SCIEX CESI 8000 Plus User manual

CESI 8000 Plus High Performance
Separation-ESI Module
User Manual
RUO-IDV-05-3897-B
February 2019

AB Sciex LLC
500 Old Connecticut Path
Framingham, Massachusetts 01701
USA
This document is provided to customers who have purchased SCIEX equipment to use in the
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© 2019 AB Sciex
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Contents
CHAPTER 1: Safety, Notices and Labels, 13
Overview, 13
Alerts for Warning, Caution, Important, and Note, 14
Instrument Safety Precautions, 15
Moving Parts or Sharp Objects, 16
Electrical Safety, 16
Laser Safety (for Optional Laser Device), 17
Class 1 Laser Caution Label, 17
Chemical Precautions, 17
Safety Symbols and Labels, 18
High Voltage Electric Shock Risk Symbol, 18
Attention Safety Symbol, 18
Sharp Object Label, 18
Mobile Cart Caution Label, 19
Cancer and Reproductive Harm Label, 19
RoHS Notices, 19
China RoHS Caution Label, 19
Other Instrument Labels, 20
Recycling Label (WEEE), 20
Disposal of Devices Containing Mercury Components, 21
CE Mark Label, 21
RCM Mark Label, 21
CSA Mark Label, 21
章 2: 安全、通知和标签 , 23
综述 , 23
警告、注意、重要事项以及注释的提示 , 24
仪器安全防护措施 , 25
活动部件或尖锐物 , 26
电气安全 , 26
激光安全 （适用于可选激光设备） , 26
1 类激光小心标签 (1 级激光警告标签 ), 26

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化学品注意事项 , 27
安全符号和标签 , 27
高压电击危险符号 , 27
注意安全符号 , 27
尖锐物标签 , 28
流动车警告标签 , 28
致癌和生殖危害标签 , 28
RoHS 通知 , 28
中国 RoHS 警告标签 , 29
其他仪器标签 , 29
环保标签 (WEEE), 29
处理包含加汞组件的设备 , 30
CE 标志标签 , 30
RCM 标志标签 , 30
CSA 标识标签 , 30
CHAPITRE 3: Sécurité, Consignes et étiquettes, 31
Présentation, 31
Alertes « Avertissement, Mise en garde, Important et Remarque », 32
Précautions de sécurité pour l'instrument, 33
Pièces mobiles ou Objets tranchants, 34
Sécurité électrique, 34
Sécurité laser (pour les appareils avec laser en option), 35
Étiquette de mise en garde : produit laser de classe 1, 35
Précautions chimiques, 36
Symboles et étiquettes de sécurité, 36
Symbole « Haute tension, risque de choc électrique », 36
Symbole de sécurité Attention, 37
Étiquette Objet tranchant, 37
Étiquette de mise en garde chariot mobile, 37
Étiquette concernant les risques de cancer et de malformations
congénitales, 37
Consignes RoHS, 38
Étiquette de mise en garde RoHS (Chine), 38
Autres étiquettes de l'instrument,38
Étiquette de recyclage (WEEE), 39
Élimination des appareils contenant des composants au
mercure, 39
Étiquette marque CE, 39
Étiquette marque MRC, 40
Étiquette marque CSA, 40
CHAPTER 4: System Overview, 41
About This Manual, 41

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Optional Detectors, 41
Introduction, 42
Instrument, 43
Sample Handling System, 44
Syringe Pump, Power Supply, LEDs and Interlock, 46
Syringe Pump, 46
High Voltage (HV) Power Supply, 46
LED Indicators, 46
Cartridge and Sample Cover Interlocks, 47
OptiMS Cartridge, 48
CHAPTER 5: Integrating the CESI 8000 Plus System with a Mass
Spectrometer, 51
CESI-MS Integration Procedures, 51
CESI 8000 Plus System: Installing OptiMS Cartridge, 53
OptiMS Cartridge Installation, 53
Thermo Scientific Mass Spectrometer: Integration with the CESI 8000 Plus
System, 57
Physical Integration with the CESI 8000 Plus System, 57
OptiMS Cartridge Sprayer Tip Installation into a Thermo
Scientific NanoSpray II Ion Source, 59
Establishing Communication Between the CESI 8000 Plus
Controller and the Thermo Scientific Mass Spectrometer, 65
Aligning the CESI 8000 Plus System with a Thermo Scientific
Mass Spectrometer, 66
SCIEX TripleTOF®5600 Mass Spectrometer: Integration with the CESI 8000
Plus System, 71
Physical Connections with the CESI 8000 Plus System, 71
OptiMS Cartridge Sprayer Tip Installation into the SCIEX
Nanospray® III Source, 73
Establishing Communication Between the CESI 8000 Plus
Controller and the SCIEX Mass Spectrometer, 80
Aligning the CESI 8000 Plus System with the SCIEX TripleTOF®
5600 Mass Spectrometer, 81
CHAPTER 6: 32 Karat Software Overview, 87
Overview of 32 Karat Software, 87
System Administration, 87
Controller and Instrument Start Up, 88
Controller/Network Login, 88
License Key, 89
Demo Mode, 89
Launching 32 Karat Software, 89
Instrument Start Up, 89

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Instruments and Projects, 90
Configuration, 90
Online Versus Offline, 90
Using the Direct Control Window to Load the Cartridge and Samples, 91
TripleTOF®5600 Mass Spectrometer Using AAO, 93
Methods and Sequences, 94
Creating and Editing a Method, 95
Instrument Setup Window, 95
Instrument Setup — Initial Conditions, 95
Instrument Setup — Time Program, 97
Separate Dialog, 98
Rinse Dialog, 100
Inject Dialog, 100
Stop Data, 102
End, 102
Saving a Method, 102
Overview of Creating a Sequence, 103
Single Run and Sequence Runs, 103
Programming a Sequence, 104
Sequence Table, 108
Sequence Validation, 109
CHAPTER 7: CESI 8000 Software, 111
Overview of the CESI 8000 Software, 111
Launching the CESI 8000 Software, 112
Login and Logout, 113
Lock and Unlock, 114
About Dialog, 114
Help, 114
Users, 114
Run Application, 115
Application Selection, 115
Samples and Vials, 118
Samples/Vials Dialog,118
Insert Option, 120
Sequence Dialog, 121
Sequence Table Rows, 123
Fill Down Option, 127
Display Options, 128
Vial Legend, 129
Tray Detail View, 129
Vial Preview, 130

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Run Acquisition, 131
SCIEX TripleTOF®5600 Mass Spectrometer Using AAO, 133
Graph Options, 134
Sequence Transfer Overview, 135
Sequence Transfer, 135
Describe Sequence, 141
Sequence Verification, 144
Sequence Display Options, 144
CHAPTER 8: Using a SCIEX TripleTOF®5600 Mass Spectrometer with
the CESI 8000 Plus System, 147
Introduction, 147
Stock Reagents and Other Consumables Required, 148
Preparation of Reagent Solutions and Test Sample, 149
Preparation of 10% (v/v) HAc—Background Electrolyte
(BGE), 150
Preparation of 20% (v/v) Acetic Acid (HAc)—For LE pH
Adjustment, 150
Preparation of 200 mM LE (Leading Electrolyte) Buffer, 150
Reconstitution of 1 μM Beta-Galactosidase Digest Solution
(Beta-Galactosidase Stock Solution), 151
Preparation of Beta-Galactosidase Test Sample, 151
Preparation of Beta-Galactosidase for Auto-calibration, 152
Buffer Tray Setup, 152
Sample Tray Setup, 153
Procedure for Installation of Adapter and OptiMS Cartridge, 154
Methods for the CESI 8000 Plus System, 155
CESI-MS Beta-Galactosidase System Performance Test, 159
Capillary Conditioning, 162
Establishing a Stable Spray and Determining Optimum ESI Voltage, 165
Running CESI-MS, 172
Create a Sequence in the Analyst®TF Software, 173
Start a Sequence in the Analyst®TF Software, 176
Load Sample and Reagents on the CESI 8000 Plus System, 177
Sample Tray Setup, 177
Create a Sequence in the CESI 8000 Software,179
Start a Sequence in the CESI 8000 Software, 183
Automatic Rinse Feature, 184
Beta-Galactosidase Analysis, 185
CHAPTER 9: Using a Thermo Scientific Mass Spectrometer with the
CESI 8000 Plus System, 189
Introduction, 189

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Stock Reagents and Other Consumables Required, 190
Preparation of Reagent Solutions and Test Sample, 191
Preparation of 10% (v/v) Acetic Acid (HAc)—Background
Electrolyte (BGE), 191
Preparation of 20% (v/v) Acetic Acid (HAc) — For LE Buffer pH
Adjustment, 192
Preparation of 200 mM LE (Leading Electrolyte) Buffer, 192
Reconstitution of 1 μM Beta-Galactosidase Digest Solution
(Beta-Galactosidase Stock Solution), 193
Preparation of Beta-Galactosidase Test Sample, 193
Sample Tray Setup for System Performance Test, 193
Procedure for Installation of Adapter and OptiMS Cartridge, 194
Capillary Conditioning, 195
Buffer Tray Setup, 195
Capillary Conditioning Procedure, 196
Establishing a Stable Spray and Determining Optimum ESI Voltage, 198
Tuning, 202
Running CESI-MS, 203
Create a Method with the Xcalibur Software, 204
Create a Sequence with the Xcalibur Software, 207
Start a Sequence with the Xcalibur Software, 208
Load Sample and Reagents on the CESI 8000 System, 209
Create a Sequence in the CESI 8000 Software, 211
Automatic Rinse Feature, 212
Start a Sequence in the CESI 8000 Software, 213
Beta-Galactosidase Analysis, 214
CHAPTER 10: Shutdown Procedures and Decoupling Instruments, 217
Shutdown and Decoupling Overview, 217
Cartridge Removal and the CESI 8000 Plus System Shutdown, 217
Cartridge Removal and Instrument Shutdown, 217
Decoupling the CESI 8000 Plus System, 222
Decoupling from the Thermo Scientific Mass Spectrometer, 222
Decoupling from the SCIEX Mass Spectrometer, 225
APPENDIX A: Specifications, 229
CESI 8000 Plus System, 229
Validated Controller Configuration, 230
Cart Specifications, 230
Sample Temperature Control, 231
Capillary Temperature Control, 231
Pressure and Vacuum System, 231

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Detector Specifications, 232
UV Detector, 232
Laser Induced Fluorescence (LIF) Detector (Optional), 233
Photo Diode Array (PDA) Detector (Optional), 233
APPENDIX B: Nominal Network Configuration, 235
Overview, 235
Switching from the CESI 8000 Plus System to Different Mass Spectrometer
Systems, 236
Switching to the CESI 8000 Plus System from Different Mass Spectrometer
Systems, 236
Switching from a SCIEX Mass Spectrometer to Another Mass
Spectrometer, 237
Switching to a SCIEX Mass Spectrometer from Another Mass
Spectrometer, 239
Advanced Networking and Computer Configuration for the Analyst®TF 1.7
Software, 241
CE-MS Networking, 241
PC Configurations, 241
Network Sharing Setting for the Crossover Connection, 262
Setting the Mass Spectrometer Type, 264
Curtain Gas Patch Installation, 265
CE-MS Driver Installation, 267
Saving Network Configurations, 269
Analyst Hardware Profile Configuration, 270
To configure the Mass Spectrometer Hardware Profile, 270
Curtain Gas Setting and Verification, 276
Curtain Gas Setting, 276
Curtain Gas Verification, 278
APPENDIX C: TripleTOF®5600 Mass Spectrometer
Manual and Auto-Calibration Methods, 281
Overview, 281
Required Reagents, 281
Reagent and Sample Preparation, 281
Manual Calibration Before Auto-calibration, 282
Create a Reference Table for CE-MS Calibration, 282
Manual Calibration of the Mass Spectrometer, 285
Manual Calibration in TOF Mass Spectrometer Mode, 286
Manual Calibration in Product Ion Mode, 292
Methods for Auto-Calibration, 296
CE Method for Auto-Calibration, 296
MS Method for Auto-Calibration, 297
Executing Auto-Calibration, 300
Create a Sequence in the Analyst®TF Software, 300

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Start a Sequence in the Analyst®TF Software, 303
Load Sample and Reagents on the CESI 8000 System, 305
Sample Tray Setup, 305
Create a Sequence in the CESI 8000 Software, 306
Start a Sequence in the CESI 8000 Software, 310
Automatic Rinse Feature, 312
Auto-Calibration Data Analysis, 312
Troubleshooting Auto-Calibration Failure, 317
Auto-calibration Troubleshooting Table, 319
APPENDIX D: Auto Vial Increment Feature, 321
Overview, 321
Setting Auto Vial Increment on a Rinse Step, 321
Setting Auto Vial Increment on an Injection, 322
Setting Auto Vial Increment on a Separation Step, 324
Auto Vial Increment in a Method, 326
Reviewing Vial Positions before Running a Sequence, 327
APPENDIX E: Conductive Liquid Capillary Conditioning, 329
Conductive Liquid Capillary (CLC) Conditioning Procedure, 329
APPENDIX F: Using Vials and Hardware Maintenance, 331
Overview, 331
Using CESI-MS Vials and Caps, 332
CESI-MS Vials and Micro Vials, 332
Filling the Micro Vials, 333
Hardware Maintenance Procedures, 334
Capillary Cleaning Procedure (Short Term Storage), 334
Capillary Storage Procedure, 335
Removing and Re-installing OptiMS Interface Plate, 336
Opening Levers, Electrodes, and the Interface Block, 338
Clean Electrodes, Opening Levers, and the Interface Block, 341
Refilling Coolant, 343
Replacing Quad Rings, 344
Replacing Fuses, 346
APPENDIX G: Troubleshooting
and Mobile Cart Homing Procedure, 349
Overview, 349
Troubleshooting and Flow Diagrams, 349
Sample Preparation Considerations for Analysis with CESI-
MS, 350
Properties of a Method or Sequence Cannot be Modified or
Saved, 350
Blocked Sprayer Tip, 351