your new info, then click OK. To sync the instrument clock with the computer: Click Set to PC time. Checking Cartridge Status If youve got a cartridge installed in the system, you can see its serial number, the injections and batches it still has available, and a history of batches and injections its run to date. To view this info, select Instrument

> Properties. User Guide for Maurice, Maurice C. and Maurice S. page 186 Chapter 10: Controlling Maurice, Maurice C. and Maurice S. Insert image here. Viewing Log Files Runs Log To see a history of all runs your system has performed, select Instrument > Runs:

User Guide for Maurice, Maurice C. and Maurice S. Viewing Log Files page 187 To open a run file: Select a run file from the list and click Open. To save a run file: Select a run file from the list and click Save. This lets you save a copy of a com-

pleted run or one in progress to either a USB drive or the local computer. To delete a run file: Select a run file from the list and click Delete. The run file will be deleted from the history and from the Run file in the Compass for iCE directory. System Logs 1. 2. Click Error Log. A list of system logs displays:

Select Instrument > Properties to display your systems properties. User Guide for Maurice, Maurice C. and Maurice S. page 188 Chapter 10: Controlling Maurice, Maurice C. and Maurice S. 3. To view a log, select it in the list and click View. User Guide for Maurice, Maurice C. and Maurice S. Viewing Log Files page 189 4. Click Save File As to save a copy of the log file. Error Log 1. 2. Click Error Log. A list of system logs displays:

Select Instrument > Properties to display your systems properties. User Guide for Maurice, Maurice C. and Maurice S. page 190 Chapter 10: Controlling Maurice, Maurice C. and Maurice S. 3. Select the error.log youre interested in from the list and click View. User Guide for Maurice, Maurice C. and Maurice S. Viewing Log Files page 191 4. Click Save File As to save a copy of the log file. User Guide for Maurice, Maurice C. and Maurice S. page 192 Chapter 10: Controlling Maurice, Maurice C. and Maurice S. Self Test Logs 1. 2. Click Test Log. A list of dates each self test was run displays:

Select Instrument > Properties. User Guide for Maurice, Maurice C. and Maurice S. Viewing Log Files page 193 3. Select a test date in the list and click View to see the individual test results:

4. Click Save File As to save a copy of the test log file. User Guide for Maurice, Maurice C. and Maurice S. page 194 Chapter 10: Controlling Maurice, Maurice C. and Maurice S. Command Log 1. 2. Click Command Log. A list of system commands displays:

Select Instrument > Properties to display your systems properties. User Guide for Maurice, Maurice C. and Maurice S. page 195 Chapter 11:

CE-SDS Data Analysis Viewing Run Data Exporting Run Files Chapter Overview Analysis Screen Overview Opening Run Files How Run Data is Displayed Data Notifications and Warnings Checking Your Results Group Statistics Copying Results Tables and Graphs Changing Sample Protein Identification Changing the Electropherogram View Closing Run Files Analysis Settings Overview Advanced Analysis Settings Markers Analysis Settings Peak Fit Analysis Settings Peak Names Settings Injection Reports Importing and Exporting Analysis Settings User Guide for Maurice, Maurice C. and Maurice S. page 196 Chapter 11: CE-SDS Data Analysis Analysis Screen Overview You can use the Analysis screen to view electropherograms and tabulated results for your injections. If any post-run analysis is needed, you can do it here too. To get to this screen, click the Analysis screen tab:

Analysis Screen Panes The Analysis screen has four panes:

Experiment - Lists the injection number, sample IDs, sample locations and methods for each injec-

tion in the run and lets you get a quick view of method parameters. Graph - Displays the electropherograms for sample proteins or standards. Peaks - Shows the tabulated results for sample proteins, internal standards and CE-SDS MW Markers. Injections - Displays a list of the sample proteins Compass for iCE names automatically using the user-defined peak name analysis parameters. User Guide for Maurice, Maurice C. and Maurice S. Analysis Screen Overview page 197 Software Menus Active in the Analysis Screen These main menu items are active in the Analysis Screen:

Window Help File Edit View Instrument (when Compass for iCE is connected to Maurice, Maurice C. or Maurice S.) File Menu These File menu options are active:

Open Run - Opens a run file. Add Run - Lets you open and view other run files besides the one thats already open. Close - Closes the run file currently being viewed. Close All - Closes all open run files. Save/Save As - If you made changes in the Analysis screen before you went to the Run Summary screen, this saves your changes to the run file. Export Tables - Exports the results for all injections in the run in .txt format. Export Spectra - Exports the raw and analyzed data traces and background for each injection in the run in .txt or .cdf format. Injection Report - Exports the raw and analyzed data, IV plot, peaks table, sample and system info for individual injections as PDF files. You can also export the run history with all analysis events. User Guide for Maurice, Maurice C. and Maurice S. page 198 Chapter 11: CE-SDS Data Analysis Exit - Closes Compass for iCE. Edit Menu These Edit menu options are active:

Copy - Copies the information in the History pane so you can paste it into other documents. Analysis - Displays the analysis settings used to analyze the run data and lets you change them as needed. See Analysis Settings Overview on page 244 for more information. Preferences - Lets you set and save your preferences for data export, graph colors, grouped data and Twitter settings. See Chapter 13, Setting Your Preferences for more information. View Menu These View menu options are active:

Single View - Displays the data for only the injections selected. Multiple View - Displays data for all injections so you can scroll through them. Standards - Lets you view data just for the internal standards in your injections. Samples - Lets you view data just for sample proteins in your injections. Grouping - Displays data for injection groups. View Region - Lets you change the x-axis range of the data displayed. Show Hidden- Shows injections that are hidden from the data view. User Guide for Maurice, Maurice C. and Maurice S. Opening Run Files page 199 Opening Run Files You can open one run file or multiple files at the same time to compare information between runs. Opening One Run File 1. Select File in the main menu and click Open Run. 2. A list of the last 10 runs opened will display. Select one of these runs or click Browse to open the Runs folder and select a different file. Opening Multiple Run Files 1. To open the first run file, select File in the main menu and click Open Run. 2. A list of the last 10 runs opened will display. Select one of these runs or click Browse to open the Runs folder and select a different file. User Guide for Maurice, Maurice C. and Maurice S. page 200 Chapter 11: CE-SDS Data Analysis 3. To open another run file, select File in the main menu and click Add Run. 4. A list of CE-SDS runs will display. Select one of these runs or click Browse to open the Runs folder and select a different file. When a run is added, its data appends to the open run file and displays as a second set of injections in all screen panes. The second run file name also appears in the title bar:

5. Repeat the last two steps to add additional runs. User Guide for Maurice, Maurice C. and Maurice S. How Run Data is Displayed page 201 How Run Data is Displayed Data in the run file is organized for easy review. Experiment Pane: Batch Injection Information The Experiment pane lists all the injections performed in the run, which samples were used for each, the sample location in the 96-well plate or 48-vial tray and the method used. To view all columns - Use the scroll bar or click Maximize in the upper right corner. To resize columns - Roll the mouse over a column border until the sizing arrow appears, then click and drag to resize. To view method parameters - Hover the mouse over a method name. NOTE: Data notification icons will display in the Injection column if Compass for iCE detects a potential analysis issue or data was manually modified by the user. For more information see Data Notifications and Warnings on page 214. Graph Pane: Electropherogram Data The Graph pane displays the electropherogram(s) for sample proteins or internal standards depending on the view options youve selected. User Guide for Maurice, Maurice C. and Maurice S. page 202 Chapter 11: CE-SDS Data Analysis You can get more info on graph view options in Changing the Electropherogram View on page 226. Peaks Pane: Calculated Results The Peaks pane shows the tabulated results for your sample proteins or internal standards. Each row in the table has the individual results for each peak detected in an injection. Results shown will either be for one injection or multiple injections, samples or standards depending on the view options youre using. Check out Viewing Run Data on page 205 for more info. NOTES:

Peaks that Compass for iCE names automatically with user-defined peak name settings are color-coded. When the Standards view is selected, the information in the Peaks table includes only injection, sample, peak, time and height. Internal standards the software has identified are marked with an S. To view all rows - Use the scroll bar or click Maximize in the upper right corner. User Guide for Maurice, Maurice C. and Maurice S. How Run Data is Displayed page 203 To resize columns - Roll the mouse over a column border until the sizing arrow appears, then click and drag to resize. The following results and info are listed in the Peaks table:

Injection - Injection number. Sample - If sample names were entered in the batch, those names will display here. Otherwise, Sample

(default name) will display. Peak - Peaks are numbered in order of detection. Name - Displays peaks Compass for iCE named automatically using the user-defined peak name anal-

ysis parameters. These cells are blank if the software wasnt able to name the peak or if you didnt enter naming parameters. Time - Peak detection time (seconds). This is the elapsed time between the start of the separation and when the peak is detected. RMT - Relative migration time of the peak to the Internal Standard which has an RMT of 1.0. MW (kDa) - Displays the relative molecular weight in kDa for sample peaks. MW only displays if youve run the CE-SDS MW Markers as one of the injections in the run and identified that injection in your analysis parameters. Height - The calculated peak height. Raw Area - Displays the uncorrected peak area. Area - Displays the time-corrected peak area. This includes corrections for big and/or slow moving peaks which can be artificially large when uncorrected.

% Total - Displays the peak area ratio compared to the sum of all peak areas (excluding the Internal Standard peak). This value results from dividing the individual peak area by the sum of all peak areas for the injection and multiplying by 100.

% Area - Displays the calculated percent area for the named peak compared to all named peaks. This value results from dividing the individual peak area by the sum of all named peak areas for the injec-

tion and multiplying by 100 (shown for named peak sample data only). Width - Displays the calculated peak width (sample data only). Baseline - Displays the raw baseline signal of each peak. Resolution - Displays resolution of the peak compared to neighboring peaks. Two peaks that are baseline resolved will have a resolution value of 1.5. Smaller values means the peaks are not com-

pletely resolved, larger values mean the peaks are fully resolved. User Guide for Maurice, Maurice C. and Maurice S. page 204 Chapter 11: CE-SDS Data Analysis Injections Pane: User-Specified Peak Names The Injections pane shows tabulated results for sample proteins Compass for iCE labels automatically using user-defined peak name settings. Each row in the table shows the individual results for the named peaks detected in each injection. NOTES:

Peaks that Compass for iCE names automatically with user-defined peak name settings are color-coded. When the Standards view is selected, the information in the Injections table includes only injection, sam-

ple and std 1 (the migration time of the standard peak). To view all rows - Use the scroll bar or click Maximize in the upper right corner. To resize columns - Roll the mouse over a column border until the sizing arrow appears, then click and drag to resize. The following results and info are listed in the Injections table:

Injection - Injection number. Sample - If sample names were entered in the batch, those names will display here. Otherwise, Sample

(default name) will display. Peak Name Columns - An individual column per peak name will display for every peak identified by name or as a MW Marker peak in the run data. Cells for injections in these columns will be blank if Compass for iCE didnt find peaks automatically using the user-defined peak name analysis and maker parameters (or none were entered). To view peak area in the peak name columns (default) - Select Area in the upper right corner of the pane. This displays calculated peak area for the individual peak only. To view % total in the peak name columns - This displays the calculated percent area for the named peak compared to all named peaks. This value results from dividing the individual peak area by the sum of all named peak areas for the injection and multiplying by 100. User Guide for Maurice, Maurice C. and Maurice S. Viewing Run Data page 205 NOTE: The sum of the named peak percentages can be less than 100% if some peaks arent named. To view % area in the peak name columns - This displays the peak area ratio compared to the sum of all named peak areas. This value results from dividing the individual peak area by the sum of all peak areas for the injection and multiplying by 100. Viewing Run Data The Analysis screen lets you view data for just one injection, specific injections or all injections in the run. Each run file has data for the sample proteins and the Internal Standard detected in each injection. Switching Between Samples and Standards Data Views Heres how you switch between viewing data for your samples and standards:

To view sample data - Click Samples in the View bar or select View in the main menu and click Samples. Data in this view is for sample proteins only. User Guide for Maurice, Maurice C. and Maurice S. page 206 Chapter 11: CE-SDS Data Analysis The graph displays electropherograms with a y-axis of Absorbance units (mAU) and an x-axis of RMT (relative migration time). Results for each protein are shown in the Peaks and Injections panes. For information on checking and identifying sample peaks, see Checking Your Data on page 139. To view Internal Standard data - Click Standards in the View bar or select View in the main menu and click Standards. Data in this view is for analyzing standards only. This is the Internal Standard you add to your sam-

ples during prep. The graph displays electropherograms with a y-axis of Absorbance units (mAU) and an x-axis of time in seconds. User Guide for Maurice, Maurice C. and Maurice S. Viewing Run Data page 207 The Internal Standard is identified in the Peaks pane with an S and as Std1 in the Injections pane. For information on checking and identifying the Internal Standard peak, see Checking Your Data on page 139. User Guide for Maurice, Maurice C. and Maurice S. page 208 Chapter 11: CE-SDS Data Analysis Selecting and Displaying Injection Data You can view data from one, multiple, or all injections at once. To look at data for one injection - Click an injection row in the Experiment pane. Data for just that injection displays in the graph and tables. User Guide for Maurice, Maurice C. and Maurice S. Viewing Run Data page 209 To look at data for specific injections - Hold the Ctrl key and select just the injection rows you want to view in the Experiment pane. Data for only the injections selected display in the graph and tables. User Guide for Maurice, Maurice C. and Maurice S. page 210 Chapter 11: CE-SDS Data Analysis To look at data for sequential injections - Select the first injection row in the Experiment pane that you want to view, then hold the Shift key and select the last. This selects all rows between the two injections. Data for only the injections selected display in the graph and tables. User Guide for Maurice, Maurice C. and Maurice S. Viewing Run Data page 211 To look at data for all injections - Just click View All in the View bar. Data for all injections displays in the graph and tables. Switching Between Single and Multiple Views of Injections You can switch between displaying run data in a single, per-injection format or a multi-injection format. To view data per in a per-injection format - Click Single View in the View bar or select View in the main menu and click Single View. Data for the injection row(s) selected in the Experiment pane:

Displays with electropherograms either overlaid or stacked in the Graph pane depending on the option youve got chosen. User Guide for Maurice, Maurice C. and Maurice S. page 212 Chapter 11: CE-SDS Data Analysis Shows only results for the selected row(s) in the Peaks and Injections panes. To view data in a multi-injection format - Click View All in the View bar or select View in the main menu and click Multiple View:

Data for the injection row(s) selected in the Experiment pane:

Displays with the electropherograms of the selected injections highlighted in the Graph pane. Shows the results for the selected injections highlighted in the Peaks and Injections panes. User Guide for Maurice, Maurice C. and Maurice S. Viewing Run Data page 213 Hiding Injection Data You can hide injection data from the view if needed. To hide injections - Select the injection rows you want to hide in the Experiment pane, then right click one and select Hide. Data for the injections will be hidden in all data views and results tables. User Guide for Maurice, Maurice C. and Maurice S. page 214 Chapter 11: CE-SDS Data Analysis To view hidden injections - Select View in the main menu and click Show Hidden. Hidden rows will become visible again in all panes, and are marked with an X in the Experiment pane. To unhide injections - Select the hidden row(s). Right click on one and click Unhide. Data Notifications and Warnings If Compass for iCE detects a potential data issue, a notification or warning icon will display next to the injec-

tion row in the Experiment pane. Manual correction of sample data notification - This means the sample data was manually changed by a user, for example to add or remove a sample peak. Roll your mouse over the icon to display the type of modification that was made. Standards warning - This means the Internal Standard may not be identified properly. You can fix this by manually identifying the standard using the steps in Step 1: Check Your Internal Standard on page 139. Roll your mouse over the icon to display warning details. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Results page 215 Manual correction of standards data notification - This means a user changed the stan-

dards data manually. Roll your mouse over the icon to display the type of modification that was made. Peak fit warning - Means that a peak cant be fit properly. This can sometimes be caused when a broad peak is fitted as multiple narrow peaks. Changing the peak width can help in this case. The warning is also caused by very small peaks around main peaks, or small peaks that are close to the end of the separation range. You can often fix this by removing the peak(s) using the steps in Step 3: Checking Sample Peaks on page 147. Roll your mouse over the icon to display warning details. Checking Your Results Compass for iCE detects your sample protein, CE-SDS MW Markers and Internal Standard peaks and reports results automatically. But, we always recommend you review and check your data as a good general practice to make sure your results are accurate. Please see the step by step procedure in Checking Your Data on page 139 to do this. If you see a data warning in the Experiment pane, these steps will also help you identify and correct any issues. User Guide for Maurice, Maurice C. and Maurice S. page 216 Chapter 11: CE-SDS Data Analysis Group Statistics You can use the Grouping view to have Compass for iCE do a statistical analysis of named proteins in your injections (see Peak Names Settings on page 271 for more info on setting named peaks up). Statistics for each protein are also plotted for easy comparison. Using Groups 1. Groups are automatically created for injections that use the same sample name and method, so to use this feature, you need to make sure youve got sample names entered. a. Go to the Batch screen. b. Click the Sample ID cells in the Injection pane and type a name for any samples you want to calcu-

late statistics for. 2. Go back to the Analysis screen. Click View in the main menu and select Grouping. NOTE: To turn Grouping off, select View in the main menu and deselect Grouping. User Guide for Maurice, Maurice C. and Maurice S. Group Statistics page 217 Viewing Sample Injection Groups Compass for iCE automatically groups all injections using the same sample name together in the Injection Groups pane. To expand a group - Click the arrow next to a group to see the individual injections in the group and reported data for each To expand all groups - Click Expand All (+) in the upper right corner of the pane. To collapse all groups - Click Collapse All (-) in the upper right corner of the pane. Viewing Statistics Peak and Method Groups The Peak Groups pane reports statistics for each named protein in every group. Each group shows the statis-

tics for named proteins which includes average area, standard deviation, %CV and SEM (standard error mea-

surement). The number in parenthesis after the sample name is the number of injections in the group. User Guide for Maurice, Maurice C. and Maurice S. page 218 Chapter 11: CE-SDS Data Analysis To display results using area - Click Area in the upper right corner of the pane. To display results using % total - Click % Total in the upper right corner of the pane to display the calculated percent area for the named peak compared to the total area measured in the injection. This value results from dividing the individual peak area by the sum of all peak areas for the injection and multiplying by 100. To display results using % area - Click % Area in the upper right corner of the pane to display the calculated percent area for the named peak compared to all named peaks. This value results from dividing the individual peak area by the sum of all named peak areas for the injection and multiplying by 100 (shown for named peak sample data only). To expand a group - Click the arrow next to a group to see the individual injections in the group and reported data for each To expand all groups - Click Expand All (+) in the upper right corner of the pane. To collapse all groups - Click Collapse All (-) in the upper right corner of the pane. The Method Groups pane pivots the Peak Groups pane results to show statistics for named protein peaks in individual columns. User Guide for Maurice, Maurice C. and Maurice S. Group Statistics page 219 Group Plots The mean values for named peaks using the same method in each injection group are plotted in bar graphs with error bars showing the standard deviation in the Group Plots pane. Youll also get plots that compare samples using the same method in the run. Hiding or Removing Injections in Group Analysis Hidden injections are not included in injection groups. But, hiding injections gives you an easy way to reject individual injections from the statistical analysis. See Hiding Injection Data on page 213 for details on how to do this. User Guide for Maurice, Maurice C. and Maurice S. page 220 Chapter 11: CE-SDS Data Analysis Copying Results Tables and Graphs You can copy and paste data and results tables into other documents, or save the electropherogram as a graphic file. Copying Results Tables 1. Click in the Peaks or Injections pane. 2. 3. 4. Open a document (Microsoft Word, Excel, PowerPoint, etc.). Right click in the document and select Select one or multiple rows. Select Edit in the main menu and click Copy, or right click on row(s) you selected and click Copy. Paste. Data for the rows selected will be pasted into the document. Copying the Graph 1. 2. 3. Select the Graph pane. Select Edit in the main menu and click Copy, or right click in the Graph pane and select Copy. Select an image option (EMF, PNG or PDF) in the pop-up window, then click Copy. 4. Open a document (Microsoft Word, Excel, PowerPoint, etc.). Right click in the document and select Paste. A graphic of the copied electropherogram will be pasted into the document. Saving the Graph as an Image File 1. 2. 3. Select the Graph pane. Select Edit in the main menu and click Copy, or right click in the Graph pane and select Copy. Select an image option (EMF, PNG or PDF) in the pop-up window, then click Save. User Guide for Maurice, Maurice C. and Maurice S. Exporting Run Files page 221 4. Select a directory to save the file to, enter a file name, then click OK. Exporting Run Files Results tables and raw plot data can be exported for use in other applications. Exporting Results Tables To export the information in the Peaks and Injections tables:

1. Click File in the main menu and click Export Tables. 2. Select a directory to save the files to and click OK. Data will be exported in .txt format. NOTE: To exclude export of standards data or export results table data in .csv format, see Setting Data Export Options on page 379. Exporting Raw Sample Electropherogram Data To export raw sample plot and background data:

1. Click File in the main menu and click Export Spectra. User Guide for Maurice, Maurice C. and Maurice S. page 222 Chapter 11: CE-SDS Data Analysis To export data in .txt format - Select Text Format. Data will be exported in one file for all injec-

tions. To export data in .cdf format - Select Andi Format. Data will be exported in one file per injec-

tion. 2. Select a directory to save the files to and click OK. Data will be exported in the selected format. Changing Sample Protein Identification Compass for iCE lets you customize what sample proteins are reported in the results tables by making man-

ual adjustments in the electropherogram or Peaks table. Adding or Removing Sample Data 1. Click Show Samples in the View bar. 2. Click Single View in the View bar. 3. Click on the row in the experiment pane that has the injection you want to correct, then click the Graph tab. To remove a peak from the data - Right click the peak in the electropherogram or Peaks table and select Remove peak. The software will no longer identify it as a sample peak in the elec-

tropherogram, and the peak data will be removed in the results tables. User Guide for Maurice, Maurice C. and Maurice S. Changing Sample Protein Identification page 223 A check mark will appear next to the injection in the Experiment pane to indicate a manual correc-

tion was made. To add an unidentified peak to the data - Right click the peak in the electropherogram or peaks table and select Add Peak. The software will calculate and display the results for the peak in the results tables and identify the peak in the electropherogram. A check mark will appear next to the injection in the Experiment pane to indicate a manual cor-

rection was made. User Guide for Maurice, Maurice C. and Maurice S. page 224 Chapter 11: CE-SDS Data Analysis NOTE: To remove sample peak assignments that were made manually and go back to the original peak data, right-click the peak in the electropherogram and select Clear for the current injection or Clear All for all injections in the batch. Hiding Sample Data You can hide the results for a sample protein in the results tables without completely removing it from the reported results. 1. Click Show Samples in the View bar. 2. Click Single View in the View bar. 3. Click on the row in the experiment pane that contains the injection you want to correct, then click the 4. Graph tab. Right click the peak in the electropherogram or Peaks table and select Hide. Compass for iCE will hide the peak data in the results tables. User Guide for Maurice, Maurice C. and Maurice S. Changing Sample Protein Identification page 225 5. To view hidden peak data, click View in the main menu and click Show Hidden. Hidden peak data will display in the results table and be marked with an X. 6. To unhide a peak, right click on the peak in the electropherogram or peaks table and select Unhide. Changing Peak Names for Sample Data If Compass for iCE did not automatically name a sample protein peak, you can do it manually. 1. Click Show Samples in the View bar. 2. Click Single View in the View bar. 3. Click on the row in the experiment pane that has the sample you want to correct, then click the Graph pane. User Guide for Maurice, Maurice C. and Maurice S. page 226 Chapter 11: CE-SDS Data Analysis 4. Right click the peak in the electropherogram or Peaks table and click Name, then select a name from the list. Compass for iCE will change the peak name in the electropherogram and results tables, and adjust peak names for other sample proteins accordingly. NOTE: For details on how to specify peak name settings, see Peak Names Settings on page 271. Changing the Electropherogram View Options in the Graph pane let you zoom and rescale electropherograms, overlay or stack plots and change the peak and plot info displayed. The Graph pane toolbar has these options:

Auto Scale Graph Options Stack the Plots Overlay the Plots User Guide for Maurice, Maurice C. and Maurice S. Changing the Electropherogram View page 227 Autoscaling the Electropherogram Click the Auto Scale button to scale the y-axis to the largest peak in the electropherogram. Click the Auto Scale button again to return to default scaling. Customizing the Data Display You can customize electropherogram peak labels, plot labels and display options. To do this, just select the Graph Options button. User Guide for Maurice, Maurice C. and Maurice S. page 228 Chapter 11: CE-SDS Data Analysis Peak Labels You can customize the labels used to identify peaks in the electropherogram with these options:

Matching Peak Names - Checking this box will draw vertical lines through each named peak. Using this option with Stack the Plots or Overlay the Plots features is helpful for visually comparing your named peaks across multiple injections. User Guide for Maurice, Maurice C. and Maurice S. Changing the Electropherogram View page 229 Peak Names - Checking this box displays peak name labels on all named peaks in the electrophero-

gram. NOTE: If more than one peak label option is selected, peak name labels will always be used for named peaks. Peak Values - Checking this box will display the molecular weight labels on all peaks in the electro-

pherogram. User Guide for Maurice, Maurice C. and Maurice S. page 230 Chapter 11: CE-SDS Data Analysis NOTE: If more than one peak label option is selected, peak name labels will always be used for named peaks. Baseline and Grid Options You can view the calculated baseline fit, peak integration and show grid lines with these options. Fitted peaks - Checking this box displays how the peaks were fit by the software. For CE-SDS runs, the software uses Gaussian fit by default. NOTE: This option is only available for sample data. User Guide for Maurice, Maurice C. and Maurice S. Changing the Electropherogram View page 231 Baseline Fit - Checking this box displays the calculated baseline for the peaks. Baseline points will also display for regions of the electropherogram considered to be at baseline. NOTE: This option is only available for sample data. User Guide for Maurice, Maurice C. and Maurice S. page 232 Chapter 11: CE-SDS Data Analysis Grid Lines - Checking this box adds grid lines in the graph. Plot Labels You can customize the plot labels displayed on the electropherogram with these options. Plot labels are shown in the upper right side of the graph. Sample - Checking this box displays the sample name used for the injection. If sample names were entered with the batch, those names will display here. If not, Sample (default name) displays. Method - Checking this box displays the method used for the injection. Exposure - Checking this box display the exposure time(s) used for the data. For CE-SDS data this value will be 0.0 seconds. Injection - Checking this box displays the injection number. For example, I4 for injection 4 in the run. Heres an example of an electropherogram with all plot labels selected:

User Guide for Maurice, Maurice C. and Maurice S. Changing the Electropherogram View page 233 Stacking Multiple Electropherograms You can stack electropherograms for multiple injections vertically in the Graph pane for comparison. 1. Click Single View. 2. 3. Click the Stack the Plots button. The individual electropherograms for each injection you selected will Select multiple injection rows in the Experiment pane. stack in the Graph pane. User Guide for Maurice, Maurice C. and Maurice S. page 234 Chapter 11: CE-SDS Data Analysis You can also customize the colors used for the stacked plot display. To do that go to Selecting Custom Plot Colors for Graph Overlay on page 380. Overlaying Multiple Electropherograms You can overlay electropherograms for multiple injections on top of each other for comparison in the Graph pane. 1. Click Single View. 2. 3. Click the Overlay the Plots button. The individual electropherograms for each injection you selected Select multiple injection rows in the Experiment pane. will overlay in the Graph pane. You can also customize the colors used for the overlay plot display. To do that go to Selecting Custom Plot Colors for Graph Overlay on page 380. User Guide for Maurice, Maurice C. and Maurice S. Changing the Electropherogram View page 235 Zooming To zoom in on a specific area of the electropherogram, hold the mouse button down and draw a box around the area with your mouse:

To return to default scaling, right click in the electropherogram and click Zoom Out. User Guide for Maurice, Maurice C. and Maurice S. page 236 Chapter 11: CE-SDS Data Analysis Selecting Data Viewing Options The graph view menu gives you multiple options for changing what type of electropherogram data is dis-

played. Just click the down arrow next to the graph pane toolbar to view the menu:

A check mark next to the menu option indicates its currently selected, and you can select multiple options at once. NOTE: Unless noted otherwise, graph view menu options are available for sample data only. Sample Raw - Clicking this option displays the basic detector values used to calculate peak absor-

bance. To view this youll need to select Auto Scale in the Graph pane tool bar. User Guide for Maurice, Maurice C. and Maurice S. Changing the Electropherogram View page 237 Sample Background - Clicking this option displays the basic detector values used to calculate base-

line absorbance. To view this youll need to select Auto Scale in the Graph pane tool bar. User Guide for Maurice, Maurice C. and Maurice S. page 238 Chapter 11: CE-SDS Data Analysis Sample - Clicking this option displays raw, uncorrected sample data. Sample Baseline Corrected - Clicking this option displays sample data with the baseline subtracted

(zeroed). This is the default view. Baseline Fit - Clicking this option displays the calculated baseline for the raw sample data. In this next example, both Baseline Fit and Sample are selected. User Guide for Maurice, Maurice C. and Maurice S. Changing the Electropherogram View page 239 NOTE: This option is selected automatically when Baseline Fit is selected in graph options. Baseline Points - Clicking this option displays regions of the electropherogram considered to be at baseline. In this example, both Baseline Points and Sample are selected. NOTE: This option is selected automatically when Baseline Fit is selected in graph options. User Guide for Maurice, Maurice C. and Maurice S. page 240 Chapter 11: CE-SDS Data Analysis Fit - Clicking this option displays the bounding envelope of the fitted peaks as calculated by the soft-

ware for the raw sample data. In this example, both Fit and Sample Baseline Corrected are selected. Fit Baseline Corrected - Clicking this option displays the fitted peaks as calculated by the software for the sample baseline corrected data. In this example, both Fit Baseline Corrected and Sample are selected, the fit plot is on the bottom. Adding and Removing Baseline Points Points in the baseline can be added or removed as needed. User Guide for Maurice, Maurice C. and Maurice S. Changing the Electropherogram View page 241 1. Click the Graph Options button in the graph pane toolbar and check Baseline Points. This will display baseline points for the raw sample data. 2. Use the mouse to draw a box around the area you want to correct. This will zoom in on the area. 3. Right click a baseline point and select Add Baseline Point or Remove Baseline Point. NOTE: To clear the manual addition or removal of baseline points and go back to the original view of the data, right click in the electropherogram and click Clear All. Selecting the Graph X-axis Range The RMT (relative migration time) range used for the x-axis can be changed. Just select View in the main menu and click View Region. User Guide for Maurice, Maurice C. and Maurice S. page 242 Chapter 11: CE-SDS Data Analysis Analysis sets the x-axis range of the electropherogram to what is selected in the Peak Fit range set-

tings. To view or change these analysis settings, go to Edit > Analysis and click Peak Fit in the left sidebar. In this example, the lower and upper range settings are 0.9 and 2.5. Full displays the entire separation in the electropherogram. This is the default setting. In this example the lower and upper range settings are 0 and 2.6. Custom lets you manually enter the lower and upper range settings to display in the electrophero-

gram. In this example the lower and upper range settings are 0.9 and 2.0. User Guide for Maurice, Maurice C. and Maurice S. Closing Run Files page 243 NOTE: You can change the default x-axis range that Compass for iCE uses. Go to Advanced Analysis Set-

tings on page 246 for more info. Closing Run Files If more than one run file is open, you can close just one file or all the open files at the same time. To close one run file - In the Experiment pane, click on one of the sample rows in the file. Then click File from the main menu and click Close. To close all open run files - Select File from the main menu and click Close All. User Guide for Maurice, Maurice C. and Maurice S. page 244 Chapter 11: CE-SDS Data Analysis Analysis Settings Overview Compass for iCE has many analysis features and settings that you can change to enhance your run data. Select Edit in the main menu and click Analysis. If more than one run file is open, select the run file you want to view settings for from the list:

This opens the Analysis window:

User Guide for Maurice, Maurice C. and Maurice S. Analysis Settings Overview page 245 To move between pages in the window, click on an option in the left sidebar. Advanced - Lets you customize analysis settings for the Internal Standard. Markers - Lets you customize the Internal Standard migration time, and the molecular weight and RMT Compass for iCE uses to identify your CE-SDS MW Markers. Peak Fit - Lets you customize peak fit settings for sample data. Peak Names - Lets you enter custom naming settings for sample proteins and have Compass for iCE automatically label the peaks in the run data. On all pages in the Analysis window:

Click Import to import an analysis settings file. Go to Importing Analysis Settings on page 283 to learn how to do this. Click Export to export the current analysis settings file. Go to Exporting Analysis Settings on page 283 to learn how to do this. Click Apply to apply changes to the run file and update results in real time. Click OK to save changes to the run file and exit. Click Cancel to exit without saving changes. User Guide for Maurice, Maurice C. and Maurice S. page 246 Chapter 11: CE-SDS Data Analysis Advanced Analysis Settings This page lets you view and change analysis settings for the Internal Standard data. Select Edit in the main menu and click Analysis, then click Advanced in the left sidebar:

NOTE: Settings can be changed in batches before you start the run, or in run files once theyre completed. If you make analysis settings changes to an executing run, they wont be saved to the final run file. Internal Standard Settings Peak Width - The approximate width (at full width half max) used to filter out absorbance artifacts which improves recognition of standards. Allowable Drift - The distance the Internal Standard is expected to move compared to the entered number of seconds on the Markers page. This setting helps with recognition of the Internal Standard. User Guide for Maurice, Maurice C. and Maurice S. Advanced Analysis Settings page 247 Advanced Analysis Settings Groups Advanced analysis settings are saved as a group, and you can create multiple settings groups. Specific group settings can be applied to methods, injections, sample names or other attributes in the run data. NOTES:

We recommend using the Compass for iCE default values for advanced analysis settings. These settings are included in the default Advanced group. Analysis settings are run-file specific. But, settings can be imported or exported for use with other run files. See Importing and Exporting Analysis Settings on page 283 for more info. Analysis groups are displayed in the analysis settings box:

The Advanced group shown contains the Compass for iCE default analysis settings. You can make changes to this group and create new groups. To view settings for a group, click on the group name. Creating a New Analysis Group 1. 2. Click Add under the analysis settings box. A new group will be created:

Select Edit > Analysis, and select Advanced in the left sidebar. 3. Click on the new group and enter a new name. User Guide for Maurice, Maurice C. and Maurice S. page 248 Chapter 11: CE-SDS Data Analysis 4. Change the settings in the Standards box as needed. 5. To use the new group as the default analysis settings for the run data, click the arrow in the drop down list next to Apply Default, then click the new group from the list. Analysis settings in the new group will then be applied to the run data. 6. Click OK to save changes. Changing the Default Analysis Group 1. 2. Click the arrow in the drop down list next to Apply Default, then click a new default group from the list. Select Edit > Analysis, and select Advanced in the left sidebar. User Guide for Maurice, Maurice C. and Maurice S. Advanced Analysis Settings page 249 3. Click OK to save changes. Analysis settings in the group selected will be applied to the run data. Modifying an Analysis Group 1. 2. Click on the group in the analysis settings box you want to modify. Select Edit > Analysis, and select Advanced in the left sidebar. 3. Change the settings in the Standards box as needed. 4. Click OK to save changes. The new analysis settings will be applied to the run data. Deleting an Analysis Group 1. 2. Click on the group in the analysis settings box you want to delete and click Remove. Select Edit > Analysis, and select Advanced in the left sidebar. User Guide for Maurice, Maurice C. and Maurice S. page 250 Chapter 11: CE-SDS Data Analysis 3. Click OK to save changes. Applying Analysis Groups to Specific Run Data 1. 2. Click on the group in the analysis settings box you want to apply to specific run data. Select Edit > Analysis, and select Advanced in the left sidebar. 3. Application of analysis groups to specific run data is done in the override box. Click Add under the over-

ride box. A default override data set will be created from sample information found in the run file. 4. Click the cell in the Apply To column, then click the down arrow. User Guide for Maurice, Maurice C. and Maurice S. Advanced Analysis Settings page 251 5. Select an option from the drop down list. This applies the settings group selected to specific run data as follows:

Methods - All methods in the run file display in the list. Selecting a method applies the group settings to all injections that used that method. Sample names - All sample names in the run file display in the list, otherwise the default name of Sample shows. Selecting a sample name applies the group settings to all injections that used that sample name. Wells or vials - All well or vial numbers used in the run display in the list. Selecting a well/vial number applies the group settings to all injections that used that well/vial. Custom settings - Lets you choose specific injections to apply the group settings to. When you select this in the list, a pop-up box displays to let you enter a specific injection number or range of injections:

6. If you need to change the analysis group used for a data set, click the cell in the Settings column and click the down arrow. Select a group from the drop down list. User Guide for Maurice, Maurice C. and Maurice S. page 252 Chapter 11: CE-SDS Data Analysis Repeat the previous steps to apply other groups to specific run data. To remove a data set, click on its cell in the Apply To column, then click Remove. 7. 8. 9. Click OK to save changes. Markers Analysis Settings This page lets you select the injection for your CE-SDS MW Markers, enter a list of molecular weights and RMTs for each marker peak, and set the expected migration time of the Internal Standard for all injections. Select Edit in the main menu and click Analysis, then click Markers in the left sidebar. NOTE: Settings can be changed in the batch default analysis before you start the run, or in run files once theyre completed. If you make analysis settings changes to an executing run, they wont be saved to the final run file. User Guide for Maurice, Maurice C. and Maurice S. Markers Analysis Settings page 253 Markers Settings Internal Standard Time - The approximate migration time (in seconds) of the Internal Standard. This is applied to all injections. Changing the Injection Used for the CE-SDS MW Markers You can use known markers to calculate molecular weights of your unknown sample proteins. You can select the injection you ran your CE-SDS MW Markers in, or opt to not use one. NOTE: When the markers injection is set to no markers, the molecular weight for sample proteins in the run isnt displayed. User Guide for Maurice, Maurice C. and Maurice S. page 254 Chapter 11: CE-SDS Data Analysis To change the markers injection:

1. 2. Click the arrow in the drop down list next to Markers Injection, then select an injection number or no Select Edit > Analysis, and select Markers in the left sidebar. markers from the list. Compass for iCE will use the data in the selected injection to calculate molecular weights for sample proteins in the run data using the information in the table. If no markers is selected, Compass for iCE doesnt display molecular weight for sample proteins. Standards Analysis Settings Groups Standards settings are saved as a group, and you can create multiple settings groups. Specific group settings can be applied to methods, injections, sample names or other attributes in the run data. NOTES:

We recommend using the Compass for iCE default values. These settings are included in the default Stan-

dards group. Analysis settings are run-file specific. But, settings can be imported or exported for use with other run files. For more information see Importing and Exporting Analysis Settings on page 283. Standards groups are displayed in the analysis settings box:

User Guide for Maurice, Maurice C. and Maurice S. Markers Analysis Settings page 255 The Standards group shown uses the Compass for iCE default settings. You can make changes to this group and create new groups. To view settings for a group, click on the group name. Creating a New Standards Group 1. 2. Click Add under the analysis settings box. A new group will be created:

Select Edit > Analysis, and select Markers in the left sidebar. 3. Click on the new group and enter a new name. 4. Change the Internal Standard time as needed. 5. Click the arrow in the drop down list next to Markers Injection, then click an injection number or no markers from the list. User Guide for Maurice, Maurice C. and Maurice S. page 256 Chapter 11: CE-SDS Data Analysis 6. Compass for iCE will use the data in the selected injection to recalculate molecular weights for sample proteins in the run data using the information in the table. If no markers is selected, Compass for iCE doesnt display molecular weight for sample proteins. If a markers injection was selected, the default Maurice CE-SDS MW Markers molecular weights and rela-

tive migration time (RMT) values are already populated in the table. If youd like to use these values, skip to the next step. If youre using different markers, heres how to change the values:

a. Click in the first cell in the MW column in the table and enter the molecular weight (in kDa) for the marker. b. Click in the first cell in the RMT column and enter a value for the marker. User Guide for Maurice, Maurice C. and Maurice S. Markers Analysis Settings page 257 NOTE: Marker peak positions are relative to each other. Only the difference in RMT is used to help identify them. When entering marker peak information for the first time, review the marker data in the Analysis screen to find the correct peak RMT. c. Repeat the steps above for the remaining markers in the table. To add another marker - Click Add under the table, then change the information in the new row. To remove a marker - Select its row and click Remove. 7. To use the new group as the default settings for the run, click the arrow in the drop down list next to Apply Default, then click the new group in the list. The settings in the new group will then be applied to the run data. 8. Click OK to save changes. User Guide for Maurice, Maurice C. and Maurice S. page 258 Chapter 11: CE-SDS Data Analysis Changing the Default Standards Group 1. 2. Click the arrow in the drop down list next to Apply Default, then select a new default group from the list. Select Edit > Analysis, and click Markers in the left sidebar. 3. Click OK to save changes. Analysis settings in the group selected will be applied to the run data. Modifying a Standards Group 1. 2. Click on the group in the analysis settings box you want to modify. Select Edit > Analysis, and click Markers in the left sidebar. 3. Change the marker info as needed as in Creating a New Standards Group on page 255. 4. Click OK to save changes. The new analysis settings will be applied to the run data. Deleting a Standards Group 1. 2. Click on the group in the analysis settings box you want to delete and click Remove. Select Edit > Analysis, and click Markers in the left sidebar. User Guide for Maurice, Maurice C. and Maurice S. Markers Analysis Settings page 259 3. Click OK to save changes. Applying Standards Groups to Specific Run Data 1. 2. Click on the group in the analysis settings box you want to apply to specific run data. Select Edit > Analysis, and select Markers in the left sidebar. 3. Application of standards groups to specific run data is done in the override box. Click Add under the override box. A default override data set will be created from sample information found in the run file. 4. Click the cell in the Apply To column, then click the down arrow. User Guide for Maurice, Maurice C. and Maurice S. page 260 Chapter 11: CE-SDS Data Analysis 5. Select an option from the drop down list. This applies the settings group selected to specific run data as follows:

Methods - All methods in the run file display in the list. Selecting a method applies the group settings to all injections that used that method. Sample names - All sample names in the run file display in the list, otherwise the default name of Sample shows. Selecting a sample name applies the group settings to all injections that used that sample name. Wells or vials - All well or vial numbers used in the run display in the list. Selecting a well/vial number applies the group settings to all injections that used that well/vial. Custom settings - Lets you choose specific injections to apply the group settings to. When you select this in the list, a pop-up box displays to let you enter a specific injection number or range of injections:

6. If you need to change the analysis group used for a data set, click the cell in the Settings column and click the down arrow. Select a group from the drop down list. User Guide for Maurice, Maurice C. and Maurice S. Peak Fit Analysis Settings page 261 Repeat the previous steps to apply other groups to specific run data. To remove a data set, click on its cell in the Apply To column, then click Remove. 7. 8. 9. Click OK to save changes. Peak Fit Analysis Settings This page lets you view and change peak fit settings for sample data. Select Edit in the main menu and click Analysis, then click Peak Fit in the left sidebar:

User Guide for Maurice, Maurice C. and Maurice S. page 262 Chapter 11: CE-SDS Data Analysis NOTE: Settings can be changed in the batch default analysis before you start the run, or in run files once theyre completed. If you make analysis settings changes to an executing run, they wont be saved to the final run file. Range Settings Minimum - The RMT value below which peaks wont be identified. This value is also used as the default lower RMT range for data displayed in the electropherogram. Maximum - The RMT value above which peaks wont be identified. This value is also used as the default upper RMT range for data displayed in the electropherogram. View - Sets the default range to either Full or Analysis for the electropherogram x-axis range in the View Region window (select View in the main menu and click View Region). User Guide for Maurice, Maurice C. and Maurice S. Peak Fit Analysis Settings page 263 Analysis sets the x-axis range of the electropherogram to the Peak Fit range minimum and max-

imum settings in the electropherogram. Full displays the entire separation range of the run data in the electropherogram. This is the default setting. Baseline Settings Threshold - The variance, or roughness, in a baseline data segment below which a point is called part of the baseline. Window - How long baseline data segments are expected to be in pixels. Shorter segments let the baseline follow plateau sections of the signal. Stiffness - The amount the baseline is allowed to vary from a straight line. Settings between 0.1 and 1.0 make the baseline fit closer to a straight line. Settings from 1.0 to 10.0 will make the baseline fit fol-

low the data more closely. Peak Find Settings Threshold - The minimum signal to noise ratio required for a peak to be identified. A setting of 1.0 will detect many peaks, a setting of 10.0 will detect fewer peaks. Width - The approximate peak width (at full width half max) in pixels used to detect peaks. The mini-

mum value for this setting is 3.0. Larger widths help eliminate the detection of shoulder and noise peaks. Area Calculation - Two fits are used, either Gaussian Fit or Dropped Lines. These settings can be changed before or after the run is finished. For CE-SDS applications, peak area is calculated using Dropped Lines by default. This type of area calculation is also often called the perpendicular drop method. This is the preferred method when peaks overlap or are close to each other. It draws two vertical lines from the left and right bounds of the peak down to the x-axis and then measures the total area bounded by the signal curve, the x-axis (y=0 line), and the two vertical lines. User Guide for Maurice, Maurice C. and Maurice S. page 264 Chapter 11: CE-SDS Data Analysis This next view is of the same data using Gaussian fit instead:

Peak Fit Analysis Settings Groups Peak fit settings are saved as a group, and you can create multiple settings groups. Specific group settings can then be applied to methods, injections, sample names or other attributes in the run data. User Guide for Maurice, Maurice C. and Maurice S. Peak Fit Analysis Settings page 265 NOTES:

We recommend using the Compass for iCE default values for peak fit analysis settings. These settings are included in the default Peak Fit group. Analysis settings are run-file specific. But, settings can be imported or exported for use with other run files. For more information see Importing and Exporting Analysis Settings on page 283. Peak fit groups are displayed in the analysis settings box:

The Peak Fit group shown contains the Compass for iCE default analysis settings. You can make changes to this group and create new groups. To view settings for a group, click on the group name. Creating a New Peak Fit Group 1. 2. Click Add under the analysis settings box. A new group will be created:

Select Edit > Analysis, and select Peak Fit in the left sidebar. 3. Click on the new group and enter a new name. User Guide for Maurice, Maurice C. and Maurice S. page 266 Chapter 11: CE-SDS Data Analysis 4. Change the settings in the range, baseline or peak find boxes as needed. 5. To use the new group as the default peak fit settings for the run file data, click the arrow in the drop down list next to Apply Default, then click the new group from the list. Peak fit settings in the new group will then be applied to the run data. User Guide for Maurice, Maurice C. and Maurice S. Peak Fit Analysis Settings page 267 6. Click OK to save changes. Changing the Default Peak Fit Group 1. 2. Click the arrow in the drop down list next to Apply Default, then click a new default group from the list. Select Edit > Analysis, and select Peak Fit in the left sidebar. 3. Click OK to save changes. Peak fit settings in the group selected will be applied to the run data. Modifying a Peak Fit Group 1. 2. Click on the group in the analysis settings box you want to modify. Select Edit > Analysis, and click Peak Fit in the left sidebar. 3. Change the settings in the range, baseline or peak find boxes as needed. User Guide for Maurice, Maurice C. and Maurice S. page 268 Chapter 11: CE-SDS Data Analysis 4. Click OK to save changes. The new peak fit settings will be applied to the run data. Deleting a Peak Fit Group 1. 2. Click on the group in the analysis settings box you want to delete and click Remove. Select Edit > Analysis, and select Peak Fit in the left sidebar. 3. Click OK to save changes. Applying Peak Fit Groups to Specific Run Data 1. 2. Click on the group in the analysis settings box you want to apply to specific run data. Select Edit > Analysis, and select Peak Fit in the left sidebar. User Guide for Maurice, Maurice C. and Maurice S. Peak Fit Analysis Settings page 269 3. Application of analysis groups to specific run data is done in the override box. Click Add under the over-

ride box. A default override data set will be created from sample information found in the run file. 4. Click the cell in the Apply To column, then click the down arrow. 5. Select an option from the drop down list. This applies the settings group selected to specific run data as follows:

Methods - All methods in the run file display in the list. Selecting a method applies the group settings to all injections that used that method. Sample names - All sample names in the run file display in the list, otherwise the default name of Sample shows. Selecting a sample name applies the group settings to all injections that used that sample name. User Guide for Maurice, Maurice C. and Maurice S. page 270 Chapter 11: CE-SDS Data Analysis Wells or vials - All well or vial numbers used in the run display in the list. Selecting a well/vial number applies the group settings to all injections that used that well/vial. Custom settings - Lets you choose specific injections to apply the group settings to. When you select this in the list, a pop-up box displays to let you enter a specific injection number or range of injections:

6. If you need to change the analysis group used for a data set, click the cell in the Settings column and click the down arrow. Select a group from the drop down list. Repeat the previous steps to apply other groups to specific run data. To remove a data set, click on its cell in the Apply To column, then click Remove. 7. 8. 9. Click OK to save changes. User Guide for Maurice, Maurice C. and Maurice S. Peak Names Settings page 271 Peak Names Settings This page lets you view and change custom naming settings for sample proteins. Select Edit in the main menu and click Analysis, then click Peak Names in the left sidebar. NOTE: Settings can be changed in the batch default analysis before you start the run, or in run files once theyre completed. If you make analysis settings changes to an executing run, they wont be saved to the final run file. Peak Names Analysis Settings Groups Peak name settings are saved as a group, and you can create multiple settings groups. Specific group set-

tings can be applied to methods, injections, sample names or other attributes in the run data. User Guide for Maurice, Maurice C. and Maurice S. page 272 Chapter 11: CE-SDS Data Analysis NOTE: Analysis settings are run-file specific. But, settings can be imported or exported for use with other run files. For more information see Importing and Exporting Analysis Settings on page 283. Peak name groups are displayed in the analysis settings box:

There arent any Compass for iCE default settings groups, but you can make changes to groups youve cre-

ated and create new groups. To view settings for a group, click on the group name in the analysis settings box. Creating a Peak Names Group 1. 2. Click Add under the analysis settings box. Select Edit > Analysis, and select Peak Names in the left sidebar. 3. Enter a new name for the group. User Guide for Maurice, Maurice C. and Maurice S. Peak Names Settings page 273 4. Click in the first cell in the Name column in the analysis settings peak table and enter a sample protein name. 5. Click in the first cell in the RMT column and enter the relative migration time for the sample protein. 6. Click in the first cell in the Color column, then click the button. User Guide for Maurice, Maurice C. and Maurice S. page 274 Chapter 11: CE-SDS Data Analysis The color selection box displays:

7. The color you pick is used to identify the sample protein peak in the Peaks and Injections panes in the Analysis screen. Click a color or define a custom color and click OK. The color selection will update in the table:

8. Click in the first cell in the Range column. 9. Enter a % range for the RMT entered. Compass for iCE will automatically name peaks found within this percent of the RMT. For example, if the RMT entered is 2 and a 10% range is used, all peaks with RMTs between 1.8 and 2.2 will be identified with this peak name and color. 10. To add another sample protein, click Add under the peak table. Repeat the previous steps for other sam-

ple proteins. In this example, three proteins were entered:

User Guide for Maurice, Maurice C. and Maurice S. Peak Names Settings page 275 To remove a sample protein, select its row and click Remove. 11. Click OK to save changes. Modifying a Peak Names Group Select Edit > Analysis, then click Peak Names in the left sidebar. 1. 2. Click on the group in the analysis settings box you want to modify. 3. Change the information in the analysis settings peak table as described in Creating a Peak Names Group on page 272. 4. Click OK to save changes. Deleting a Peak Names Group 1. 2. Click on the group in the analysis settings box you want to delete and click Remove. Select Edit > Analysis, then click Peak Names in the left sidebar. 3. Click OK to save changes. User Guide for Maurice, Maurice C. and Maurice S. page 276 Chapter 11: CE-SDS Data Analysis Applying Peak Names Groups to Run Data 1. 2. Click on the group in the analysis settings box you want to apply to specific run data. Select Edit > Analysis, then click Peak Names in the options list. 3. Application of peak names groups to specific run data is done in the apply settings box. A default data set automatically gets created whenever you create a new group and its applied to all injections in the run. You can either modify the default group or click Add under the box to create a new one. 4. Click the cell in the Apply To column, then click the down arrow. 5. Select an option from the drop down list. This applies the peak names group selected to specific run data as follows:

User Guide for Maurice, Maurice C. and Maurice S. Peak Names Settings page 277 All - Selecting this applies peak names group settings to all injections. Methods - All methods in the run file display in the list. Selecting a method applies the group settings to all injections that used that method. Sample names - All sample names in the run file display in the list, otherwise the default name of Sample shows. Selecting a sample name applies the group settings to all injections that used that sample name. Wells or vials - All well or vial numbers used in the run display in the list. Selecting a well/vial number applies the group settings to all injections that used that well/vial. Custom settings - Lets you choose specific injections to apply the group settings to. When you select this in the list, a pop-up box displays to let you enter a specific injection number or range of injections:

6. If you need to change the peak names group used for a data set, click the cell in the Settings column and click the down arrow. Select a group from the drop down list. Repeat the previous steps to apply other groups to specific run data. To remove a data set, click on its cell in the Apply To column, then click Remove. 7. 8. 9. Click OK to save changes. Named peaks will be identified with a peak name label in the electrophero-

gram and color-coded in the Peaks and Injections panes:

User Guide for Maurice, Maurice C. and Maurice S. page 278 Chapter 11: CE-SDS Data Analysis Injection Reports You can export PDF files of the raw and analyzed data, IV plot, peaks table, sample and system info for indi-

vidual or all injections in a run file. You can also export the run history with all analysis events. 1. Click File > Open Run and select a run file. 2. If you want reports for all injections, skip to the next step. If you only want reports for certain injections, in the Experiment pane:

To select sequential injections: Select the first injection, then hold the Shift key and select the last injection you want a report for. This selects all rows between the two injections. To select specific injections: Hold the Ctrl key and select just the injections you want reports for. 3. Select File from the main menu in either screen and click Injection Report. User Guide for Maurice, Maurice C. and Maurice S. Injection Reports page 279 4. In the Injection Reports window:

d. Choose either Selected injections or All injections. e. Select the Analysis log checkbox if you want a run history report with all analysis events. f. The report name defaults to the run file name. If you want to change it, type in the Report Name box to make updates. g. Click OK. 5. The Injection Report PDF(s) are exported to the Runs folder in the Compass for iCE directory. Theyll be in a folder with the report name used in the prior step. When the reports are done, the folder opens for you automatically. User Guide for Maurice, Maurice C. and Maurice S. page 280 Chapter 11: CE-SDS Data Analysis Example Analysis and Injection Report User Guide for Maurice, Maurice C. and Maurice S. Injection Reports page 281 User Guide for Maurice, Maurice C. and Maurice S. page 282 Chapter 11: CE-SDS Data Analysis User Guide for Maurice, Maurice C. and Maurice S. Importing and Exporting Analysis Settings page 283 Importing and Exporting Analysis Settings The analysis settings in a run file can be exported as a separate file. This allows the same analysis settings to be imported into other batches or run files at a later time, rather than you having to re-enter them manually. Importing Analysis Settings NOTE: Importing an analysis settings file populates the settings in all analysis pages. Select Edit in the main menu and click Default Analysis (Batch screen) or Analysis (Analysis screen). 1. Open the run file or batch you want to import analysis settings to. 2. 3. Click Import on any page. 4. Select a settings file (*.settings) and click OK. The imported settings will display in all analysis pages. Exporting Analysis Settings NOTE: Exporting an analysis settings file exports the settings in all analysis pages. 1. Open the run file or batch you want to export analysis settings from. 2. 3. Click Export on any page. The following window displays:

Select Edit in the main menu and click Default Analysis (Batch screen) or Analysis (Analysis screen). User Guide for Maurice, Maurice C. and Maurice S. page 284 Chapter 11: CE-SDS Data Analysis 4. 5. The default directory is Compass for iCE/Runs. Change the directory if needed. Enter a file name and click Save. The settings will be saved as a *.settings file. User Guide for Maurice, Maurice C. and Maurice S.

page 285 Chapter 12:

cIEF Data Analysis Viewing Run Data Exporting Run Files Chapter Overview Analysis Screen Overview Opening Run Files How Run Data is Displayed Data Notifications and Warnings Checking Your Results Group Statistics Copying Results Tables and Graphs Changing Sample Protein Identification Changing the Electropherogram View Closing Run Files Analysis Settings Overview Advanced Analysis Settings Detection Settings Peak Fit Analysis Settings Peak Names Settings pI Markers Analysis Settings Injection Reports Importing and Exporting Analysis Settings User Guide for Maurice, Maurice C. and Maurice S. page 286 Chapter 12: cIEF Data Analysis Analysis Screen Overview You can use the Analysis screen to view electropherograms and tabulated results for your injections. If any post-run analysis is needed, you can do it here too. To get to this screen, click the Analysis screen tab:

Analysis Screen Panes The Analysis screen has four panes:

Experiment - Lists the injection number, sample IDs, sample locations and methods for each injec-

tion in the run and lets you get a quick view of method parameters. Graph - Displays the electropherograms for sample proteins or pI markers. Peaks - Shows the tabulated results for sample proteins and pI markers. Injections - Displays a list of the sample proteins Compass for iCE names automatically using the user-defined peak name analysis parameters. User Guide for Maurice, Maurice C. and Maurice S. Analysis Screen Overview page 287 Software Menus Active in the Analysis Screen These main menu items are active in the Analysis Screen:

Window Help File Edit View Instrument (when Compass for iCE is connected to Maurice, Maurice C. or Maurice S.) File Menu These File menu options are active:

Open Run - Opens a run file. Add Run - Lets you open and view other run files besides the one thats already open. Close - Closes the run file currently being viewed. Close All - Closes all open run files. Save/Save As - If you made changes in the Analysis screen before you went to the Run Summary screen, this saves your changes to the run file. Export Tables - Exports the results for all injections in the run in .txt format. Export Spectra - Exports the raw and analyzed data traces and background for each injection in the run in .txt or .cdf format. Injection Report - Exports the raw and analyzed data, IV plot, peaks table, sample and system info for individual injections as PDF files. You can also export the run history with all analysis events. User Guide for Maurice, Maurice C. and Maurice S. page 288 Chapter 12: cIEF Data Analysis Exit - Closes Compass for iCE. Edit Menu These Edit menu options are active:

Copy - Copies the information in the History pane so you can paste it into other documents. Analysis - Displays the analysis settings used to analyze the run data and lets you change them as needed. See Analysis Settings Overview on page 334 for more information. Preferences - Lets you set and save your preferences for data export, graph colors, grouped data and Twitter settings. See Chapter 13, Setting Your Preferences for more information. View Menu These View menu options are active:

Single View - Displays the data for only the injections selected. Multiple View - Displays data for all injections so you can scroll through them. Markers - Lets you view data just for the pI markers in your injections. Grouping - Displays data for injection groups. View Region - Lets you change the x-axis range of the data displayed. Show Hidden- Shows injections that are hidden from the data view. Samples - Lets you view data just for sample proteins in your injections. User Guide for Maurice, Maurice C. and Maurice S. Opening Run Files page 289 Opening Run Files You can open one run file or multiple files at the same time to compare information between runs. Opening One Run File 1. Select File in the main menu and click Open Run. 2. A list of the last 10 runs opened will display. Select one of these runs or click Browse to open the Runs folder and select a different file. Opening Multiple Run Files 1. To open the first run file, select File in the main menu and click Open Run. 2. A list of the last 10 runs opened will display. Select one of these runs or click Browse to open the Runs folder and select a different file. User Guide for Maurice, Maurice C. and Maurice S. page 290 Chapter 12: cIEF Data Analysis 3. To open another run file, select File in the main menu and click Add Run. 4. A list of cIEF runs will display. Select one of these runs or click Browse to open the Runs folder and select a different file. When a run is added, its data appends to the open run file and displays as a second set of injections in all screen panes. The second run file name also appears in the title bar:

5. Repeat the last two steps to add additional runs. User Guide for Maurice, Maurice C. and Maurice S. How Run Data is Displayed page 291 How Run Data is Displayed Data in the run file is organized for easy review. Experiment Pane: Batch Injection Information The Experiment pane lists all the injections performed in the run, which samples were used for each, the sample location in the 96-well plate or 48-vial tray and the method used. To view all columns - Use the scroll bar or click Maximize in the upper right corner. To resize columns - Roll the mouse over a column border until the sizing arrow appears, then click and drag to resize. To view method parameters - Hover the mouse over a method name. NOTE: Data notification icons will display in the Injection column if Compass for iCE detects a potential analysis issue or data was manually modified by the user. For more information see Data Notifications and Warnings on page 304. Graph Pane: Electropherogram Data The Graph pane displays the electropherogram(s) for sample proteins or pI markers depending on the view options youve selected. User Guide for Maurice, Maurice C. and Maurice S. page 292 Chapter 12: cIEF Data Analysis You can get more info on graph view options in Changing the Electropherogram View on page 316. Peaks Pane: Calculated Results The Peaks pane shows the tabulated results for your sample proteins or pI markers. Each row in the table has the individual results for each peak detected in an injection. Results shown will either be for one injection or multiple injections, samples or pI markers depending on the view options youre using. Check out Viewing Run Data on page 295 for more info. NOTES:

Peaks that Compass for iCE names automatically with user-defined peak name settings are color-coded. When the Markers view is selected, the information in the Peaks table includes only injection, sample, peak, position and height. pI markers the software has identified are marked with an M. To view all rows - Use the scroll bar or click Maximize in the upper right corner. User Guide for Maurice, Maurice C. and Maurice S. How Run Data is Displayed page 293 To resize columns - Roll the mouse over a column border until the sizing arrow appears, then click and drag to resize. The following results and info are listed in the Peaks table:

Injection - Injection number. Sample - If sample names were entered in the batch, those names will display here. Otherwise, Sample

(default name) will display. Peak - Peaks are numbered in order of detection. Name - Displays peaks Compass for iCE named automatically using the user-defined peak name anal-

ysis parameters. These cells are blank if the software wasnt able to name the peak or if you didnt enter naming parameters. Position - Peak location in pixels. pI - Displays the calculated peak pI based on the migration time of the peak to the pI markers. Height - The calculated peak height. Area - Displays the time-corrected peak area. This includes corrections for big and/or slow moving peaks which can be artificially large when uncorrected.

% Total - Displays the peak area ratio compared to the sum of all peak areas. This value results from dividing the individual peak area by the sum of all peak areas for the injection and multiplying by 100.

% Area - Displays the calculated percent area for the named peak compared to all named peaks. This value results from dividing the individual peak area by the sum of all named peak areas for the injec-

tion and multiplying by 100 (shown for named peak sample data only). Width - Displays the calculated peak width (sample data only). Baseline - Displays the raw baseline signal of each peak. Resolution - Displays resolution of the peak compared to neighboring peaks. Two peaks that are baseline resolved will have a resolution value of 1.5. Smaller values means the peaks are not com-

pletely resolved, larger values mean the peaks are fully resolved. Injections Pane: User-Specified Peak Names The Injections pane shows tabulated results for sample proteins Compass for iCE labels automatically using user-defined peak name settings. Each row in the table shows the individual results for the named peaks detected in each injection. User Guide for Maurice, Maurice C. and Maurice S. page 294 Chapter 12: cIEF Data Analysis NOTES:

Peaks that Compass for iCE names automatically with user-defined peak name settings are color-coded. When the Markers view is selected, the information in the Injections table includes only injection, sample and the positions of the pI marker (Mkr) peaks. To view all rows - Use the scroll bar or click Maximize in the upper right corner. To resize columns - Roll the mouse over a column border until the sizing arrow appears, then click and drag to resize. The following results and info are listed in the Injections table:

Injection - Injection number. Sample - If sample names were entered in the batch, those names will display here. Otherwise, Sample

(default name) will display. Peak Name Columns - An individual column per peak name will display for every peak identified by name or as a pI marker peak in the run data. Cells for injections in these columns will be blank if Com-

pass for iCE didnt find peaks automatically using the user-defined peak name analysis and maker parameters (or none were entered). To view peak area in the peak name columns (default) - Select Area in the upper right corner of the pane. This displays calculated peak area for the individual peak only. To view % total in the peak name columns - This displays the calculated percent area for the named peak compared to all named peaks. This value results from dividing the individual peak area by the sum of all named peak areas for the injection and multiplying by 100. NOTE: The sum of the named peak percentages can be less than 100% if some peaks arent named. User Guide for Maurice, Maurice C. and Maurice S. Viewing Run Data page 295 To view % area in the peak name columns - This displays the peak area ratio compared to the sum of all named peak areas. This value results from dividing the individual peak area by the sum of all peak areas for the injection and multiplying by 100. Viewing Run Data The Analysis screen lets you view data for just one injection, specific injections or all injections in the run. Each run file has data for the sample proteins and the pI markers detected in each injection. Switching Between Samples and Markers Data Views Heres how you switch between viewing data for your samples and pI markers:

To view sample data - Click Samples in the View bar or select View in the main menu and click Samples. Data in this view is for sample proteins only. The graph displays electropherograms with a y-axis of either Absorbance units (mAU) or Fluores-

cence units and an x-axis of pI. Go to Detection Settings on page 343 for more info on how to change the detection method to view either absorbance or native fluorescence data. User Guide for Maurice, Maurice C. and Maurice S. page 296 Chapter 12: cIEF Data Analysis Results for each protein are shown in the Peaks and Injections panes. For information on checking and identifying sample peaks, see Checking Your Data on page 105. To view pI marker data - Click Markers in the View bar or select View in the main menu and click Markers. Data in this view is for analyzing pI markers only. These are the pI markers you add to your sam-

ples during prep. The graph displays electropherograms with a y-axis of either Absorbance units (mAU) or Fluores-

cence units and an x-axis of pixels. Go to Detection Settings on page 343 for more info on how to change the detection method to view either absorbance or native fluorescence data. User Guide for Maurice, Maurice C. and Maurice S. Viewing Run Data page 297 pI markers are identified in the Peaks pane with an M and as Mkr in the Injections pane. For information on checking and identifying the pI marker peaks, see Checking Your Data on page 105. User Guide for Maurice, Maurice C. and Maurice S. page 298 Chapter 12: cIEF Data Analysis Selecting and Displaying Injection Data You can view data from one, multiple, or all injections at once. To look at data for one injection - Click an injection row in the Experiment pane. Data for just that injection displays in the graph and tables. User Guide for Maurice, Maurice C. and Maurice S. Viewing Run Data page 299 To look at data for specific injections - Hold the Ctrl key and select just the injection rows you want to view in the Experiment pane. Data for only the injections selected display in the graph and tables. User Guide for Maurice, Maurice C. and Maurice S. page 300 Chapter 12: cIEF Data Analysis To look at data for sequential injections - Select the first injection row in the Experiment pane that you want to view, then hold the Shift key and select the last. This selects all rows between the two injections. Data for only the injections selected display in the graph and tables. User Guide for Maurice, Maurice C. and Maurice S. Viewing Run Data page 301 To look at data for all injections - Just click View All in the View bar. Data for all injections displays in the graph and tables. Switching Between Single and Multiple Views of Injections You can switch between displaying run data in a single, per-injection format or a multi-injection format. To view data per in a per-injection format - Click Single View in the View bar or select View in the main menu and click Single View. Data for the injection row(s) selected in the Experiment pane:

Displays with electropherograms either overlaid or stacked in the Graph pane depending on the option youve got chosen. User Guide for Maurice, Maurice C. and Maurice S. page 302 Chapter 12: cIEF Data Analysis Shows only results for the selected row(s) in the Peaks and Injections panes. To view data in a multi-injection format - Click View All in the View bar or select View in the main menu and click Multiple View:

Data for the injection row(s) selected in the Experiment pane:

Displays with the electropherograms of the selected injections highlighted in the Graph pane. Shows the results for the selected injections highlighted in the Peaks and Injections panes. User Guide for Maurice, Maurice C. and Maurice S. Viewing Run Data page 303 Hiding Injection Data You can hide injection data from the view if needed. To hide injections - Select the injection rows you want to hide in the Experiment pane, then right click one and select Hide. Data for the injections will be hidden in all data views and results tables. User Guide for Maurice, Maurice C. and Maurice S. page 304 Chapter 12: cIEF Data Analysis To view hidden injections - Select View in the main menu and click Show Hidden. Hidden rows will become visible again in all panes, and are marked with an X in the Experiment pane. To unhide injections - Select the hidden row(s). Right click on one and click Unhide. Data Notifications and Warnings If Compass for iCE detects a potential data issue, a notification or warning icon will display next to the injec-

tion row in the Experiment pane. Manual correction of sample data notification - This means the sample data was manually changed by a user, for example to add or remove a sample peak. Roll your mouse over the icon to display the type of modification that was made. Markers warning - This means one or more of the pI markers may not be identified properly. You can fix this by manually identifying the pI marker using the steps in Step 2: Check Your pI Markers on page 105. Roll your mouse over the icon to display warning details. User Guide for Maurice, Maurice C. and Maurice S. Checking Your Results page 305 Manual correction of markers data notification - This means a user changed the pI marker data manually. Roll your mouse over the icon to display the type of modification that was made. Peak fit warning - Means that a peak cant be fit properly. This can sometimes be caused when a broad peak is fitted as multiple narrow peaks. Changing the peak width can help in this case. The warning is also caused by very small peaks around main peaks, or small peaks that are close to the end of the separation range. You can often fix this by removing the peak(s) using the steps in Step 3: Checking Sample Peaks on page 108. Roll your mouse over the icon to display warning details. Checking Your Results If you see a data warning in the Experiment pane, these steps will also help you identify and correct any issues. Compass for iCE detects your sample protein and pI marker peaks and reports results automatically. But, we always recommend you review your data using the steps in this section as a good general practice to make sure your results are accurate. Please see the step by step procedure in Checking Your Data on page 105 to do this.If you see a data warning in the Experiment pane, these steps will also help you identify and correct any issues. Group Statistics You can use the Grouping view to have Compass for iCE do a statistical analysis of named proteins in your injections (see Peak Names Settings on page 354 for more info on setting named peaks up). Statistics for each protein are also plotted for easy comparison. User Guide for Maurice, Maurice C. and Maurice S. page 306 Chapter 12: cIEF Data Analysis Using Groups 1. Groups are automatically created for injections that use the same sample name and method, so to use this feature, you need to make sure youve got sample names entered. a. Go to the Batch screen. b. Click the Sample ID cells in the Injection pane and type a name for any samples you want to calcu-

late statistics for. 2. Go back to the Analysis screen. Click View in the main menu and select Grouping. NOTE: To turn Grouping off, select View in the main menu and deselect Grouping. Viewing Sample Injection Groups Compass for iCE automatically groups all injections using the same sample name together in the Injection Groups pane. To expand a group - Click the arrow next to a group to see the individual injections in the group and reported data for each User Guide for Maurice, Maurice C. and Maurice S. Group Statistics page 307 To expand all groups - Click Expand All (+) in the upper right corner of the pane. To collapse all groups - Click Collapse All (-) in the upper right corner of the pane. Viewing Statistics Peak and Method Groups The Peak Groups pane reports statistics for each named protein in every group. Each group shows the statis-

tics for named proteins which includes average area, standard deviation, %CV and SEM (standard error mea-

surement). The number in parenthesis after the sample name is the number of injections in the group. To display results using area - Click Area in the upper right corner of the pane. To display results using % total - Click % Total in the upper right corner of the pane to display the calculated percent area for the named peak compared to the total area measured in the injection. This value results from dividing the individual peak area by the sum of all peak areas for the injection and multiplying by 100. To display results using % area - Click % Area in the upper right corner of the pane to display the calculated percent area for the named peak compared to all named peaks. This value results from dividing the individual peak area by the sum of all named peak areas for the injection and multiplying by 100 (shown for named peak sample data only). To expand a group - Click the arrow next to a group to see the individual injections in the group and reported data for each User Guide for Maurice, Maurice C. and Maurice S. page 308 Chapter 12: cIEF Data Analysis To expand all groups - Click Expand All (+) in the upper right corner of the pane. To collapse all groups - Click Collapse All (-) in the upper right corner of the pane. The Method Groups pane pivots the Peak Groups pane results to show statistics for named protein peaks in individual columns. Group Plots The mean values for named peaks using the same method in each injection group are plotted in bar graphs with error bars showing the standard deviation in the Group Plots pane. Youll also get plots that compare samples using the same method in the run. User Guide for Maurice, Maurice C. and Maurice S. Group Statistics page 309 Hiding or Removing Injections in Group Analysis Hidden injections are not included in injection groups. But, hiding injections gives you an easy way to reject individual injections from the statistical analysis. See Hiding Injection Data on page 303 for details on how to do this. User Guide for Maurice, Maurice C. and Maurice S. page 310 Chapter 12: cIEF Data Analysis Copying Results Tables and Graphs You can copy and paste data and results tables into other documents, or save the electropherogram as a graphic file. Copying Results Tables 1. Click in the Peaks or Injections pane. 2. 3. 4. Open a document (Microsoft Word, Excel, PowerPoint, etc.). Right click in the document and select Select one or multiple rows. Select Edit in the main menu and click Copy, or right click on row(s) you selected and click Copy. Paste. Data for the rows selected will be pasted into the document. Copying the Graph 1. 2. 3. Select the Graph pane. Select Edit in the main menu and click Copy, or right click in the Graph pane and select Copy. Select an image option (EMF, PNG or PDF) in the pop-up window, then click Copy. 4. Open a document (Microsoft Word, Excel, PowerPoint, etc.). Right click in the document and select Paste. A graphic of the copied electropherogram will be pasted into the document. Saving the Graph as an Image File 1. 2. 3. Select the Graph pane. Select Edit in the main menu and click Copy, or right click in the Graph pane and select Copy. Select an image option (EMF, PNG or PDF) in the pop-up window, then click Save. User Guide for Maurice, Maurice C. and Maurice S. Exporting Run Files page 311 4. Select a directory to save the file to, enter a file name, then click OK. Exporting Run Files Results tables and raw plot data can be exported for use in other applications. Exporting Results Tables To export the information in the Peaks and Injections tables:

1. Click File in the main menu and click Export Tables. 2. Select a directory to save the files to and click OK. Data will be exported in .txt format. NOTE: To exclude export of standards (pI markers) data or export results table data in .csv format, see Set-

ting Data Export Options on page 379. Exporting Raw Sample Electropherogram Data To export raw sample plot and background data:

1. Click File in the main menu and click Export Spectra. User Guide for Maurice, Maurice C. and Maurice S. page 312 Chapter 12: cIEF Data Analysis To export data in .txt format - Select Text Format. Data will be exported in one file for all injec-

tions. To export data in .cdf format - Select Andi Format. Data will be exported in one file per injec-

tion. 2. Select a directory to save the files to and click OK. Data will be exported in the selected format. Changing Sample Protein Identification Compass for iCE lets you customize what sample proteins are reported in the results tables by making man-

ual adjustments in the electropherogram or Peaks table. Adding or Removing Sample Data 1. Click Show Samples in the View bar. 2. Click Single View in the View bar. 3. Click on the row in the experiment pane that has the injection you want to correct, then click the Graph tab. To remove a peak from the data - Right click the peak in the electropherogram or Peaks table and select Remove peak. The software will no longer identify it as a sample peak in the elec-

tropherogram, and the peak data will be removed in the results tables. User Guide for Maurice, Maurice C. and Maurice S. Changing Sample Protein Identification page 313 A check mark will appear next to the injection in the Experiment pane to indicate a manual correc-

tion was made. To add an unidentified peak to the data - Right click the peak in the electropherogram or peaks table and select Add Peak. The software will calculate and display the results for the peak in the results tables and identify the peak in the electropherogram. A check mark will appear next to the injection in the Experiment pane to indicate a manual cor-

rection was made. NOTE: To remove sample peak assignments that were made manually and go back to the original peak data, right-click the peak in the electropherogram and select Clear for the current injection or Clear All for all injections in the batch. User Guide for Maurice, Maurice C. and Maurice S. page 314 Chapter 12: cIEF Data Analysis Hiding Sample Data You can hide the results for a sample protein in the results tables without completely removing it from the reported results. 1. Click Show Samples in the View bar. 2. Click Single View in the View bar. 3. Click on the row in the experiment pane that contains the injection you want to correct, then click the 4. Graph tab. Right click the peak in the electropherogram or Peaks table and select Hide. Compass for iCE will hide the peak data in the results tables. User Guide for Maurice, Maurice C. and Maurice S. Changing Sample Protein Identification page 315 5. To view hidden peak data, click View in the main menu and click Show Hidden. Hidden peak data will display in the results table and be marked with an X. 6. To unhide a peak, right click on the peak in the electropherogram or peaks table and select Unhide. Changing Peak Names for Sample Data If Compass for iCE did not automatically name a sample protein peak, you can do it manually. 1. Click Show Samples in the View bar. 2. Click Single View in the View bar. 3. Click on the row in the experiment pane that has the sample you want to correct, then click the Graph pane. User Guide for Maurice, Maurice C. and Maurice S. page 316 Chapter 12: cIEF Data Analysis 4. Right click the peak in the electropherogram or Peaks table and click Name, then select a name from the list. Compass for iCE will change the peak name in the electropherogram and results tables, and adjust peak names for other sample proteins accordingly. NOTE: For details on how to specify peak name settings, see Peak Names Settings on page 354. Changing the Electropherogram View Options in the Graph pane let you zoom and rescale electropherograms, overlay or stack plots and change the peak and plot info displayed. The Graph pane toolbar has these options:

Auto Scale Graph Options Stack the Plots Overlay the Plots User Guide for Maurice, Maurice C. and Maurice S. Changing the Electropherogram View page 317 Autoscaling the Electropherogram Click the Auto Scale button to scale the y-axis to the largest peak in the electropherogram. Click the Auto Scale button again to return to default scaling. Customizing the Data Display You can customize electropherogram peak labels, plot labels and display options. To do this, just select the Graph Options button. User Guide for Maurice, Maurice C. and Maurice S. page 318 Chapter 12: cIEF Data Analysis Peak Labels You can customize the labels used to identify peaks in the electropherogram with these options:

Matching Peak Names - Checking this box will draw vertical lines through each named peak. Using this option with Stack the Plots or Overlay the Plots features is helpful for visually comparing your named peaks across multiple injections. User Guide for Maurice, Maurice C. and Maurice S. Changing the Electropherogram View page 319 Peak Names - Checking this box displays peak name labels on all named peaks in the electrophero-

gram. NOTE: If more than one peak label option is selected, peak name labels will always be used for named peaks. Peak Values - Checking this box will display the molecular weight labels on all peaks in the electro-

pherogram. User Guide for Maurice, Maurice C. and Maurice S. page 320 Chapter 12: cIEF Data Analysis NOTE: If more than one peak label option is selected, peak name labels will always be used for named peaks. Baseline and Grid Options You can view the calculated baseline fit, peak integration and show grid lines with these options. Fitted peaks - Checking this box displays how the peaks were fit by the software. For cIEF runs, the software uses Dropped Lines by default. NOTE: This option is only available for sample data. User Guide for Maurice, Maurice C. and Maurice S. Changing the Electropherogram View page 321 Baseline Fit - Checking this box displays the calculated baseline for the peaks. Baseline points will also display for regions of the electropherogram considered to be at baseline. NOTE: This option is only available for sample data. User Guide for Maurice, Maurice C. and Maurice S. page 322 Chapter 12: cIEF Data Analysis Grid Lines - Checking this box adds grid lines in the graph. Plot Labels You can customize the plot labels displayed on the electropherogram with these options. Plot labels are shown in the upper right side of the graph. Sample - Checking this box displays the sample name used for the injection. If sample names were entered with the batch, those names will display here. If not, Sample (default name) displays. Method - Checking this box displays the method used for the injection. Heres an example of an electropherogram with all plot labels selected:

Exposure - Checking this box display the exposure time(s) used for the data. Injection - Checking this box displays the injection number. For example, I4 for injection 4 in the run. User Guide for Maurice, Maurice C. and Maurice S. Changing the Electropherogram View page 323 Stacking Multiple Electropherograms You can stack electropherograms for multiple injections vertically in the Graph pane for comparison. 1. Click Single View. 2. 3. Click the Stack the Plots button. The individual electropherograms for each injection you selected will Select multiple injection rows in the Experiment pane. stack in the Graph pane. User Guide for Maurice, Maurice C. and Maurice S. page 324 Chapter 12: cIEF Data Analysis You can also customize the colors used for the stacked plot display. To do that go to Selecting Custom Plot Colors for Graph Overlay on page 380. Overlaying Multiple Electropherograms You can overlay electropherograms for multiple injections on top of each other for comparison in the Graph pane. 1. Click Single View. 2. 3. Click the Overlay the Plots button. The individual electropherograms for each injection you selected Select multiple injection rows in the Experiment pane. will overlay in the Graph pane. You can also customize the colors used for the overlay plot display. To do that go to Selecting Custom Plot Colors for Graph Overlay on page 380. User Guide for Maurice, Maurice C. and Maurice S. Changing the Electropherogram View page 325 Zooming To zoom in on a specific area of the electropherogram, hold the mouse button down and draw a box around the area with your mouse:

To return to default scaling, right click in the electropherogram and click Zoom Out. User Guide for Maurice, Maurice C. and Maurice S. page 326 Chapter 12: cIEF Data Analysis Selecting Data Viewing Options The graph view menu gives you multiple options for changing what type of electropherogram data is dis-

played. Just click the down arrow next to the graph pane toolbar to view the menu:

A check mark next to the menu option indicates its currently selected, and you can select multiple options at once. NOTE: Unless noted otherwise, graph view menu options are available for sample data only. Sample Raw - Clicking this option displays the basic detector values used to calculate peak absor-

bance. User Guide for Maurice, Maurice C. and Maurice S. Changing the Electropherogram View page 327 Sample Background - Clicking this option displays the basic detector values used to calculate base-

line absorbance. User Guide for Maurice, Maurice C. and Maurice S. page 328 Chapter 12: cIEF Data Analysis Sample - Clicking this option displays raw, uncorrected sample data. Sample Baseline Corrected - Clicking this option displays sample data with the baseline subtracted

(zeroed). This is the default view. In this next example, both Sample and Sample Baseline Corrected are selected. Baseline Fit - Clicking this option displays the calculated baseline for the raw sample data. In this next example, both Baseline Fit and Sample are selected. User Guide for Maurice, Maurice C. and Maurice S. Changing the Electropherogram View page 329 NOTE: This option is selected automatically when Baseline Fit is selected in graph options. Baseline Points - Clicking this option displays regions of the electropherogram considered to be at baseline. In this example, both Baseline Points and Sample are selected. NOTE: This option is selected automatically when Baseline Fit is selected in graph options. User Guide for Maurice, Maurice C. and Maurice S. page 330 Chapter 12: cIEF Data Analysis Fit - Clicking this option displays the bounding envelope of the fitted peaks as calculated by the soft-

ware for the raw sample data. In this example, both Fit and Sample Baseline Corrected are selected. Fit Baseline Corrected - Clicking this option displays the fitted peaks as calculated by the software for the sample baseline corrected data. In this example, both Fit Baseline Corrected and Sample Raw are selected, the fit plot is on the bottom. Adding and Removing Baseline Points Points in the baseline can be added or removed as needed. User Guide for Maurice, Maurice C. and Maurice S. Changing the Electropherogram View page 331 1. Click the Graph Options button in the graph pane toolbar and check Baseline Points. This will display baseline points for the raw sample data. 2. Use the mouse to draw a box around the area you want to correct. This will zoom in on the area. 3. Right click a baseline point and select Add Baseline Point or Remove Baseline Point. NOTE: To clear the manual addition or removal of baseline points and go back to the original view of the data, right click in the electropherogram and click Clear All. Selecting the Graph X-axis Range The pI range used for the x-axis can be changed. Just select View in the main menu and click View Region. User Guide for Maurice, Maurice C. and Maurice S. page 332 Chapter 12: cIEF Data Analysis Analysis sets the x-axis range of the electropherogram to what is selected in the Peak Fit range set-

tings. To view or change these analysis settings, go to Edit > Analysis and click Peak Fit in the left sidebar. In this example, the lower and upper range settings are 3.0 and 10.5. Full displays the entire separation in the electropherogram. This is the default setting. In this example the lower and upper range settings are 1.5 and 11.4. Custom lets you manually enter the lower and upper range settings to display in the electrophero-

gram. In this example the lower and upper range settings are 5.0 and 9.0. User Guide for Maurice, Maurice C. and Maurice S. Closing Run Files page 333 NOTE: You can change the default x-axis range that Compass for iCE uses. Go to Advanced Analysis Set-

tings on page 336 for more info. Closing Run Files If more than one run file is open, you can close just one file or all the open files at the same time. To close one run file - In the Experiment pane, click on one of the sample rows in the file. Then click File from the main menu and click Close. To close all open run files - Select File from the main menu and click Close All. User Guide for Maurice, Maurice C. and Maurice S. page 334 Chapter 12: cIEF Data Analysis Analysis Settings Overview Compass for iCE has many analysis features and settings that you can change to enhance your run data. Select Edit in the main menu and click Analysis. If more than one run file is open, select the run file you want to view settings for from the list:

This opens the Analysis window:

User Guide for Maurice, Maurice C. and Maurice S. Analysis Settings Overview page 335 To move between pages in the window, click on an option in the left sidebar. Advanced - Lets you customize analysis settings for the pI markers. Detection - Lets you choose to view absorbance or native fluorescence data for the run and choose data at different fluorescence exposures. Peak Fit - Lets you customize peak fit settings for sample data. Peak Names - Lets you enter custom naming settings for sample proteins and have Compass for iCE automatically label the peaks in the run data. pI Markers - Lets you customize the pI markers and positions Compass for iCE identifies for each method in your run. On all pages in the Analysis window:

Click Import to import an analysis settings file. Go to Importing Analysis Settings on page 374 to learn how to do this. Click Export to export the current analysis settings file. Go to Exporting Analysis Settings on page 374 to learn how to do this. Click Apply to apply changes to the run file and update results in real time. Click OK to save changes to the run file and exit. Click Cancel to exit without saving changes. User Guide for Maurice, Maurice C. and Maurice S. page 336 Chapter 12: cIEF Data Analysis Advanced Analysis Settings This page lets you view and change analysis settings for the pI marker data. Select Edit in the main menu and click Analysis, then click Advanced in the left sidebar:

NOTE: Settings can be changed in batches before you start the run, or in run files once theyre completed. If you make analysis settings changes to an executing run, they wont be saved to the final run file. pI Markers Settings Peak Width - The approximate width (at full width half max) used to filter out absorbance and fluo-

rescence artifacts which improves recognition of pI markers. Allowable Drift - The distance the pI marker(s) are expected to move compared to the position entered on the pI Markers page. This setting helps with recognition of the pI marker. User Guide for Maurice, Maurice C. and Maurice S. Advanced Analysis Settings page 337 Advanced Analysis Settings Groups Advanced analysis settings are saved as a group, and you can create multiple settings groups. Specific group settings can be applied to methods, injections, sample names or other attributes in the run data. NOTES:

We recommend using the Compass for iCE default values for advanced analysis settings. These settings are included in the default Advanced group. Analysis settings are run-file specific. But, settings can be imported or exported for use with other run files. See Importing and Exporting Analysis Settings on page 374 for more info. Analysis groups are displayed in the analysis settings box:

The Advanced group shown contains the Compass for iCE default analysis settings. You can make changes to this group and create new groups. To view settings for a group, click on the group name. Creating a New Analysis Group 1. 2. Click Add under the analysis settings box. A new group will be created:

Select Edit > Analysis, and select Advanced in the left sidebar. 3. Click on the new group and enter a new name. User Guide for Maurice, Maurice C. and Maurice S. page 338 Chapter 12: cIEF Data Analysis 4. Change the settings in the Markers box as needed. 5. To use the new group as the default analysis settings for the run data, click the arrow in the drop down list next to Apply Default, then click the new group from the list. Analysis settings in the new group will then be applied to the run data. 6. Click OK to save changes. Changing the Default Analysis Group 1. 2. Click the arrow in the drop down list next to Apply Default, then click a new default group from the list. Select Edit > Analysis, and select Advanced in the left sidebar. User Guide for Maurice, Maurice C. and Maurice S. Advanced Analysis Settings page 339 3. Click OK to save changes. Analysis settings in the group selected will be applied to the run data. Modifying an Analysis Group 1. 2. Click on the group in the analysis settings box you want to modify. Select Edit > Analysis, and select Advanced in the left sidebar. 3. Change the settings in the Markers box as needed. 4. Click OK to save changes. The new analysis settings will be applied to the run data. Deleting an Analysis Group 1. 2. Click on the group in the analysis settings box you want to delete and click Remove. Select Edit > Analysis, and select Advanced in the left sidebar. User Guide for Maurice, Maurice C. and Maurice S. page 340 Chapter 12: cIEF Data Analysis 3. Click OK to save changes. Applying Analysis Groups to Specific Run Data 1. 2. Click on the group in the analysis settings box you want to apply to specific run data. Select Edit > Analysis, and select Advanced in the left sidebar. 3. Application of analysis groups to specific run data is done in the override box. Click Add under the over-

ride box. A default override data set will be created from sample information found in the run file. 4. Click the cell in the Apply To column, then click the down arrow. User Guide for Maurice, Maurice C. and Maurice S. Advanced Analysis Settings page 341 5. Select an option from the drop down list. This applies the settings group selected to specific run data as follows:

Methods - All methods in the run file display in the list. Selecting a method applies the group settings to all injections that used that method. Sample names - All sample names in the run file display in the list, otherwise the default name of Sample shows. Selecting a sample name applies the group settings to all injections that used that sample name. Wells or vials - All well or vial numbers used in the run display in the list. Selecting a well/vial number applies the group settings to all injections that used that well/vial. Custom settings - Lets you choose specific injections to apply the group settings to. When you select this in the list, a pop-up box displays to let you enter a specific injection number or range of injections:

6. If you need to change the analysis group used for a data set, click the cell in the Settings column and click the down arrow. Select a group from the drop down list. User Guide for Maurice, Maurice C. and Maurice S. page 342 Chapter 12: cIEF Data Analysis Repeat the previous steps to apply other groups to specific run data. To remove a data set, click on its cell in the Apply To column, then click Remove. 7. 8. 9. Click OK to save changes. User Guide for Maurice, Maurice C. and Maurice S. Detection Settings page 343 Detection Settings This page lets you see the absorbance and native fluorescence exposures taken during the run, and select different exposures for data viewing in the Analysis screen. Select Edit in the main menu and click Analysis, then click Detection in the left sidebar. Changing the Detection Method You can choose to display either absorbance or fluorescence data for your run in the Analysis screen. 1. 2. Select Edit > Analysis, and select Detection in the left sidebar. Select either the Absorbance or Fluorescence radio button. User Guide for Maurice, Maurice C. and Maurice S. page 344 Chapter 12: cIEF Data Analysis Changing the Detection Exposure You can change the exposure used for the sample data displayed in the Analysis screen. NOTES:

Youll only be able to choose exposures for the detection method currently selected. The number of exposures taken and exposure times shown are specified in the method when you set up your batch. They cant be changed after the run has executed. The Absorbance exposure at 0.005 seconds is an instrument default exposure setting. No other absor-

bance exposures are available. Select Edit > Analysis, and select Detection in the left sidebar. 1. 2. Click the arrow in the exposure button you wan to change and select an exposure setting:

User Guide for Maurice, Maurice C. and Maurice S. Peak Fit Analysis Settings page 345 3. Click OK to save changes. Sample data for the exposure selected will display in the Analysis screen. Peak Fit Analysis Settings This page lets you view and change peak fit settings for sample data. Select Edit in the main menu and click Analysis, then click Peak Fit in the left sidebar:

NOTE: Settings can be changed in the batch default analysis before you start the run, or in run files once theyre completed. If you make analysis settings changes to an executing run, they wont be saved to the final run file. User Guide for Maurice, Maurice C. and Maurice S. page 346 Chapter 12: cIEF Data Analysis Range Settings Minimum - The pI value below which peaks wont be identified. This value is also used as the default lower pI range for data displayed in the electropherogram. Maximum - The pI value above which peaks wont be identified. This value is also used as the default upper pI range for data displayed in the electropherogram. View - Sets the default range to either Full or Analysis for the electropherogram x-axis range in the View Region window (select View in the main menu and click View Region). Analysis sets the x-axis range of the electropherogram to the Peak Fit range minimum and max-

imum settings in the electropherogram. Full displays the entire separation range of the run data in the electropherogram. This is the default setting. Baseline Settings Threshold - The variance, or roughness, in a baseline data segment below which a point is called part of the baseline. Window - How long baseline data segments are expected to be in pixels. Shorter segments let the baseline follow plateau sections of the signal. Stiffness - The amount the baseline is allowed to vary from a straight line. Settings between 0.1 and 1.0 make the baseline fit closer to a straight line. Settings from 1.0 to 10.0 will make the baseline fit fol-

low the data more closely. Peak Find Settings Threshold - The minimum signal to noise ratio required for a peak to be identified. A setting of 1.0 will detect many peaks, a setting of 10.0 will detect fewer peaks. Width - The approximate peak width (at full width half max) in pixels used to detect peaks. The mini-

mum value for this setting is 3.0. Larger widths help eliminate the detection of shoulder and noise peaks. User Guide for Maurice, Maurice C. and Maurice S. Peak Fit Analysis Settings page 347 Area Calculation - Two fits are used, either Gaussian Fit or Dropped Lines. These settings can be changed before or after the run is finished. For cIEF applications, peak area is calculated using Dropped Lines by default. This next view is of the same data using the Dropped Lines method instead.This type of area cal-

culation is also often called the perpendicular drop method. This is the preferred method when peaks overlap or are close to each other. It draws two vertical lines from the left and right bounds of the peak down to the x-axis and then measures the total area bounded by the signal curve, the x-axis (y=0 line), and the two vertical lines. User Guide for Maurice, Maurice C. and Maurice S. page 348 Chapter 12: cIEF Data Analysis Peak Fit Analysis Settings Groups Peak fit settings are saved as a group, and you can create multiple settings groups. Specific group settings can then be applied to methods, injections, sample names or other attributes in the run data. NOTES:

We recommend using the Compass for iCE default values for peak fit analysis settings. These settings are included in the default Peak Fit group. Analysis settings are run-file specific. But, settings can be imported or exported for use with other run files. For more information see Importing and Exporting Analysis Settings on page 374. Peak fit groups are displayed in the analysis settings box:

The Peak Fit group shown contains the Compass for iCE default analysis settings. You can make changes to this group and create new groups. To view settings for a group, click on the group name. Creating a New Peak Fit Group 1. 2. Click Add under the analysis settings box. A new group will be created:

Select Edit > Analysis, and select Peak Fit in the left sidebar. 3. Click on the new group and enter a new name. User Guide for Maurice, Maurice C. and Maurice S. Peak Fit Analysis Settings page 349 4. Change the settings in the range, baseline or peak find boxes as needed. 5. To use the new group as the default peak fit settings for the run file data, click the arrow in the drop down list next to Apply Default, then click the new group from the list. Peak fit settings in the new group will then be applied to the run data. User Guide for Maurice, Maurice C. and Maurice S. page 350 Chapter 12: cIEF Data Analysis 6. Click OK to save changes. Changing the Default Peak Fit Group 1. 2. Click the arrow in the drop down list next to Apply Default, then click a new default group from the list. Select Edit > Analysis, and select Peak Fit in the left sidebar. 3. Click OK to save changes. Peak fit settings in the group selected will be applied to the run data. Modifying a Peak Fit Group 1. 2. Click on the group in the analysis settings box you want to modify. Select Edit > Analysis, and click Peak Fit in the left sidebar. 3. Change the settings in the range, baseline or peak find boxes as needed. User Guide for Maurice, Maurice C. and Maurice S. Peak Fit Analysis Settings page 351 4. Click OK to save changes. The new peak fit settings will be applied to the run data. Deleting a Peak Fit Group 1. 2. Click on the group in the analysis settings box you want to delete and click Remove. Select Edit > Analysis, and select Peak Fit in the left sidebar. 3. Click OK to save changes. Applying Peak Fit Groups to Specific Run Data 1. 2. Click on the group in the analysis settings box you want to apply to specific run data. Select Edit > Analysis, and select Peak Fit in the left sidebar. User Guide for Maurice, Maurice C. and Maurice S. page 352 Chapter 12: cIEF Data Analysis 3. Application of analysis groups to specific run data is done in the override box. Click Add under the over-

ride box. A default override data set will be created from sample information found in the run file. 4. Click the cell in the Apply To column, then click the down arrow. 5. Select an option from the drop down list. This applies the settings group selected to specific run data as follows:

Methods - All methods in the run file display in the list. Selecting a method applies the group settings to all injections that used that method. Sample names - All sample names in the run file display in the list, otherwise the default name of Sample shows. Selecting a sample name applies the group settings to all injections that used that sample name. User Guide for Maurice, Maurice C. and Maurice S. Peak Fit Analysis Settings page 353 Wells or vials - All well or vial numbers used in the run display in the list. Selecting a well/vial number applies the group settings to all injections that used that well/vial. Custom settings - Lets you choose specific injections to apply the group settings to. When you select this in the list, a pop-up box displays to let you enter a specific injection number or range of injections:

6. If you need to change the analysis group used for a data set, click the cell in the Settings column and click the down arrow. Select a group from the drop down list. Repeat the previous steps to apply other groups to specific run data. To remove a data set, click on its cell in the Apply To column, then click Remove. 7. 8. 9. Click OK to save changes. User Guide for Maurice, Maurice C. and Maurice S. page 354 Chapter 12: cIEF Data Analysis Peak Names Settings This page lets you view and change custom naming settings for sample proteins. Select Edit in the main menu and click Analysis, then click Peak Names in the left sidebar. NOTE: Settings can be changed in the batch default analysis before you start the run, or in run files once theyre completed. If you make analysis settings changes to an executing run, they wont be saved to the final run file. Peak Names Analysis Settings Groups Peak name settings are saved as a group, and you can create multiple settings groups. Specific group set-

tings can be applied to methods, injections, sample names or other attributes in the run data. User Guide for Maurice, Maurice C. and Maurice S. Peak Names Settings page 355 NOTE: Analysis settings are run-file specific. But, settings can be imported or exported for use with other run files. For more information see Importing and Exporting Analysis Settings on page 374. Peak name groups are displayed in the analysis settings box:

There arent any Compass for iCE default settings groups, but you can make changes to groups youve cre-

ated and create new groups. To view settings for a group, click on the group name in the analysis settings box. Creating a Peak Names Group 1. 2. Click Add under the analysis settings box. Select Edit > Analysis, and select Peak Names in the left sidebar. 3. Enter a new name for the group. User Guide for Maurice, Maurice C. and Maurice S. page 356 Chapter 12: cIEF Data Analysis 4. Click in the first cell in the Name column in the analysis settings peak table and enter a sample protein name. 5. Click in the first cell in the pI column and enter the expected pI for the sample protein. 6. Click in the first cell in the Color column, then click the button. User Guide for Maurice, Maurice C. and Maurice S. Peak Names Settings page 357 The color selection box displays:

7. The color you pick is used to identify the sample protein peak in the Peaks and Injections panes in the Analysis screen. Click a color or define a custom color and click OK. The color selection will update in the table:

8. Click in the first cell in the Range column. 9. Enter a % range for the pI entered. Compass for iCE will automatically name peaks found within this per-

cent of the pI. For example, if the pI entered is 2 and a 10% range is used, all peaks with pIs between 1.8 and 2.2 will be identified with this peak name and color. 10. To add another sample protein, click Add under the peak table. Repeat the previous steps for other sam-

ple proteins. In this example, eight proteins were entered:

User Guide for Maurice, Maurice C. and Maurice S. page 358 Chapter 12: cIEF Data Analysis To remove a sample protein, select its row and click Remove. 11. Click OK to save changes. Modifying a Peak Names Group Select Edit > Analysis, then click Peak Names in the left sidebar. 1. 2. Click on the group in the analysis settings box you want to modify. 3. Change the information in the analysis settings peak table as described in Creating a Peak Names Group on page 355. 4. Click OK to save changes. Deleting a Peak Names Group 1. 2. Click on the group in the analysis settings box you want to delete and click Remove. Select Edit > Analysis, then click Peak Names in the left sidebar. User Guide for Maurice, Maurice C. and Maurice S. Peak Names Settings page 359 3. Click OK to save changes. Applying Peak Names Groups to Run Data 1. 2. Click on the group in the analysis settings box you want to apply to specific run data. Select Edit > Analysis, then click Peak Names in the options list. 3. Application of peak names groups to specific run data is done in the apply settings box. A default data set automatically gets created whenever you create a new group and its applied to all injections in the run. You can either modify the default group or click Add under the box to create a new one. 4. Click the cell in the Apply To column, then click the down arrow. User Guide for Maurice, Maurice C. and Maurice S. page 360 Chapter 12: cIEF Data Analysis 5. Select an option from the drop down list. This applies the peak names group selected to specific run data as follows:

All - Selecting this applies peak names group settings to all injections. Methods - All methods in the run file display in the list. Selecting a method applies the group settings to all injections that used that method. Sample names - All sample names in the run file display in the list, otherwise the default name of Sample shows. Selecting a sample name applies the group settings to all injections that used that sample name. Wells or vials - All well or vial numbers used in the run display in the list. Selecting a well/vial number applies the group settings to all injections that used that well/vial. Custom settings - Lets you choose specific injections to apply the group settings to. When you select this in the list, a pop-up box displays to let you enter a specific injection number or range of injections:

6. If you need to change the peak names group used for a data set, click the cell in the Settings column and click the down arrow. Select a group from the drop down list. User Guide for Maurice, Maurice C. and Maurice S. Peak Names Settings page 361 Repeat the previous steps to apply other groups to specific run data. To remove a data set, click on its cell in the Apply To column, then click Remove. 7. 8. 9. Click OK to save changes. Named peaks will be identified with a peak name label in the electrophero-

gram and color-coded in the Peaks and Injections panes:

User Guide for Maurice, Maurice C. and Maurice S. page 362 Chapter 12: cIEF Data Analysis pI Markers Analysis Settings This page lets you define the pI and position of the pI Markers youre using in your samples. Select Edit in the main menu and click Analysis, then click pI Markers in the left sidebar. NOTE: Settings can be changed in the batch default analysis before you start the run, or in run files once theyre completed. If you make analysis settings changes to an executing run, they wont be saved to the final run file. Markers Analysis Settings Groups pI marker settings are saved as a group, and you can create multiple settings groups. Specific group settings can be applied to methods, injections, sample names or other attributes in the run data. User Guide for Maurice, Maurice C. and Maurice S. pI Markers Analysis Settings page 363 NOTES:

We recommend using the Compass for iCE default values. These settings are included in the default Mark-

ers group. When you edit the pI markers in the method for a batch, Compass for iCE automatically creates a Markers group in the pI Markers Analysis settings for you. Analysis settings are run-file specific. But, settings can be imported or exported for use with other run files. For more information see Importing and Exporting Analysis Settings on page 374. Markers groups are displayed in the analysis settings box:

The Markers group shown uses the Compass for iCE default settings. You can make changes to this group and create new groups. To view settings for a group, click on the group name. Creating a New Markers Group 1. 2. Click Add under the analysis settings box. A new group will be created:

Select Edit > Analysis, and select pI Markers in the left sidebar. 3. Click on the new group and enter a new name. User Guide for Maurice, Maurice C. and Maurice S. page 364 Chapter 12: cIEF Data Analysis 4. The default Maurice cIEF pI marker pI and position values are already populated in the pI Marker Peaks table. If youd like to use these values, skip to the next step. If youre using different markers, heres how to change the values:

a. Click in the first cell in the pI column in the table and enter the pI for the marker. b. Click in the first cell in the Position column and enter a value for the marker. User Guide for Maurice, Maurice C. and Maurice S. pI Markers Analysis Settings page 365 NOTE: pI marker peak positions are relative to each other. Only the difference in position is used to help identify them. When entering pI marker peak information for the first time, review the marker data in the Analysis screen to find the correct peak positions. c. Repeat the steps above for the remaining markers in the table. To add another marker - Click Add under the table, then change the information in the new row. To remove a marker - Select its row and click Remove. 5. To use the new group as the default settings for the run, click the arrow in the drop down list next to Apply Default, then click the new group in the list. The settings in the new group will then be applied to the run data. 6. Click OK to save changes. Changing the Default Markers Group 1. 2. Click the arrow in the drop down list next to Apply Default, then select a new default group from the list. Select Edit > Analysis, and click pI Markers in the left sidebar. User Guide for Maurice, Maurice C. and Maurice S. page 366 Chapter 12: cIEF Data Analysis 3. Click OK to save changes. Analysis settings in the group selected will be applied to the run data. Modifying a Markers Group 1. 2. Click on the group in the analysis settings box you want to modify. Select Edit > Analysis, and click Markers in the left sidebar. 3. Change the marker info as needed as in Creating a New Markers Group on page 363. 4. Click OK to save changes. The new analysis settings will be applied to the run data. Deleting a Markers Group 1. 2. Click on the group in the analysis settings box you want to delete and click Remove. Select Edit > Analysis, and click pI Markers in the left sidebar. User Guide for Maurice, Maurice C. and Maurice S. pI Markers Analysis Settings page 367 3. Click OK to save changes. Applying Markers Groups to Specific Run Data 1. 2. Click on the group in the analysis settings box you want to apply to specific run data. Select Edit > Analysis, and select pI Markers in the left sidebar. 3. Application of markers groups to specific run data is done in the override box. Click Add under the over-

ride box. A default override data set will be created from sample information found in the run file. 4. Click the cell in the Apply To column, then click the down arrow. User Guide for Maurice, Maurice C. and Maurice S. page 368 Chapter 12: cIEF Data Analysis 5. Select an option from the drop down list. This applies the settings group selected to specific run data as follows:

Methods - All methods in the run file display in the list. Selecting a method applies the group settings to all injections that used that method. Sample names - All sample names in the run file display in the list, otherwise the default name of Sample shows. Selecting a sample name applies the group settings to all injections that used that sample name. Wells or vials - All well or vial numbers used in the run display in the list. Selecting a well/vial number applies the group settings to all injections that used that well/vial. Custom settings - Lets you choose specific injections to apply the group settings to. When you select this in the list, a pop-up box displays to let you enter a specific injection number or range of injections:

6. If you need to change the analysis group used for a data set, click the cell in the Settings column and click the down arrow. Select a group from the drop down list. User Guide for Maurice, Maurice C. and Maurice S. Injection Reports page 369 Repeat the previous steps to apply other groups to specific run data. To remove a data set, click on its cell in the Apply To column, then click Remove. 7. 8. 9. Click OK to save changes. Injection Reports You can export PDF files of the raw and analyzed data, IV plot, peaks table, sample and system info for indi-

vidual or all injections in a run file. You can also export the run history with all analysis events. 1. Click File > Open Run and select a run file. 2. If you want reports for all injections, skip to the next step. If you only want reports for certain injections, in the Experiment pane:

To select sequential injections: Select the first injection, then hold the Shift key and select the last injection you want a report for. This selects all rows between the two injections. To select specific injections: Hold the Ctrl key and select just the injections you want reports for. 3. Select File from the main menu in either screen and click Injection Report. User Guide for Maurice, Maurice C. and Maurice S. page 370 Chapter 12: cIEF Data Analysis 4. In the Injection Reports window:

d. Choose either Selected injections or All injections. e. Select the Analysis log checkbox if you want a run history report with all analysis events. f. The report name defaults to the run file name. If you want to change it, type in the Report Name box to make updates. g. Click OK. 5. The Injection Report PDF(s) are exported to the Runs folder in the Compass for iCE directory. Theyll be in a folder with the report name used in the prior step. When the reports are done, the folder opens for you automatically. User Guide for Maurice, Maurice C. and Maurice S. Injection Reports page 371 Example Analysis and Injection Report User Guide for Maurice, Maurice C. and Maurice S. page 372 Chapter 12: cIEF Data Analysis User Guide for Maurice, Maurice C. and Maurice S. Injection Reports page 373 User Guide for Maurice, Maurice C. and Maurice S. page 374 Chapter 12: cIEF Data Analysis Importing and Exporting Analysis Settings The analysis settings in a run file can be exported as a separate file. This allows the same analysis settings to be imported into other batches or run files at a later time, rather than you having to re-enter them manually. Importing Analysis Settings NOTE: Importing an analysis settings file populates the settings in all analysis pages. Select Edit in the main menu and click Default Analysis (Batch screen) or Analysis (Analysis screen). 1. Open the run file or batch you want to import analysis settings to. 2. 3. Click Import on any page. 4. Select a settings file (*.settings) and click OK. The imported settings will display in all analysis pages. Exporting Analysis Settings NOTE: Exporting an analysis settings file exports the settings in all analysis pages. 1. Open the run file or batch you want to export analysis settings from. 2. 3. Click Export on any page. The following window displays:

Select Edit in the main menu and click Default Analysis (Batch screen) or Analysis (Analysis screen). User Guide for Maurice, Maurice C. and Maurice S. Importing and Exporting Analysis Settings page 375 4. 5. The default directory is Compass for iCE/Runs. Change the directory if needed. Enter a file name and click Save. The settings will be saved as a *.settings file. User Guide for Maurice, Maurice C. and Maurice S. page 376 Chapter 12: cIEF Data Analysis User Guide for Maurice, Maurice C. and Maurice S. page 377 Chapter 13:

Setting Your Preferences Chapter Overview Customize Your Preferences Grouping Options Enabling Access Control Setting Data Export Options Selecting Custom Plot Colors for Graph Overlay Setting Up Maurice Systems to Send Tweets User Guide for Maurice, Maurice C. and Maurice S. page 378 Chapter 13: Setting Your Preferences Customize Your Preferences You can set and save several custom preferences in Compass for iCE. To view and change these settings, select Edit in the main menu and click Preferences. To move between preferences pages, click on an option in the left sidebar. Heres what you can customize:

Access Control - Lets you log on to Compass for iCE through an Authorization Server. Analysis - Lets you customize data export options. Graph - Lets you customize graph color displays. Grouping - Groups samples with the same name together across runs, so you can get statistics for the same sample in multiple runs. Twitter - Lets you configure Compass for iCE to tweet Maurice, Maurice C. and Maurice S. run status. In all preferences windows:

Click Apply to apply changes to any open run files in Compass for iCE. Click Restore Defaults to restore the values on the page to default settings. Click OK to save changes and exit. Click Cancel to exit without saving changes. User Guide for Maurice, Maurice C. and Maurice S. Enabling Access Control page 379 Enabling Access Control You can use the Access Control feature to help satisfy 21CFR Part 11 data security requirements when using Maurice instruments. Please go to Enabling Access Control on page 391 to get more info. Setting Data Export Options Select Analysis in the sidebar. Export Standards - This option exports data for the standards in each injection when run data is exported. Its selected by default. If its not selected, only sample injection data is exported. Export using a comma as the column deliminator - This option exports run data with a comma separator in .csv format. When its not selected, data is exported in .txt format with a tab separator

(this is the default setting). User Guide for Maurice, Maurice C. and Maurice S. page 380 Chapter 13: Setting Your Preferences Selecting Custom Plot Colors for Graph Overlay Select Graph in the sidebar. Apply colors to stacked plots - This option applies the color scheme shown to individual plots when Stack the plots is selected in the Analysis screens Graph pane. When this option isnt selected, all plots use the same color (this is the default setting). NOTE: If Apply colors to stacked plots isnt selected, the colors shown are only applied to plots when Overlay the plots is selected in the Graph pane. User Guide for Maurice, Maurice C. and Maurice S. Selecting Custom Plot Colors for Graph Overlay page 381 Changing Plot Colors 1. Click the button next to a Plot color number. Youll get a color selection box:

User Guide for Maurice, Maurice C. and Maurice S. page 382 Chapter 13: Setting Your Preferences 2. Select a color or define a custom color and click OK. The color button will update to the new color selected. Repeat the steps above for any other plot colors. 3. 4. Check Apply Colors to Stacked Plots if you also want the new color settings to be used for the Stack the plots option in the Graph pane. 5. Click Apply to apply the new color settings to the plots currently displayed. This lets you see the changes without having to close the Graph window. 6. Click OK to save changes and exit. 7. Select Overlay the plots in the Graph pane. The new color scheme will be used. Grouping Options Select Grouping in the sidebar. Selecting the Group Across Runs box groups samples with the same name together even if theyre in dif-

ferent runs, so you can get statistics for the same samples across multiple runs. When the box isnt selected, only samples with the same name within the same run are grouped for statistics (this is the default setting). NOTE: To activate grouping and get statistics for runs you have open in the Analysis Screen, select View in the main menu and click Grouping. User Guide for Maurice, Maurice C. and Maurice S. Setting Up Maurice Systems to Send Tweets page 383 Setting Up Maurice Systems to Send Tweets Select Twitter in the sidebar. NOTES:

To set your Maurice system up to tweet, the computer youre using needs to be connected to the internet through a network connection or the local lab computer. We recommend setting up separate Twitter accounts for each system. This lets multiple people in the lab follow run progress. User Guide for Maurice, Maurice C. and Maurice S. page 384 Chapter 13: Setting Your Preferences 1. Click Set Account. A set account window will display in Compass for iCE and a browser window will open:

User Guide for Maurice, Maurice C. and Maurice S. Setting Up Maurice Systems to Send Tweets page 385 2. 3. Enter a user name or email and password, then click Authorize app. A new page will display in the browser with a PIN number. Enter the PIN number in the Compass for iCE set account window and click OK:

4. The user name will now appear in the Twitter User Name box. Select your Tweet When options and click Apply. User Guide for Maurice, Maurice C. and Maurice S. page 386 Chapter 13: Setting Your Preferences 5. To confirm the Twitter account is receiving messages, click Tweet Message. Enter a test message and click OK. 6. If the test Tweet was successful, youll get this message:

User Guide for Maurice, Maurice C. and Maurice S. Setting Up Maurice Systems to Send Tweets page 387 7. Click OK to save changes and exit. Maurice, Maurice C. and Maurice S. will automatically tweet as the selected options occur:

Changing the Twitter Account To change the Twitter account your system uses:

1. 2. Click Clear. 3. Select Edit > Preferences, then select Twitter in the left sidebar. Follow the same steps to set up the account as in Setting Up Maurice Systems to Send Tweets on page 383. User Guide for Maurice, Maurice C. and Maurice S. page 388 Chapter 13: Setting Your Preferences User Guide for Maurice, Maurice C. and Maurice S. page 389 Chapter 14:

Compass Access Control and 21 CFR Part 11 Compliance Chapter Overview Overview Authorization Server Enabling Access Control Logging In to Compass for iCE Saving Changes Signing Files Instrument Command Log Run File History Troubleshooting Problems and Suggested Solutions User Guide for Maurice, Maurice C. and Maurice S. page 390 Chapter 14: Compass Access Control and 21 CFR Part 11 Compliance Overview The Compass Access Control feature can be used to help satisfy the 21CFR Part 11 data security require-

ments when using Maurice instruments. When Access Control is enabled and the Authorization Server has been installed (see "Authorization Server" on page 399):

Users are required to log in to Compass for iCE when the software is launched A history of all actions is maintained Data files are signed and encrypted to prevent unauthorized changes (e.g., all files are controlled) Compass for iCE can be run with or without Access Control enabled. When Access Control is disabled, no user log in is required and files are not encrypted or signed. The instrument history and file history are still maintained but the entries are not signed. Each instrument maintains a history of user commands Each batch and data file includes a history of signed changes to the file User Guide for Maurice, Maurice C. and Maurice S. Enabling Access Control page 391 Enabling Access Control Access Control is enabled in Preferences. Select Edit in the main menu, click Preferences, then select Access Control. To enable Access Control:

1. Check the Enable box. 2. Enter the IP address of the Authorization server. Use format X.X.X.X or LocalHost if installing the server on the local machine. NOTE: Always use the default port setting of 8000, this should not be changed. 3. Close Compass for iCE. The next time the software is launched, a user log in will be required. NOTE: Access Control can only be disabled by logging into Compass for iCE and deselecting the Enable box in the Access Control page of Preferences. User Guide for Maurice, Maurice C. and Maurice S. page 392 Chapter 14: Compass Access Control and 21 CFR Part 11 Compliance Logging In to Compass for iCE With Access Control enabled, all users must log in to Compass for iCE whenever the software is launched. Enter your user name and password previously setup by your Compass for iCE Administrator. NOTE: Your account will be blocked after a certain number of login failures. If this happens, contact your administrator to unblock the account. A successful log in will display the Compass for iCE main window with the user information in the lower sta-

tus bar. The full user name is displayed with the unique user ID in parenthesis:

User Guide for Maurice, Maurice C. and Maurice S. Logging In to Compass for iCE page 393 Locking and Unlocking the Application You can click the Lock button to lock Compass for iCE and prevent access by other users. To unlock the application, users must re-enter their password. If there is no activity in Compass for iCE for 20 minutes, the application automatically locks. Users must re-

enter their passwords to perform any controlled actions:

Resolving Log In Issues Log in failures may occur when:

Compass for iCE is using the wrong IP address When this happens, the following message displays:

The server is temporarily unavailable User Guide for Maurice, Maurice C. and Maurice S. page 394 Chapter 14: Compass Access Control and 21 CFR Part 11 Compliance Click Disable to restart Compass for iCE with Access Control disabled. Verify or correct the server IP address then close and restart the software to log in with Access Control enabled. Saving Changes When Save is selected from the File menu, a dialog box will display to allow you to enter a comment before saving the signed file:

The comment is added to the signature entry in the file History:

User Guide for Maurice, Maurice C. and Maurice S. Signing Files page 395 Signing Files Select e-Signature from the File menu to add an electronic signature to a file. The signed entry will be added to the file History with the meaning of the signature entered in the com-

ment, such as Approved or Verified. Instrument Command Log The Instrument Command Log can be viewed at any time by selecting the Instrument menu and clicking Properties, and then clicking the Command Log button:

User Guide for Maurice, Maurice C. and Maurice S. page 396 Chapter 14: Compass Access Control and 21 CFR Part 11 Compliance The Command Log lists all the commands sent to the instrument that were signed by the user who sent the command. If you want to copy the Command Log at any time, right click in the table and select Copy, then paste into another document. User Guide for Maurice, Maurice C. and Maurice S. Instrument Command Log page 397 User Guide for Maurice, Maurice C. and Maurice S. page 398 Chapter 14: Compass Access Control and 21 CFR Part 11 Compliance Run File History Select the Run Summary screen tab and then the History tab to see the file History. To copy the file History, right click in the table and select Copy, then paste into another document. Troubleshooting Problems and Suggested Solutions If any of the following error messages are encountered, follow the recommended steps below to resolve the issue. Unknown user name or password. Check if the Caps Lock is on, user name and password are case sensitive. Ask a Compass for iCE administrator to confirm your user name. If your password is unknown then the administrator can reset your password (see "Resetting User Passwords" on page 405 for more information). User Guide for Maurice, Maurice C. and Maurice S. Authorization Server page 399 Server not available. From the Edit menu, click Preferences and then Access Control to confirm the server address is set to the correct Authorization server address. Compass for iCE must be able to reach the server on the network. The server must have inbound access to port 8000 enabled. Controlled file cannot be opened without log in. To open a controlled Run file, enable Access Control by clicking Edit, then Preferences and Access Control. Select Enable, close Compass for iCE, then re-launch the software with a valid log in. Uncontrolled file cannot be opened when logged in. To open an uncontrolled Run file, disable Access Control by clicking Edit, then Preferences and Access Control. Deselect Enable, close Com-

pass for iCE then re-launch the software. NOTE: Uncontrolled files can be opened when Compass Access Control is enabled (controlled mode). Command disabled. Certain commands are only available when a user with the correct permissions is logged in. To change user permissions, use a web browser to log in to the Authorization server web interface at the address shown on the Access Control page in Preferences, such as: 10.1.3.231:8000. Compass for iCE does not prompt for log in. Compass for iCE will only prompt for a log in on launch when Access Control is enabled in Preferences. Enable Access Control by clicking Edit, then Preferences and Access Control. Select Enable, close Compass for iCE, then re-launch the software. You should now be prompted for a log in. Authorization Server The Authorization Server controls the log in access to Compass for iCE. In the simplest configuration, the server is run on the same computer as Compass for iCE and only that copy of Compass for iCE is controlled. A single server can also be used to control access to multiple copies of Compass for iCE running on different computers, so long as they have network access to the server. Multiple copies of the server may be run on the same network, and each server will have its own user database. To enable Compass for iCE to use a particular Authorization Server, click Edit, then Preferences and Access Control and enter the server IP address using format X.X.X.X. User Guide for Maurice, Maurice C. and Maurice S. page 400 Chapter 14: Compass Access Control and 21 CFR Part 11 Compliance NOTES:

Always use the default port setting of 8000, this should not be changed. If the server is installed on the same computer as Compass for iCE (e.g., the local machine), enter Local-

Host instead of the IP address. Contact your local IT Administrator to assist with installing the Authoriza-

tion Server in your preferred format. Server Administration The Authorization Server is configured through a web interface at the IP address of the server on port 8000. To access the Server home page, open any browser and type the IP address on port 8000 in a X.X.X.X:8000 or http://X.X.X.X:8000 format. Use LocalHost instead of the IP address if the Server is installed on the local machine. The default server administrator is:

User: admin After installing the Authorization Server, the administrator user name and password can be changed. Password: admin Adding Non-admin Users Add a user to the server to allow that user to log in to Compass for iCE. To do this:

1. Select Users from the Site Administration home page:

User Guide for Maurice, Maurice C. and Maurice S. Authorization Server page 401 2. From the Users page, select Add User:

3. Fill in the fields to create a new user:

After adding a new user more information can be added:

User Guide for Maurice, Maurice C. and Maurice S. page 402 Chapter 14: Compass Access Control and 21 CFR Part 11 Compliance NOTE: Users are blocked after the number of login failures defined in the Password policy setting. Permissions All users can log in to Compass for iCE, but the commands available within Compass for iCE are controlled by Permission settings. Commands a user does not have permission to use will be disabled. After user permis-

sions have been changed on the server the user must close and re-open Compass for iCE to use the new permissions. Users can belong to groups that have multiple permissions such as Operator or Scientist:

User Guide for Maurice, Maurice C. and Maurice S. Authorization Server page 403 Use the Groups page to change the permissions in a group or create new groups:

To change permissions for a group click Change, then select a group:

User Guide for Maurice, Maurice C. and Maurice S. page 404 Chapter 14: Compass Access Control and 21 CFR Part 11 Compliance Move individual group permissions in or out of the Available Permissions and Chosen Permissions boxes by selecting a permission in either box. Click the left or right arrow button to move the permission into the other box. Adding Admin Users To create a user with administrator permissions:

1. 2. Under permissions, select Staff status and Superuser status:

Follow the steps described in "Adding Non-admin Users" on page 400 to create the admin user. 3. Assign the admin user to a group. NOTE: Selecting Superuser status enables server permissions only. Admin users must be also be assigned to a group to in order to have Compass for iCE permissions. User Guide for Maurice, Maurice C. and Maurice S. Authorization Server page 405 Resetting User Passwords NOTE: Users are blocked after the number of login failures defined in the Password policy setting. To reset a user password:

1. Select Users from the Site Administration home page, then select the user to change. The following screen displays:

2. Raw passwords are not stored, they must be changed manually. Click the text link to access the pass-

word change form:

3. Enter the new password, then click Change password. User Guide for Maurice, Maurice C. and Maurice S. page 406 Chapter 14: Compass Access Control and 21 CFR Part 11 Compliance Audit Trail Admin users with Staff Status can view, print and download the Audit Trail. Select View Audit Trail from the Site Administration home page to access it. Password Policy Settings These settings let administrators set password policies. Select Password policy settings from the Site Administration home page to make changes. User Guide for Maurice, Maurice C. and Maurice S. Authorization Server page 407 LDAP Settings LDAP settings allow you to connect the Compass Authorization Server to your own networks domain con-

troller, so users can log on with their existing network password. With LDAP, passwords are not maintained by the Compass Authorization Server, they are administered by the network admin. First select LDAP settings from the Site Administration page and set your LDAP settings. Next, add users as described in "Adding Non-admin Users" on page 400 and select the LDAP User checkbox. Passwords arent required for LDAP users. Encryption Details Compass for iCE uses the SHA1 hash algorithm to generate a 160 bit hash code that is unique for all files. All files saved by Compass for iCE are encrypted with a digital key. This key along with the hash codes guaran-

tees the file history is correct and no other edits were made. All changes saved to a file have the electronic signature of the user who saved the file. The e-Signature command allows a user to sign off on a state such as approved or verified. There is no individual ownership of files, all users who log into Compass for iCE can open any file. User Guide for Maurice, Maurice C. and Maurice S. page 408 Chapter 14: Compass Access Control and 21 CFR Part 11 Compliance User Guide for Maurice, Maurice C. and Maurice S. page 409 Chapter 15:

Maintenance and Troubleshooting Chapter Overview Cartridge Handling and Care Maintenance Spare Parts Software Updates Instrument Software (Embedded) Updates Frequently Asked Questions: cIEF Applications Frequently Asked Questions: cIEF Applications User Guide for Maurice, Maurice C. and Maurice S. Cartridge Handling and Care page 410 Cartridge Handling and Care The cIEF and CE-SDS Cartridges were developed for use with Maurice systems. Each cartridge is individually tested and shipped with a Certificate of Analysis, are also online at http://www.proteinsimple.com/certifi-

cates.html. The cartridges are shipped dry and should be stored free of liquid. Cartridges need to be used, cleaned and stored properly to reach their maximum lifetime. Store cartridges in their original packaging at room temperature when you receive them. Hold cartridges using the blue or orange finger holds on either side of the cartridge. Dont touch the recessed optical windows of the cartridge. Finger Holds Optical Windows Whenever you handle the cartridge or remove it from its packaging, make sure the cartridge inlet doesn't come in contact with any surfaces. Each cartridge is guaranteed for 100 injections. Maurice reads the cartridges RFID and keeps track of how many injections are left for you automatically. Always clean the cartridge before storing. See page 103 for the cIEF Cartridge cleaning steps and page 137 for the CE-SDS Cartridge cleaning steps. Always store the cartridge in its original packaging at room temperature when not in use. cIEF Cartridge The cartridge is designed for use with common cIEF reagents like methyl cellulose, ampholytes, urea, anolyte and catholyte, but over exposure or high concentrations of certain components can harm it. The cartridge also requires 0.35% methyl cellulose in the sample mixture. Make sure to always add Catholyte solution to the OH- electrolyte tank (white port) and Anolyte solu-

tion to the H+ electrolyte tank (red port). If you add electrolytes to the wrong tank, it can damage to the cartridge. User Guide for Maurice, Maurice C. and Maurice S. Cartridge Handling and Care page 411 Make sure to not get any liquid on the cartridge's optical window. Maurice cleans the cIEF Cartridge automatically at the end of the run. If youll use the cartridge again within 24 hours of your last run, you can leave the cartridge in Maurice. Otherwise youll need to clean and store it. See page 103 for cleaning steps. Always clean the electrolyte tanks before storing. See page 103 for the cIEF Cartridge cleaning steps. Compatibility with Sample Components Methyl Cellulose (MC): The sample mix must contain 0.35% methyl cellulose. The cartridge must be flushed with 0.5% methyl cellulose between runs. Solvents: The cartridge is not compatible with organic solvents. Do not rinse with solvents and mini-

mize the amount of solvent in the sample mix. Salt and surfactants: High current can harm the internal coating in the cartridge capillary. High con-

centrations of salt and surfactants in the sample mix can generate high currents above 40 micro-

amps. This high current will compress the pH gradient and also damage the cartridge. Please take care to minimize the concentration of salts in the final sample mix to below 15 mM. To keep current at a minimum, we suggested using only non-ionic or zwitterionic surfactants. Dont use aromatic sur-

factants as they can interfere with sample detection. Cleaning the Outside of the Cartridge If you see spikes in your data, the outside of the cartridge should be cleaned with canned air. Youll need to use residue- and moisture-free canned air to prevent fouling of the optical path through the separation cap-

illary. 1. Place the can's nozzle or tube opening 10-12 inches from the cartridge surface. Then depress the aero-

sol actuator down about halfway so you get a gentle flow of air. Sweep the air stream across the entire length of the optical window. Flip the cartridge over and repeat the prior steps. Flip the cartridge over again and gently clean the top surface one last time before reinstalling in Mau-

rice. 2. 3. 4. CE-SDS Cartridge If you see any separation matrix sticking to the cartridge inlet, soak the inlet in DI water for 5 minutes. Then wipe it using a lint-free laboratory wipe that's been moistened with DI water. Other than this, no external cleaning of the cartridge is required. User Guide for Maurice, Maurice C. and Maurice S. Maintenance page 412 Check the saturation sensor on the back of the cartridge insert after every run. If it's red, you'll need to use a new cartridge insert for your next batch. If the saturation sensor isn't red, you can keep using the current cartridge insert. Saturation Sensor OK to keep using insert. Replace cartridge insert. If youll use the cartridge again within 2 hours of your last run, you can leave the cartridge in Maurice. Otherwise youll need to clean and store it. Always run the cartridge cleanup before storing. See page 137 for the CE-SDS Cartridge cleanup steps. Compatibility with Sample Components Salt: The salt concentration in your sample should be <50 mM. Higher concentrations will adversely affect electrokinetic injections. Dilute your sample with CE-SDS Sample Buffer to reach the recom-

mended salt concentration. If the protein concentration in your samples is low, we recommend desalting the sample. Maintenance Daily Empty out any condensation in the sample plate or sample tray inserts. Wipe out the sample block too if needed. Dispose of your samples and reagent vials after each run. Compass for iCE will let you know when a cartridge is at the end of its useful life and should be discarded. User Guide for Maurice, Maurice C. and Maurice S. Maintenance page 413 Yearly We recommend Maurice has annual preventive maintenance performed by an authorized ProteinSimple engineer. Please contact Technical Support to schedule a visit. Changing the Fuse 1. 2. Power down Maurice and unplug his power cord. Locate the fuse holder on his rear panel. Power Cord Fuse Holder 3. Use a flat-head screwdriver to gently pry the fuse holder open and remove the fuse holder. Spare Fuse Box Old Fuse 4. Remove the old fuse. User Guide for Maurice, Maurice C. and Maurice S. Spare Parts page 414 5. Theres a spare fuse in the small box. Pull the box out, pull the new fuse out and use it to replace defec-

tive fuse. Spare Fuse 6. 7. Reinsert the fuse holder. Plug Maurices power cord back in and turn his power on. Spare Parts Maurice, Maurice C. and Maurice S. dont have any user replaceable parts except for the power fuse. Please contact ProteinSimple Technical Support if they get sick and need repair.

!WARNING!

You cant replace or service any parts on Maurice systems except for the power entry fuse. Software Updates To check for software updates, first make sure the computer youre using has an active internet connection. Then go to Compass for iCE software, select Help in the main menu and click Check for Updates. If you dont have internet access, call your FAS for assistance on getting the latest update. User Guide for Maurice, Maurice C. and Maurice S. Instrument Software (Embedded) Updates page 415 Instrument Software (Embedded) Updates To check for embedded updates, go to Compass for iCE software, select Instrument in the main menu, then Update and select Network. If youre not on the network, call your FAS for assistance on getting the latest update. Frequently Asked Questions: cIEF Applications NOTE: Please refer to the Maurice cIEF Method Development or CE-SDS Application Guides for info on ini-

tial application conditions and method optimization. I have a new protein sample to analyze. What starting conditions should I use?

Begin with the following initial sample conditions:

Carrier ampholytes: pH 3-10 Pharmalytes (4%) Additive: 0.35% methyl cellulose Sample analyte: 0.1 mg/mL concentration in final solution. The balance of the solution should be HPLC-grade deionized water. 10 mM arginine 1X pI 4.05 and 9.99 markers NOTES:

If you want to use pI markers below pI 4.05, we suggest adding 10 mM IDA to the sample solution ProteinSimple provides a 1% methyl cellulose solution (P/N 101876). Another way to start is to simply use the same sample conditions used if you were successful in running this sample on slab gel IEF. Use the same carrier ampholytes and additives for analysis on Maurice systems. What carrier ampholytes are commercially available, and which one is best for my sample?

At present, carrier ampholytes are commercially available from four different manufacturers under the fol-

lowing brand names:

Pharmalytes (GE) Servalyts (Serva) User Guide for Maurice, Maurice C. and Maurice S. Frequently Asked Questions: cIEF Applications page 416 Other carrier ampholytes exist, however, they are all repackaged and resold using one of the products listed above. Each brand may give slightly different separation resolution due to slight differences in ampholytic composi-

tions. Identification of the optimal carrier ampholytes for a given protein sample is best determined experi-

mentally. Along with native fluorescence, Maurice systems use UV absorption detection at 280 nm. All carrier ampholytes exhibit some degree of absorption at this wavelength, which causes some baseline noise. Phar-

malytes have low and uniform UV absorption and produce no background signal in native fluorescence along the entire pH range. Because of the low background noise of Pharmalytes, these ampholytes are rec-

ommended for initial sample conditions. Does my sample matrix affect my results?

Yes. However, the sample is diluted 20X in carrier ampholytes, methyl cellulose and HPLC-grade deionized water, which minimizes matrix effects. For example, if the concentration of your sample stock solution is 2 mg/mL, 10 mL of the sample can be directly diluted by adding 112 mL of HPLC-grade deionized water, 8 mL of pH 3-10 Pharmalytes and 70 mL of 1% methyl cellulose. The final solution is 200 mL with a sample con-

centration of 0.1 mg/mL. In this example, the original sample matrix will not affect analysis. If the original stock sample concentration is >2 mg/mL and contains high salt concentrations, then diluting further and using native fluorescence to boost signal is recommended. If detection in both absorbance and fluorescence is required, desalting may be necessary. I cannot get reproducible peaks due to sample precipitation, what should I do?

1. Dilute the sample. 2. The native fluorescence detection mode provides higher sensitivity and can be used for low concentra-

tion samples. Doing either or both of the above reduces the potential for aggregation or precipitation. If the issue is still observed, several additives can be tested to increase protein solubility. The following additives have been successfully tested with Maurice systems and should help stabilize proteins during analysis:

Up to 4M urea Up to 20% formamide Up to 25% sorbitol Up to 25% sucrose Up to 25% glycerol Denaturing conditions, such as 8 M urea User Guide for Maurice, Maurice C. and Maurice S. Frequently Asked Questions: cIEF Applications page 417 In rare cases, sample precipitation may be caused by the carrier ampholytes. To avoid this problem, try using a different brand of carrier ampholytes. If additive conditions for stable sample runs have been established for gel IEF, then these additive conditions can often be successfully used for cIEF analysis on Maurice sys-

tems. NOTE: All additives may change the pI value of the protein slightly, especially if the method uses pI markers in the acidic range of the pH gradient. How do I prepare sample solutions in 8 M Urea?

For a 200 L final sample solution:

Weigh 96 mg of urea powder in a 1.5 mL centrifuge tube. Add 32 L HPLC-grade deionized water, 70 L of 1% methyl cellulose, 8 L of carrier ampholytes and 10 L of sample to the urea powder in the centrifuge tube. This will make a final volume of 200 L (96 mg urea powder and 120 L liquid). If more than 10 L or less than 10 L of sample is added, the volume of water should be adjusted to ensure a final volume of 120 L. NOTE: Urea must always be prepared fresh before use. When running samples in 8 M urea, the focusing time should be increased 1-2 minutes compared to normal conditions. This is due to the higher viscosity of the urea-containing solution. How can I identify peaks in different runs and different samples?

A reliable way to identify peaks in electropherograms is to use internal pI Markers. First run the sample with-

out internal pI Markers. The pI values of sample peaks can be estimated from their peak positions relative to the full pI range of the carrier ampholytes. In Compass for iCE graphs, the left side of the electropherogram is the anodic end of the capillary (acidic) and the right side is the cathodic end (basic). For example, if pH 3-10 Pharmalytes are used as the carrier ampholytes, the x-axis of the electropherogram represents pI 3 to pI 10 from left to right. The pI value of a peak at the middle of the trace should be about 6.5. Two pI Markers are mixed into the sample solution. Ideally, the peaks of the two markers should bracket the sample peaks and the two marker peaks should be as close as possible in order to achieve good precision in peak identification. The electropherograms of the sample mixed with pI Markers are processed using Compass for iCE for pI determination. The software uses the method settings to automatically identify the pI markers to convert from pixel position in the Markers View to pI in the Samples View. User Guide for Maurice, Maurice C. and Maurice S. Frequently Asked Questions: cIEF Applications page 418 In this way, the sample peaks are identified by their measured pI values. The precision of peak identification by measuring the pI values using Maurice systems is less than +0.03 pH units. Since the measured pI value of a protein is affected by many factors such as sample matrix and the type of carrier ampholytes used, to correctly identify peaks in different samples or different runs, all runs should be done under the exact same conditions. What kind of pI markers can I use?

ProteinSimple recommends using low molecular weight amphoteric compounds with well defined isoelec-

tric points and strong UV absorbance when using Maurice systems. Conversely, we do not recommend using protein pI markers since they often produce multiple isoelectric points and, on occasion, may interact with the sample analyte. ProteinSimple offers a selection of absorbance- and fluorescence-compatible pI markers at pI 3.38, 4.05, 5.85, 6.14, 7.05, 8.40, 9.99, and 10.17. The distance between the two pI Markers in my sample electropherograms is different from run to run even though I use the same pI Markers and carrier ampholytes. What is the reason for this?

Usually this is caused by different salt concentrations in the sample solutions. Salt can compress the pH gra-

dient created by the carrier ampholytes. So, the higher the salt concentration, the shorter the distance between the two pI Markers. However, since the whole pH gradient is compressed by the salt, this will not affect peak identification results as long as two pI Markers are used and their peaks bracket the sample peaks. Can I use narrow pH range carrier ampholytes to improve the resolution for my sample?

Yes. The most efficient way to do this is to use a mixture of narrow pH range carrier ampholytes and wide pH range carrier ampholytes. The proportion of carrier ampholytes can be from 1:1 (narrow range: wide range) up to 5:1 depending on the resolution requirement. Focusing time should be increased with the increasing proportion of the narrow pH range carrier ampholytes, from 6 to 12 minutes. The measured pI value of my sample peak is slightly different when I use different pI Markers or different carrier ampholytes with the same pI markers. What is the reason for this?

When using different pI Markers, the small difference in the measured pI value is due to the slight non-linear-

ity of the pH gradient established by the carrier ampholytes along the separation capillary. Compass for iCE pI calibration assumes that the pH gradient is perfectly linear between the two pI Markers. In reality, carrier ampholytes are not perfectly linear throughout their pH gradient. When different carrier ampholytes are used, their pH gradients may be slightly different causing a small dif-

ference in measured pI value. This effect is most obvious when using a carrier ampholyte mixture (i.e. narrow and wide pH range carrier ampholytes). Under these conditions, the pH gradient will not be linear at the edges of the overlapping pH regions of the different carrier ampholytes. Changing the ratio of the different carrier ampholytes in the mixture will affect the measured pI values of a protein. User Guide for Maurice, Maurice C. and Maurice S. Troubleshooting page 419 In conclusion, only measured pI values obtained using the same carrier ampholytes and the same pI markers can be compared. Also, as long as the run conditions are the same, the measured pI values can be used to identify protein peaks. Troubleshooting Compass for iCE lets you run a self test on Maurice, Maurice C. and Maurice S. systems. These diagnostic tests check many internal components and can help you determine if you have an instrument issue or not. Go to Instrument Software (Embedded) Updates on page 181 for details on how to get started. For more Maurice and application troubleshooting information, please contact ProteinSimple Technical Sup-

port at (888) 607-9692 (option 3), support@proteinsimple.com or visit http://www.proteinsimple.com/tech-

nical_support.html. You can also contact your local Field Application Specialist for help. cIEF Application Troubleshooting Problem Solution Error message: Calibration standard not detected The Fluorescence Calibration Standard was not stored at the proper temperature, the reagent vial is in the wrong position, or the reagent vial doesnt contain the right volume of solution. The cartridge may be clogged. The Fluorescence Calibration Standard should always be stored at 4 C. If its been stored at another temperature, replace the bottle with a new one then prepare a fresh reagent vial with the new solution. Make sure reagent vials are placed in the right positions in the sample and reagent platform. Confirm that there is 500 L of Fluores-

cence Calibration Standard in the reagent vial. Run the cIEF Cartridge Purge then start the batch again. If the error reoccurs, replace the cartridge with a new one User Guide for Maurice, Maurice C. and Maurice S. Troubleshooting page 420 Abnormal Focusing Problem cIEF Cartridge tank level low If the anolyte or catholyte tank fluid level is not high enough to make good contact with the elec-

trodes, the current will drop to < 2 A. Electrolyte contamination Current keeps increasing beyond 80 mA Solution 2 mL of electrolyte is needed in each tank. Aspirate out all the electrolyte solution and add 2 mL of anolyte and catholyte into their designated tanks. Replace the anolyte and catholyte solutions in the electrolyte tanks. Either the electrolytes are in the wrong tanks or the cartridge is defective. 1. Immediately stop the system and run the Maurice cIEF Cartridge Purge in Compass for iCE. 2. When the purge is done, remove the car-

3. 4. tridge, wash out the tanks and transfer new electrolyte solutions into the proper tanks. Rerun the System Suitability test to confirm the internal coating is intact. Replace the cartridge if the System Suitability run fails to meet resolution specifications or the current still remains high at >80 mA. Artificial Peaks Problem Solution Dust or particulates on the optical window Remove the cartridge. Use compressed air or nitro-

gen to gently clean the optical window, then rein-

stall the cartridge. NOTE: Dont wash or submerge the car-

tridges optical window in water or solvent. User Guide for Maurice, Maurice C. and Maurice S. Troubleshooting page 421 Problem Solution Particles or precipitate in sample Air bubble in capillary Use an aqueous additive to stabilize the sample solution. Always spin samples for 10 min at 1000 xg before adding them to sample vials or wells of a 96-well plate. Dispense the solution at the bottom of the vial/well to avoid trapping any air bubbles. CE-SDS Application Troubleshooting Error Message: Detected current below minimum threshold Problem Run stops before the first injection Capillary is likely clogged. Solution Discard the cartridge and use a new one. Spikes, Poor Resolution Problem Air bubble in capillary Late Peak Arrival, Poor Resolution Solution Always spin samples for 10 min at 1000 xg and use fresh reagents to minimize bubble occurrence. Problem Solution Top Running Buffer vial leak Use a new Top Running Buffer vial. Insufficient conditioning Partial capillary clog Use fresh Conditioning Buffers with each run. Run the CE-SDS Cartridge Purge. User Guide for Maurice, Maurice C. and Maurice S. Troubleshooting page 422 Current Drifts to 0, No Signal, Saturation Sensor is Red Problem Solution Non-viscous liquid in Separation Buffer vial Make sure reagent vials are placed in the right positions in the sample and reagent platform. Top Running Buffer vial is overloaded Use a new cartridge insert and new Top Top Running Buffer vial leak Running Buffer vial. Use a new cartridge insert and new Top Running Buffer vial. Low Signal Problem Solution Sample composition is affecting the electroki-

netic injection Make sure the salt and protein concentrations of your sample are within the recommended ranges. Rising Baseline Problem Solution UV lamp is approaching the life time limit Replace the lamp. User Guide for Maurice, Maurice C. and Maurice S. page 423 Chapter 16:

General Information Safety Guidelines Chapter Overview Compliance Consumables and Reagents Customer Service and Technical Support Legal Notices User Guide for Maurice, Maurice C. and Maurice S. Compliance page 424 Compliance Maurice complies with:

UL 61010-1:2001: Safety requirements for electrical equipment for measurement, control, and labo-

ratory use - Part 1: General requirements (US) EN 61010-1:2010: Safety requirements for electrical equipment for measurement, control, and labo-

ratory use - Part 1: General requirements (EU) CAN/CSA 22.2 No. 61010-1-04: Safety requirements for electrical equipment for measurement, con-

trol, and laboratory use - Part 1: General requirements (CA) EN 61326-1:2013: Electrical equipment for measurement, control and laboratory use. EMC Require-

ments. General requirements (EU) This device complies with Part 15 of the FCC Rules. Operation is subject to the following two condi-

tions:

1. 2. This device may not cause harmful interference. This device must accept any interference received, including interference that may cause undesired operation. Note: This equipment has been tested and found to comply with the limits for a Class B digital device, pur-

suant to Part 15 of the FCC Rules. These limits are designed to provide reasonable protection against harmful interference in a residential installation. This equipment generates, uses and can radiate radio frequency energy and, if not installed and used in accordance with the instructions, may cause harmful interference to radio communications. However, there is no guarantee that interference will not occur in a particular instal-

lation. If this equipment does cause harmful interference to radio or television reception, which can be determined by turning the equipment off and on, the user is encouraged to try to correct the interference by one or more of the following measures:

Connect the equipment into an outlet on a circuit different from that to which the receiver is con-

Reorient or relocate the receiving antenna. Increase the separation between the equipment and receiver. nected. Consult the dealer or an experienced radio/television technician for help. User Guide for Maurice, Maurice C. and Maurice S. Safety Guidelines page 425 Modifications: Any modifications made to this device that are not approved by ProteinSimple, Inc. may void the authority granted to the user by the FCC to operate this equipment. FCC ID: 2AHGG-MAURICE Safety Guidelines

!WARNING!

If Maurice is not used as specified by ProteinSimple, overall safety will be impaired.

!WARNING!

If Maurice is damaged and doesnt function properly, stop him safely and contact ProteinSimple Tech-

nical Support right away.

!WARNING!

You cant replace or service any parts on Maurice except for the power entry fuse.

!WARNING! SHARPS HAZARD The capillary inlet of the cartridge may present a potential sharps hazard. Dispose of used cartridges according to your organizations health and safety regulations. CAUTION Avoid using Maurice ways not specified by ProteinSimple. Although Maurice has been designed to protect you, this protection may not be effective if he isnt used properly. Chemical Hazards

!WARNING! CHEMICAL HAZARD Some chemicals used can be potentially hazardous, and can cause injury or illness. Read and understand the Product Inserts and Safety Data Sheets (SDSs) provided by the chemical manufacturer before you store, handle, or work with any chemicals or hazardous materials. User Guide for Maurice, Maurice C. and Maurice S. Safety Guidelines page 426 Minimize contact with and inhalation of chemicals. Wear appropriate personal protective equipment when handling chemicals (e.g., safety glasses, gloves, or clothing). For additional safety guidelines, consult the SDS. Do not leave chemical containers open. Check regularly for chemical leaks or spills. If a leak or spill occurs, follow the manufacturer's cleanup procedures as recommended on the SDS. Comply with all local, state/provincial, or national laws and regulations related to chemical storage, handling, and disposal. Chemical Waste Hazards

!WARNING! BIOHAZARD Cartridges, sample plates and vials should be handled by procedures recommended in the CDC/NIH manual: Biosafety in Microbiological and Biomedical Laboratories (BMBL). The manual is available from the U.S. Government Printing Office or online at http://

www.cdc.gov/biosafety/publications/bmbl5/. Depending on the samples used, the cartridges, plates and vials may constitute a chemi-

cal or a biohazard. Dispose of the cartridges, plates and vials in accordance with good lab-

oratory practices and local, state/provincial, or national environmental and health regulations. Read and understand the Safety Data Sheets (SDSs) provided by the manu-

facturers of the chemicals in the waste content before you store, handle, or dispose of chemical waste. Read and understand the Safety Data Sheets (SDSs) provided by the manufacturers of the chemicals in the waste container before you store, handle, or dispose of chemical waste. Minimize contact with chemical waste. Wear appropriate personal protective equipment when han-

dling chemicals (e.g., safety glasses, gloves, or clothing). Use precaution when emptying waste. Dispose of waste in accordance with good laboratory practices and local, state/provincial, or national environmental and health regulations. User Guide for Maurice, Maurice C. and Maurice S. Safety Guidelines page 427 Waste Production and Disposal Samples cIEF Application on Maurice and Maurice C. Maurice produces approximately 2.0 mL of waste per 100 injections run on a single cIEF cartridge and will contain the following:

Methyl cellulose (~0.5%) Carrier ampholytes Additionally, the Anolyte and Catholyte used in the cIEF cartridge will also need to be discarded and replaced after each batch and during cartridge cleanup prior to storage. Catholyte: 100 mM sodium hydroxide in 0.1% methyl cellulose, 1.5 mL Anolyte: 80 mM phosphoric acid in 0.1% methyl cellulose, 1.5 mL Fluorescence calibration standard pI markers Sample additives Samples CE-SDS Application on Maurice and Maurice S. Maurice produces approximately 0.75 mL of waste per 48 injections that is contained within the Top Run-

ning Buffer vial. It contains the following:

Conditioning Solution 1 and 2 Separation Matrix Running Buffer Wash Solution Additives such as -mercaptoethanol or iodoacetamide. Waste should be disposed of in accordance with good laboratory practices and local, state/provincial, or national environmental and health regulations. Safety Data Sheets Some chemicals used with Maurice may be listed as hazardous. Warnings are displayed on the labels of all chemicals when hazards exist. User Guide for Maurice, Maurice C. and Maurice S. Safety Guidelines page 428 SDSs provide users with safety information needed to store, handle, transport and dispose of the chemicals safely. We recommend updating laboratory SDS records periodically. Safety Data Sheets for ProteinSimple reagents are available online at www.proteinsimple.com/literature or by calling (888) 607-9692. Otherwise, call the chemical manufacturer directly or visit their web site. Instrument Safety Labels The following safety labels are located on Maurice. Each label will display a safety alert symbol indicating a potential safety hazard. Symbol Description Risk of Electric Shock. Refer to Maurice User Guide before proceeding. Danger of hazardous waste. Use caution in these areas. This warning only applies if using hazardous material. Maurice reagents are not considered hazardous waste. If you are using hazardous materials, please contact your field service representative to place labels in the appropriate locations. User Guide for Maurice, Maurice C. and Maurice S. Consumables and Reagents page 429 Consumables and Reagents Maurice CE-SDS Consumables, Kits and Reagents Item Maurice CE-SDS Cartridges Maurice CE-SDS Orange Pressure Caps Maurice CE-SDS Application Kit P/N PS-MC02-S 046-020 PS-MAK01-S Description Cartridges for CE-SDS application, 2 cartridges/pk. For use with Mau-

rice and Maurice S. systems only. Pressure screw tops with o-ring for glass reagent vials (P/N 046-017), 12/pk. Suitable for use with Maurice, Maurice S., Maurice C systems only. The CE-SDS Application Kit contains all components required to run CE-SDS application. The kit includes CE-SDS cartridges, Separation Matrix, Running Buffer, Sample Buffer, Wash Solution, Conditioning Solutions, Internal Standard, reagent vials, orange pressure caps and 96-well plates. 200 samples/kit. CE-SDS Molecular Weight Markers can be ordered separately. Maurice CE-SDS IgG Standard Maurice CE-SDS Molecular Weight Markers Maurice CE-SDS Separation Matrix Maurice CE-SDS Running Buffer -

Top Maurice CE-SDS Running Buffer -

Bottom 046-039 Lyophilized antibody standard for 8 runs. 046-038 Lyophilized molecular weight markers (10, 20, 33, 55, 103, 178 and 240 kDa) for 8 runs. 046-009 046-010 Separation Matrix for CE-SDS application, 15 mL. For use with CE-SDS cartridge (PS-MSC02) on Maurice and Maurice S. systems only. Pre-assembled vial insert containing Top Running Buffer for CE-SDS application. For use with the cartridge insert (046-124) of the CE-SDS cartridge (PS-MSC02) on Maurice and Maurice S. systems only. 10 vials. 046-011 Running Buffer for CE-SDS application, 15 mL. For use with CE-SDS cartridge (PS-MSC02) on Maurice and Maurice S. systems only. Maurice CE-SDS 1X Sample Buffer 046-012 Buffer for samples preparation for CE-SDS application, 25 mL. For use with CE-SDS cartridge (PS-MSC02) on Maurice and Maurice S. sys-

tems only. Maurice CE-SDS Wash Solution 046-013 Wash Solution for CE-SDS application, 20 mL. For use with CE-SDS cartridge (PS-MSC02) on Maurice and Maurice S. systems only. User Guide for Maurice, Maurice C. and Maurice S. Consumables and Reagents page 430 Item Maurice CE-SDS Conditioning Solu-

tion 1 Maurice CE-SDS Conditioning Solu-

tion 2 Maurice CE-SDS Internal Standard P/N 046-014 046-015 046-0144 Maurice CE-SDS Cartridge inserts 046-124 Description Conditioning Solution 1 for use with CE-SDS cartridge, 20 mL. For use with CE-SDS cartridge (PS-MSC02) on Maurice and Maurice S. systems only. Conditioning Solution 2 for use with CE-SDS cartridge, 20 mL. For use with CE-SDS cartridge (PS-MSC02) on Maurice and Maurice S. systems only. Internal Standard for addition to each sample for CE-SDS application. 2 vials/pk. For use with CE-SDS cartridge (PS-MSC02) on Maurice and Maurice S. systems only. Cartridge Inserts for holding the Top Running Buffer vial assembly

(046-010) in the Maurice CE-SDS Cartridge (PS-MSC02). 2 inserts/pk. For use with Maurice and Maurice S. systems only Maurice CE-SDS Cartridge Cleaning Vial 046-125 Clear cleaning vial for use with the Maurice CE-SDS Cartridge insert

(046-124). 2 vials/pk. User Guide for Maurice, Maurice C. and Maurice S. Consumables and Reagents page 431 Maurice cIEF Consumables, Kits and Reagents Item Maurice cIEF Cartridges P/N PS-MC02-C Maurice cIEF Blue Pressure Caps 046-332 Maurice cIEF Method Develop-

ment Kit PS-MDK01-C Maurice cIEF Chemical Test Kit 046-036 Maurice cIEF System Suitability Kit 046-044 Description Cartridges for cIEF application, 2 cartridges/pk. For use with Maurice and Maurice C. systems only. Pressure screw tops with o-ring for glass reagent vials (P/N 046-017), 12/pk. Suitable for use with Maurice, Maurice S., Maurice C systems only. The cIEF Method Development Kit provides all the reagents and instructions to help you develop fast and robust cIEF methods on Maurice and Maurice C. systems. The kit includes a Method Develop-

ment Guide as well as a selection of reagents required for cIEF method development on the system. This kit includes a Fluores-

cence Calibration Standard, System Suitability Kit, Anolyte, Catholyte, Methyl Cellulose, five types of Ampholytes (Pharmalyte pH ranges 3-

10, 2.5-5, 5-8 and 8 to 10.5 and Servalyte pH range 2-9), eight pI Markers (3.38, 4.05, 5.85, 6.14, 7.05, 8.40, 9.99 and 10.17) and additives

(lyophilized urea and arginine). 30 samples/kit. The expiration date for this kit is 12 months from date of manufacture. For use with the cIEF cartridge (PS-MC02-C) on Maurice and Maurice C. systems only. The cIEF Chemical Test Kit is designed to confirm the overall perfor-

mance of the Maurice and Maurice C. systems with the cIEF car-

tridge (PS-MC02-C) on 8 separate occasions. The kit contains Anolyte, Catholyte, Methyl Cellulose, Fluorescence Calibration Stan-

dard and a System Suitability kit. Each time, the performance can be checked up to 24 hours. The expiration date for this kit is 12 months from date of manufacture. 8 runs/kit. For use with the cIEF cartridge

(PS-MC02-C) on Maurice and Maurice C. systems only. The cIEF System Suitability Kit is used to run a control test for cIEF application on Maurice and Maurice C. systems on 8 separate occa-

sions. Each time, the performance can be checked up to 24 hours. The kit contains a vial of lyophilized Peptide Panel and a vial of Sys-

tem Suitability Test mix. 8 runs/kit. The expiration date for this kit is 12 months from date of manufacture. For use with the cIEF cartridge

(PS-MC02-C) on Maurice and Maurice C. systems only. User Guide for Maurice, Maurice C. and Maurice S. Consumables and Reagents page 432 P/N 046-025 Item Maurice cIEF Fluorescence Calibration Standard 0.5% Methyl Cellu-

lose Solution 102505 1% Methyl Cellu-

lose Solution 101876 iCE Electrolyte Kit 102506 Description Fluorescence Calibration Standard for cIEF application, 5.5 mL. For use with Maurice and Maurice C. systems only. 0.5% Methyl Cellulose Solution, 100 mL. Use this concentration for the wash cycle between injections. The solution is filtered to ensure consistent viscosity to coat the capillary lumen to minimize elec-

troosmotic flow (EOF). Conveniently packaged in 2 x 100 mL bottles. The expiration date for this kit is 12 months from date of manufac-

ture. Suitable for use with Maurice, Maurice C., iCE3 and iCE280. 1% Methyl Cellulose Solution, 100 mL. This solution is used to pre-

pare samples for cIEF applications. The expiration date for this kit is 12 months from date of manufacture. Suitable for use with Maurice, Maurice C.,iCE3 and iCE280. These 100 mL Anolyte and Catholyte solutions in 0.1% MC are used to fill the electrolyte tanks on Maurice cIEF cartridge as well as FC and HT cartridges. The labels and bottles are color coded to improve safety. The kit contains 2 x 100 mL bottles. The expiration date for this kit is 12 months from date of manufacture. Suitable for use with Maurice, Maurice C., iCE3 and iCE280. Maurice cIEF pI Marker - 3.38 Maurice cIEF pI Marker - 4.05 Maurice cIEF pI Marker - 5.85 Maurice cIEF pI Marker - 6.14 Maurice cIEF pI Marker - 7.05 Maurice cIEF pI Marker - 8.4 Maurice cIEF pI Marker - 9.99 046-028 Maurice cIEF pI Marker - 3.38, 210 L, lyophilized. 046-029 Maurice cIEF pI Marker - 4.05, 210 L, lyophilized. 046-030 Maurice cIEF pI Marker - 5.85, 210 L, lyophilized. 046-031 Maurice cIEF pI Marker - 6.14, 210 L, lyophilized. 046-032 Maurice cIEF pI Marker - 7.05, 210 L, lyophilized. 046-033 Maurice cIEF pI Marker - 8.4, 210 L, lyophilized. 046-034 Maurice cIEF pI Marker - 9.99, 210 L, lyophilized. User Guide for Maurice, Maurice C. and Maurice S. Customer Service and Technical Support page 433 Item P/N Description Maurice cIEF pI Marker - 10.17 Maurice cIEF elec-

trolyte tank caps 046-035 Maurice cIEF pI Marker - 10.17, 210 L, lyophilized. 046-123 Electrolyte tank caps, 20 mm. Red is used for the Anolyte tank and the grey cap is used for the Catholyte tank. 5 pairs/pk. Electrolyte Pipette 101788 Pipettes with soft tips for adding Anolyte and Catholyte into the electrolyte tanks in the cIEF cartridge. 10/pk. Maurice Systems Consumables and Reagents Item Maurice glass reagent vials, 2 mL Maurice sample vials with inte-

grated inserts Maurice clear screw caps P/N 046-017 046-083 Description Screw-top glass vials, 2 mL. 100/pk. Suitable for use with Maurice, Maurice S. and Maurice C. systems only. Vials with integrated inserts for samples, accommodate 200 L sam-

ple volume. 100/pk. Suitable for use with Maurice, Maurice S. and Maurice C. systems only. 046-138 Clear screw caps with round opening, 100/pk. Suitable for use with Maurice, Maurice S., Maurice C systems only. 96-well plates 046-021 96-well plate for high-throughput analysis, 10/pk. Suitable for use with Maurice, Maurice S., Maurice C systems only. Adhesive film with pre-cut slits for 96-

well plates 046-046 Adhesive film for sealing 96-well plate (046-021), 10/pk. Customer Service and Technical Support Need pricing information or want to know who your sales rep is? Our Customer Service team can help. Email: orders@proteinsimple.com Telephone: 1-408-510-5500, option 1 Toll-free (US and Canada): 1-888-607-9692, option 1 Fax: 1-408-520-4831 User Guide for Maurice, Maurice C. and Maurice S. Customer Service and Technical Support page 434 Have product-related questions? Ping our Tech Support group, they'll be happy to help!

Use our online technical support request Email: support@proteinsimple.com Telephone: 1-408-510-5500 Toll-free (US and Canada): 1-888-607-9692, option 3 Web www.proteinsimple.com Address ProteinSimple 3001 Orchard Parkway San Jose, CA 95134 USA User Guide for Maurice, Maurice C. and Maurice S. Legal Notices page 435 Legal Notices NOTE: Read the Legal Notices carefully before using Maurice. Maurice Disclaimer of Warranty EXCEPT AS EXPRESSLY PROVIDED IN ANY ProteinSimple SOFTWARE LICENSE AGREEMENT OR QUOTATION, THE PRODUCTS SOLD AND SER-

VICES PROVIDED BY ProteinSimple ARE PROVIDED ON AN AS IS AND AS AVAILABLE BASIS WITHOUT WARRANTY OF ANY KIND. ProteinSimple AND ITS SUPPLIERS DO NOT WARRANT THE SECURITY, PRIVACY, OR ACCURACY OF ANY DATA PROVIDED VIA THE PRODUCTS OR SERVICES, AND YOU AGREE THAT THE USE OF ANY SUCH DATA BY YOU IS AT YOUR SOLE RISK. TO THE MAXIMUM EXTENT ALLOWED UNDER APPLICABLE LAW, ProteinSimple AND ITS SUPPLIERS DISCLAIM ANY AND ALL WARRANTIES, WHETHER EXPRESS, IMPLIED OR STATUTORY, INCLUDING, WITHOUT LIMITATION, ANY WARRANTY OF MERCHANTABILITY, TITLE, NON-INFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE. Compass Software and Authorization Server License Agreement IMPORTANT - PLEASE READ CAREFULLY THE TERMS OF THIS COMPASS SOFTWARE AND AUTHORIZATION SERVER LICENSE AGREEMENT

(AGREEMENT). BY CLICKING ON THE I AGREE BUTTON, (1) YOU ACKNOWLEDGE THAT YOU HAVE READ, UNDERSTAND, AND AGREE TO BE BOUND BY THIS AGREEMENT AND (2) YOU REPRESENT THAT YOU HAVE THE AUTHORITY TO ENTER INTO THIS AGREEMENT, PERSONALLY OR IF YOU HAVE NAMED A COMPANY AS CUSTOMER, ON BEHALF OF THAT COMPANY (YOU OR ANY SUCH COMPANY, THE CUSTOMER), AND TO BIND THE CUSTOMER TO THE TERMS OF THIS AGREEMENT. IF YOU DO NOT AGREE TO ALL TERMS AND CONDITIONS OF THIS AGREEMENT, OR IF YOU DO NOT HAVE SUCH AUTHORITY, YOU SHOULD CLICK ON THE CANCEL BUTTON TO DISCONTINUE THE DOWNLOAD OF THE LICENSED SOFTWARE. 1. Definitions 1.1 Authorized Use Parameters means the following usage restrictions, which restrict the operation of the Licensed Software to a particular set of conditions: Customer shall (a) limit simultaneous use of the Licensed Software to a maximum of ten (10) Authorized Users; and (b) use the Licensed Software only in connection with the accompanying System purchased by Customer pursuant to the System Quotation and located at the Site. 1.2 Authorized User means one (1) User who initiates the execution of the Licensed Software and/or interacts with or directs the Licensed Software in the performance of its functions. Multiple Authorized Users may work simultaneously with one installation of the Licensed Software, as on a server, or they may each have their own installation on single-user machines, or a mix of these, provided that in all cases the total number of simultaneous Users does not exceed the applicable Authorized Use Parameters. 1.3 Company means ProteinSimple. 1.4 Documentation means Company's then-current manuals, guides, and on-line help pages, if any, applicable to the Licensed Software and made generally available by Company to its customers. 1.5 Enterprise means those organizations that have Internet addresses located at top level and second-level domain names set forth in the System Quotation. 1.6 Error means a reproducible error in the Licensed Software that prevents such Licensed Software from operating substantially in accordance with its Documentation. 1.7 Executable Code means the fully compiled binary version of Licensed Software that can be executed by a computer and used by an end user without further compilation. 1.8 Intellectual Property Rights means all copyrights, trade secrets, patents, patent applications, moral rights, contract rights, and other proprietary rights, but specifically excluding any trademarks or service marks. 1.9 Licensed Software means the Compass software program in Executable Code form, and any Updates that Company makes available to Customer in accordance with this Agreement. User Guide for Maurice, Maurice C. and Maurice S. Legal Notices page 436 1.10 Site means the facility or campus set forth in the System Quotation. 1.11 System means the proprietary NP1000, NP100, Simon, Sally, Peggy, Wes, Sally Sue, Peggy Sue and Maurice protein analysis system or any future model or successor thereto that is provided to Customer by Company pursuant to a separate agreement between the parties (the System Quotation). 1.12 Update means those releases of the Licensed Software that Company provides to customers to correct Errors, fix bugs, or create minor improvements, incremental features, or enhancements of existing features which Company designates by a change in the number to the right of the first or second decimal point. Updates do not include those releases of the Licensed Software that provide substantial new features or additional functionality which Company designates by a change in the number to the left of the first decimal point. 1.13 User means any individual that has an e-mail address within the Enterprise. 2. License and Restrictions 2.1 License Grant. Subject to the terms and conditions of this Agreement and the payment of the required fees set forth in the System Quotation, Company grants to Customer a nontransferable, nonexclusive, royalty-free, revocable, worldwide license (without the right to sublicense) to (a) install the Licensed Software on any computer located at any Site; (b) use, execute, and display the Licensed Software, in Executable Code form only; and (c) copy the Licensed Software and Documentation, solely as necessary to support Authorized Users; in each of the foregoing, solely in accordance with the Documentation and the Authorized Use Parameters. Customer agrees that it will comply with the Authorized Use Parameters. 2.2 License Restrictions. Customer acknowledges that the Licensed Software and its structure and organization constitute valuable trade secrets of Company. Accordingly, the license granted in this Agreement is subject to the following restrictions: Customer and its Authorized Users (a) may not reverse engineer, disassemble, decompile, or otherwise attempt to derive the source code of Licensed Software; (b) may not modify, adapt, alter, translate, or create derivative works from the Licensed Software; (c) may not merge the Licensed Software with other software; (d) may not use the Licensed Software in any service bureau or time-sharing arrangement, license, sell, rent, lease, transfer, assign, distribute, host, outsource, disclose, or otherwise commercially exploit or make the Licensed Software or Documentation available to any third party; (e) shall only make that number of exact copies of the Licensed Software and Documentation as delivered by Company that are necessary to support Customer's use of the Licensed Software in accordance with this Agreement; (f ) shall include any titles, trademarks, and copyright and restricted rights notices that are included on or in the Licensed Software as delivered by Company on and in any copies of the Licensed Software that it makes; and (g) shall ensure that Customer's use of the Licensed Software does not exceed the scope of the license that Customer has purchased pursuant to this Agreement. 2.3 Open Source Software. Certain items of independent, third-party code may be included in the Licensed Software that are subject to open source licenses (Open Source Software). Such Open Source Software is licensed under the terms of the license that accompanies such Open Source Software. Nothing in this Agreement limits Customer's rights under, or grants Customer rights that supersede, the terms and conditions of any applicable end user license for such Open Source Software. In particular, nothing in this Agreement restricts Customer's right to copy, modify, and distribute such Open Source Software that is subject to the terms of such open source licenses. 2.4 Ownership. Company reserves all rights not expressly granted to Customer in this Agreement. Without limiting the generality of the foregoing, Customer acknowledges and agrees that, except as expressly set forth in this Agreement, Company and its suppliers retain all Intellectual Property Rights, title and interest in and to the Licensed Software and Documentation. 3. Support and Maintenance Services 3.1 Services. Subject to Customer's payment of the Services fees, as set forth in the System Quotation, and to the terms and conditions herein, Company will use commercially reasonable efforts to provide to Customer the following support and maintenance services

(the Services) for the Licensed Software: (a) Company will answer technical questions concerning functions and features of the Licensed Software; (b) Company will provide Error verification, analysis and corrective efforts for the Licensed Software; and (c) Company will provide, without charge, Updates of the software released during the term of this Agreement. Customer will be responsible for providing, in a manner consistent with good industry practice, all Services to Users. Customer acknowledges that Company may not be able to correct all reported Errors. Any Update of the Licensed Software will be deemed part of the Licensed Software and Customer will use such Updates in accordance with the requirements and obligations in this Agreement. 3.2 Service Conditions. Company's obligation to provide the Services is conditioned on Customer: (a) notifying Company of any Error within a reasonable period of time; (b) providing Company all information relating to the Error; (c) providing access to the Licensed Software and Customer's facility where the Licensed Software is located and informing Company of any potential hazards which may User Guide for Maurice, Maurice C. and Maurice S. Legal Notices page 437 be encountered while servicing the Licensed Software. Customer may contact Company via telephone at 1-888-607-9692 or e-mail at support@proteinsimple.com during the hours of 8 a.m. (Pacific Time) and 5 p.m. (Pacific Time) Monday through Friday, excluding holidays, to report any Error. A list of standard holidays will be provided to Customer upon request. Company shall have the right to determine in its sole discretion what corrective action Company will perform to support the Licensed Software. Company may subcontract the Services to a third party contractor provided that Company will be responsible for the third party contractor's compliance with this Agreement. 3.3 Service Exclusions. Company will not be obligated to provide the Services if (a) Company determines that an Error is caused by malfunction of any hardware (other than malfunction of the System) or third party software used with the Licensed Software; or (b) Customer has failed to incorporate the latest Update previously released to Customer. 4. Warranty 4.1 Licensed Software Warranty. Company warrants that the Licensed Software, as properly installed, and under normal use, will perform substantially in accordance with its Documentation during the Warranty Period. The Warranty Period for the Licensed Software begins on date Customer downloads the Licensed Software and ends twelve (12) months thereafter. 4.2 Remedy. If Customer notifies Company in writing during the Warranty Period of an Error, Company will, at its expense and as its sole obligation for any breach of the foregoing warranty, use commercially reasonable efforts to correct the Error or replace the Licensed Software. Any Error correction or replacement of the Licensed Software will not extend the original Warranty Period. The warranty and the remedies provided above will not apply to the Licensed Software if (a) Company determines that an Error is caused by accident, abuse, misuse, negligence, fire, earthquake, flood, other force majeure event, failure of electrical power, the use of unauthorized products, or unauthorized repairs or modifications; (b) Company determines that an Error is caused during or as a result of delivery; (c) a problem arises from or is based on Company's compliance with Customer's specifications; or (d) Company determines that an Error is caused by malfunction of any hardware (other than malfunction of the System) or third party software used with the Licensed Software. 4.3 Disclaimer. THE WARRANTIES ABOVE ARE EXCLUSIVE AND IN LIEU OF ALL OTHER WARRANTIES, WHETHER EXPRESS, IMPLIED OR STATUTORY, INCLUDING WITHOUT LIMITATION THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE, AND NONINFRINGEMENT. 5. Limitation of Liability. NEITHER COMPANY NOR ITS SUPPLIERS SHALL BE RESPONSIBLE OR LIABLE WITH RESPECT TO ANY SUBJECT MATTER OF THIS AGREEMENT OR TERMS OR CONDITIONS RELATED THERETO UNDER ANY CONTRACT, NEGLIGENCE, STRICT LIABILITY OR OTHER THEORY (A) FOR LOSS OR INACCURACY OF DATA, LOSS OF PROFITS OR COST OF PROCUREMENT OF SUBSTITUTE GOODS, SERVICES OR TECHNOLOGY, OR (B) FOR ANY INDIRECT, INCIDENTAL OR CONSEQUENTIAL DAMAGES INCLUDING, BUT NOT LIMITED TO LOSS OF REVENUES AND LOSS OF PROFITS. COMPANY'S AGGREGATE CUMULATIVE LIABILITY HEREUNDER SHALL NOT EXCEED THE GREATER OF FIVE HUNDRED DOLLARS ($500.00). 6. Term and Termination 6.1 Term of Agreement. The Agreement is effective on the date Customer downloads the Licensed Software and shall remain in effect until terminated by either party as provided in this section. 6.2 Termination For Material Breach. Either party may terminate this Agreement upon written notice if the other party materially breaches this Agreement and fails to cure such breach within thirty (30) calendar days following receipt of written notice from the other party specifying the breach in detail. Notwithstanding the foregoing, Company may immediately terminate this Agreement and all licenses granted hereunder if Customer breaches Section 2 (License and Restrictions) hereof or upon termination of the System Quotation. The foregoing rights of termination are in addition to any other rights and remedies provided in this Agreement or by law. 6.3 Effect of Termination. Upon termination of this Agreement (or termination or expiration of any license granted hereunder), all rights of Customer to use the Licensed Software and Documentation will cease and (a) all license rights granted under this Agreement will immediately terminate and Customer shall promptly stop all use of the Licensed Software and Documentation; (b) all Services will terminate immediately; (c) Customer shall promptly erase all copies of the Licensed Software from Customer's computers, and destroy all copies of the Licensed Software and Documentation on tangible media in Customer's possession or control or return such copies to Company; and (d) upon request by Company, Customer shall certify in writing to Company that it has returned or destroyed such Licensed Software and Documentation. The parties' rights and obligations under Sections 1 (Definitions), 2.4 (Ownership), 4.3

(Disclaimer), 5 (Limitation of Liability), 6 (Term and Termination), and 7 (General) shall survive termination of this Agreement. User Guide for Maurice, Maurice C. and Maurice S. Legal Notices 7. General page 438 7.1 Assignment. This Agreement and Customer's rights hereunder may not be assigned to any third party by Customer except with the prior written approval of Company. Any attempted assignment of this Agreement or any rights or obligations hereunder will be null and void. 7.2 Governing Law. This Agreement is made in, governed by, and shall be construed in accordance with the laws of the State of California, without regard to any conflicts of law principles that would result in application of laws of any other jurisdiction. The United Nations Convention on Contracts for the International Sale of Goods does not apply to this contract. Any legal action or other legal proceeding relating to this contract or the enforcement of any provision of this contract must be brought in any state or federal court located in Santa Clara County, California. Customer and Company expressly and irrevocably consents and submits to the jurisdiction of such courts. 7.3 Injunctive Relief. Customer acknowledges that the Licensed Software contains valuable trade secrets and proprietary information of Company, that any actual or threatened breach of this Agreement will cause harm to Company for which monetary damages would be an inadequate remedy, and that injunctive relief is an appropriate remedy for such breach. 7.4 Modifications. Company reserves the right to change the terms and conditions of this Agreement or its policies relating to the Licensed Software at any time. Company will notify Customer of any material changes to this Agreement by sending Customer an e-

mail to the last e-mail address Customer provided to Company or by prominently posting notice of the changes on Company's website. Any material changes to this Agreement will be effective upon the earlier of thirty (30) calendar days following Company's dispatch of an e-mail notice to Customer or thirty (30) calendar days following Company's posting of notice of the changes on Company's website. These changes will be effective immediately for new users of our Licensed Software. Please note that at all times Customer is responsible for providing Company with its most current e-mail address. In the event that the last e-mail address that Customer has provided Company is not valid, or for any reason Company is not capable of delivering to Customer the notice described above, Company's dispatch of the e-mail containing such notice will nonetheless constitute effective notice of the changes described in the notice. If Customer does not agree with the changes to this Agreement, Customer must notify Company prior to the effective date of the changes that Customer wishes to terminate its license to the Licensed Software. Continued use of the Licensed Software, following notice of such changes, shall indicate Customer's acknowledgement of such changes and agreement to be bound by the terms and conditions of such changes. 7.5 Severability. In the event any provision of this Agreement is held to be invalid or unenforceable, the remaining provisions of this Agreement will remain in full force. 7.6 Waiver. The waiver by either party of any default or breach of this Agreement shall not constitute a waiver of any other or subsequent default or breach. 7.7 Export. Customer agrees not to export, reexport, or transfer, directly or indirectly, any U.S. technical data acquired from Company, or any products utilizing such data, in violation of the United States export laws or regulations. 7.8 Force Majeure. Company shall not be liable, directly or indirectly, for any delay or failure in performance of any obligation under this Agreement, including any delivery obligation, where such delay or failure arises or results from a cause beyond Company's reasonable control, or beyond the reasonable control of Company's suppliers or contractors, including, but not limited to strike, boycott or other labor disputes, embargo, governmental regulation, inability or delay in obtaining materials, acts of God, war, earthquake, fire, or flood. In the event of such force majeure, the time for delivery or other performance will be extended for a period equal to the duration of the delay caused thereby, provided that Company notifies Customer of the nature and duration of such force majeure event. 7.9 Entire Agreement; Notice. This Agreement constitutes the complete agreement between the parties and supersedes all prior or contemporaneous agreements or representations, written or oral, concerning the subject matter of this Agreement. Except as otherwise expressly provided in this Agreement, any modifications of this Agreement must be in writing and agreed to by both parties. Company may provide any notice to Customer by e-mail. Customer may provide notice to Company by sending an e-mail to info@proteinsimple.com or a letter by United States mail to ProteinSimple, 3040 Oakmead Village Drive, Santa Clara, CA 95051, or to such other address as Company may specify in writing by posting the new address on the Company website. 7.10 Relationship of the Parties. The parties are acting hereunder as independent contractors and not as partners, agents, fiduciaries, or joint venturers. Neither party has the power or authority represent, act for, bind, or otherwise create or assume any obligation on behalf of the other party. User Guide for Maurice, Maurice C. and Maurice S.