Thermo Scientific Dionex ICS-5000 User manual

Dionex ICS-5000 Ion Chromatography
System Operator's Manual
Document No. 065342
Revision 06
December 2011

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The contents of this document are subject to change without notice. All
technical information in this document is for reference purposes only. System
configurations and specifications in this document supersede all previous
information received by the purchaser.
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For research use only. Not for use in diagnostic procedures.
Revision history: Revision 01 released May 2010
Revision 02 released June 2010 Revision 03 released February 2011
Revision 04 released June 2011 Revision 05 released September 2011
Revision 06 released December 2011

Doc. 065342-06 12/11 i
1 • Introduction
1.1 Thermo Scientific Dionex ICS-5000 System Overview . . . . . . . . . . . 1
1.1.1 Dionex ICS-5000 System Components . . . . . . . . . . . . . . . . . 2
1.1.2 Dionex ICS-5000 System Control . . . . . . . . . . . . . . . . . . . . 11
1.2 Dionex ICS-5000 System Documentation . . . . . . . . . . . . . . . . . . . . . 14
1.3 The Dionex ICS-5000 System Operator’s Manual . . . . . . . . . . . . . . 15
1.4 Safety and Regulatory Information . . . . . . . . . . . . . . . . . . . . . . . . . . 16
1.4.1 Safety Messages and Notes . . . . . . . . . . . . . . . . . . . . . . . . . . 16
1.4.2 Safety Symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
1.4.3 Declaration of Conformity . . . . . . . . . . . . . . . . . . . . . . . . . . 19
1.5 Deionized Water Requirements for IC . . . . . . . . . . . . . . . . . . . . . . . . 20
2•Description
DP/SP Description. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.1 DP/SP Front Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.2 DP/SP Interior Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.2.1 Pump Heads . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2.2.2 Pressure Transducer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.2.3 Proportioning Valves (Gradient pump only) . . . . . . . . . . . . 25
2.2.4 Vacuum Degassing Module . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.2.5 Piston Seal Wash System . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Contents

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2.2.6 Static Mixer (Analytical IC only) . . . . . . . . . . . . . . . . . . . . . 27
2.2.7 Pulse Damper (Capillary IC only) . . . . . . . . . . . . . . . . . . . . 27
2.3 DP/SP Flow Schematics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
2.3.1 Isocratic Pump Flow Schematic . . . . . . . . . . . . . . . . . . . . . . 28
2.3.2 Gradient Pump Flow Schematic . . . . . . . . . . . . . . . . . . . . . . 29
2.4 DP/SP Rear Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
2.5 Eluent Reservoirs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
2.5.1 EO (Optional) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
2.5.2 Pressurizing Eluent Reservoirs . . . . . . . . . . . . . . . . . . . . . . . 34
2.5.3 Filtering Eluent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
EG Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
2.6 EG Front Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
2.7 EG Interior Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
2.8 EG Rear Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
2.9 EG Flow Schematics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
DC Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
2.10 DC Front Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
2.11 DC Interior Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
2.11.1 DC Interior Components for Capillary IC . . . . . . . . . . . . . . 54
2.11.2 IC Cube for Capillary IC . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
2.11.3 DC Interior Components for Analytical IC . . . . . . . . . . . . . 61
2.12 DC Temperature Control Zones . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
2.13 High-Pressure Valves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
2.13.1 4-Port Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

Contents
Doc. 065342-06 12/11 iii
2.13.2 6-Port Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
2.13.3 10-Port Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
2.14 CD Conductivity Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
2.14.1 Heated Conductivity Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
2.14.2 Suppressor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
2.14.3 System Flow Schematics for Conductivity Detection . . . . . 72
2.15 ED Electrochemical Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
2.15.1 Electrochemical Detector Cell . . . . . . . . . . . . . . . . . . . . . . . 75
2.15.2 Combination pH–Ag/AgCl Reference Electrode . . . . . . . . . 77
2.15.3 Palladium Hydrogen (PdH) Reference Electrode . . . . . . . . . 79
2.16 DC Rear Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
2.17 I/O Option . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
2.17.1 I/O Option Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
2.17.2 Analog Outputs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
2.17.3 Power, Relay, and TTL Outputs . . . . . . . . . . . . . . . . . . . . . . 87
2.17.4 TTL Inputs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
2.18 Automation Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
2.18.1 AM High-Pressure Switching Valves . . . . . . . . . . . . . . . . . . 96
2.18.2 AM Low-Pressure Valves . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
2.18.3 AM High- and Low-Pressure Valve Control . . . . . . . . . . . . 98
2.18.4 RCH-1 Reaction Coil Heater . . . . . . . . . . . . . . . . . . . . . . . 101
2.19 Electrochemical Detection Modes . . . . . . . . . . . . . . . . . . . . . . . . . . 102
2.19.1 DC Amperometric Detection . . . . . . . . . . . . . . . . . . . . . . . 102
2.19.2 Integrated and Pulsed Amperometric Detection . . . . . . . . 103
2.19.3 Cyclic Voltammetry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105

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2.19.4 Waveforms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
2.19.5 Storing and Reprocessing Amperometry Data . . . . . . . . . . 109
TC Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
2.20 TC Front Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
2.21 TC Interior Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
2.22 TC Rear Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
2.23 Injection Valves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
2.23.1 Injection Valve Operation . . . . . . . . . . . . . . . . . . . . . . . . . . 122
2.23.2 Injection Valve Plumbing . . . . . . . . . . . . . . . . . . . . . . . . . . 124
2.24 Column Identification (ID) System . . . . . . . . . . . . . . . . . . . . . . . . . 125
2.25 Gas and Humidity Sensors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
2.26 TC Theory of Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
2.26.1 Predictive Performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
3 • Configurations
3.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
4•Startup
4.1 Operating Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
4.1.1 EG Operating Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . 141
4.1.2 ED Cell Operating Precautions . . . . . . . . . . . . . . . . . . . . . . 143
4.2 System Startup Checklist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
4.3 Preparing Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
4.3.1 Collecting and Storing Samples . . . . . . . . . . . . . . . . . . . . . 147

Contents
Doc. 065342-06 12/11 v
4.3.2 Pretreating Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
4.3.3 Diluting Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
4.3.4 Filling the Autosampler Vials and Loading the Sample
Tray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
4.4 Starting Chromeleon 7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
4.4.1 Starting the Chromeleon 7 Instrument Controller Service . 149
4.4.2 Starting the Chromeleon 7 Client . . . . . . . . . . . . . . . . . . . . 149
4.5 Starting Chromeleon 6.8 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
4.5.1 Starting the Chromeleon 6.8 Server . . . . . . . . . . . . . . . . . . 150
4.5.2 Starting the Chromeleon 6.8 Client . . . . . . . . . . . . . . . . . . 151
DP/SP Startup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
4.6 Setting Up the Eluent Reservoirs . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
4.7 Setting Up the Piston Seal Wash System . . . . . . . . . . . . . . . . . . . . . 154
4.8 Starting the Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
EG Startup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
4.9 Entering the Eluent Concentration . . . . . . . . . . . . . . . . . . . . . . . . . . 161
4.10 Selecting an Eluent Concentration . . . . . . . . . . . . . . . . . . . . . . . . . . 162
DC Startup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
4.11 Starting the DC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
4.12 Equilibrating the System and Verifying Operational Readiness . . . 166
TC Startup. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
4.13 Starting the TC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
4.14 Equilibrating the System and Verifying Operational Readiness . . . 170

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5 • Operation
5.1 Controlling Modules Directly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
5.2 Analyzing Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
5.2.1 Creating a New Sequence in Chromeleon 7 . . . . . . . . . . . . 173
5.2.2 Creating a New Sequence in Chromeleon 6.8 . . . . . . . . . . 174
5.2.3 Starting a Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
5.3 Loading Samples Into the Sample Loop or Concentrator . . . . . . . . 178
5.3.1 Loading Samples with an Autosampler . . . . . . . . . . . . . . . 178
5.3.2 Loading Samples with a Syringe . . . . . . . . . . . . . . . . . . . . 178
5.3.3 Loading Samples with a Vacuum Syringe (Pull Method) . 179
5.4 Autosampler Commands for Loading and Injecting Samples . . . . . 180
6 • Shutdown
DP/SP Shutdown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
EG Shutdown. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
6.1 Short-term Shutdown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
6.2 Long-term Shutdown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
DC Shutdown. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
6.3 Consumables Storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
6.4 ED Cell Storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
6.4.1 Short-term Storage of the ED Cell . . . . . . . . . . . . . . . . . . . 187
6.4.2 Long-term Storage of the pH-Ag/AgCl Reference
Electrode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187

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Doc. 065342-06 12/11 vii
TC Shutdown. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
6.5 Consumables Storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
6.6 Short-term Shutdown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
6.7 Long-term Shutdown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
7 • Maintenance
7.1 System Maintenance Checklists . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
7.1.1 Daily Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
7.1.2 Weekly Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
7.1.3 Periodic Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
7.1.4 Annual Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
DP/SP Routine Maintenance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
7.2 DP/SP Daily Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
7.3 DP/SP Weekly Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
7.4 DP/SP Periodic Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
7.5 DP/SP Annual Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
EG Routine Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
7.6 EG Daily Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
7.7 EG Weekly Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
7.8 EG Annual Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
DC Routine Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
7.9 DC Daily Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
7.10 DC Weekly Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199

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7.11 DC Periodic Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
7.12 DC Annual Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
TC Routine Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
7.13 TC Daily Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
7.14 TC Weekly Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
7.15 TC Periodic Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
7.16 TC Annual Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202
8 • Troubleshooting
8.1 Audit Trail Error Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
8.1.1 DP/SP Error Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
8.1.2 EG Error Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
8.1.3 DC Error Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
8.1.4 TC Error Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
8.2 Noisy Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 214
8.3 Poor Retention Time Reproducibility . . . . . . . . . . . . . . . . . . . . . . . 218
8.4 Peak Retention Times Are Too Early . . . . . . . . . . . . . . . . . . . . . . . 220
8.5 Peak Retention Times Are Too Late . . . . . . . . . . . . . . . . . . . . . . . . 220
8.6 No Peaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220
8.7 Tailing Peaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
8.8 Low System Backpressure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223
8.9 High System Backpressure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223
8.10 Low Detector Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
8.11 High Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225

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DP/SP Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
8.12 Troubleshooting DP/SP Error Messages . . . . . . . . . . . . . . . . . . . . . 227
8.13 DP/SP Does Not Start . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
8.14 DP/SP Stops . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236
8.15 DP/SP Liquid Leaks/Leak Alarm . . . . . . . . . . . . . . . . . . . . . . . . . . 237
8.16 Vacuum Degassing Module Low Vacuum . . . . . . . . . . . . . . . . . . . 238
8.17 Vacuum Degassing Module Does Not Run . . . . . . . . . . . . . . . . . . . 238
8.18 DP/SP Digital I/O Port Inoperative . . . . . . . . . . . . . . . . . . . . . . . . . 239
EG Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
8.19 Troubleshooting EG Error Messages . . . . . . . . . . . . . . . . . . . . . . . . 241
8.20 EG ALARM LED Is Lighted . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
8.21 EG POWER LED Fails to Light . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
8.22 Liquid Leaks in the EG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
8.23 No Flow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
8.24 EG Stops Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256
DC Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
8.25 Troubleshooting DC Error Messages . . . . . . . . . . . . . . . . . . . . . . . . 259
8.26 Liquid Leaks from DC Components . . . . . . . . . . . . . . . . . . . . . . . . 270
8.27 VALVE Button Not Working . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
8.28 ED Cell Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
8.28.1 ED Cell pH Readout Always 7.0 . . . . . . . . . . . . . . . . . . . . 271
8.28.2 Cannot Set ED Cell pH Readout to 7.0 . . . . . . . . . . . . . . . . 272
8.28.3 Shift in ED Cell pH Readout . . . . . . . . . . . . . . . . . . . . . . . 272
8.28.4 No ED Cell pH Readout or Intermittent Readout . . . . . . . . 273

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8.28.5 Leak in pH-Ag/AgCl Reference Electrode Compartment . 274
8.28.6 Shift in Ag/AgCl Reference Potential . . . . . . . . . . . . . . . . . 274
TC Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
8.29 Troubleshooting TC Error Messages . . . . . . . . . . . . . . . . . . . . . . . . 275
8.30 TC ALARM LED Is Lighted . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299
8.31 Liquid Leaks from TC Components . . . . . . . . . . . . . . . . . . . . . . . . 300
8.32 TC Temperature Does Not Increase . . . . . . . . . . . . . . . . . . . . . . . . . 301
8.33 TC Temperature Stabilizer Not Operating Properly . . . . . . . . . . . . 301
9•Service
9.1 Connecting Capillary Tubing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 303
9.2 Tightening Guidelines for High-Pressure Fittings . . . . . . . . . . . . . . 305
DP/SP Service . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 306
9.3 Replacing Tubing and Fittings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 306
9.4 Cleaning Eluent Reservoirs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308
9.5 Priming the DP/SP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308
9.5.1 Priming with the PUMP PRIME Button . . . . . . . . . . . . . . . 309
9.5.2 Priming from the Chromeleon Panel . . . . . . . . . . . . . . . . . 310
9.6 Replacing the Check Valves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 312
9.6.1 Removing the Check Valves . . . . . . . . . . . . . . . . . . . . . . . . 313
9.6.2 Installing the New Check Valves . . . . . . . . . . . . . . . . . . . . 314
9.7 Replacing Piston Seals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 316
9.7.1 Removing the Pump Head and Piston . . . . . . . . . . . . . . . . 317
9.7.2 Cleaning the Piston . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 320

Contents
Doc. 065342-06 12/11 xi
9.7.3 Removing the Main Piston Seal . . . . . . . . . . . . . . . . . . . . . 320
9.7.4 Removing the Piston Seal Wash Seal . . . . . . . . . . . . . . . . . 321
9.7.5 Installing the Piston Seals and O-Ring . . . . . . . . . . . . . . . . 321
9.7.6 Reinstalling the Piston and Pump Head . . . . . . . . . . . . . . . 323
9.8 Replacing the Piston . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323
9.8.1 Removing the Pump Head and Piston . . . . . . . . . . . . . . . . 324
9.8.2 Reinstalling the New Piston . . . . . . . . . . . . . . . . . . . . . . . . 325
9.8.3 Reinstalling the Pump Head . . . . . . . . . . . . . . . . . . . . . . . . 325
9.9 Replacing the Piston Seal Wash Tubing . . . . . . . . . . . . . . . . . . . . . 326
9.10 Replacing the DP/SP Priming Valve Knob Seal . . . . . . . . . . . . . . . 329
9.11 Changing the DP/SP Main Power Fuses . . . . . . . . . . . . . . . . . . . . . 330
EG Service . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333
9.12 Replacing Tubing and Fittings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333
9.12.1 Tubing and Fittings for Capillary IC EG Channels . . . . . . 333
9.12.2 Tubing and Fittings for Analytical IC EG Channels . . . . . 335
9.13 Isolating a Restriction in the Liquid Lines . . . . . . . . . . . . . . . . . . . . 336
9.14 Replacing the EGC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 336
9.14.1 Removing the Old EGC . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
9.14.2 Disposing of the Old EGC . . . . . . . . . . . . . . . . . . . . . . . . . 339
9.14.3 Storing an Old EGC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 339
9.14.4 Installing and Conditioning a New Capillary EGC . . . . . . 340
9.14.5 Installing and Conditioning a New Analytical EGC . . . . . . 345
9.15 Replacing the CR-TC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 349
9.15.1 Removing the Old CR-TC . . . . . . . . . . . . . . . . . . . . . . . . . 350

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9.15.2 Installing and Flushing the New CR-TC . . . . . . . . . . . . . . 350
9.15.3 Completing the New CR-TC Plumbing . . . . . . . . . . . . . . . 353
9.16 Replacing the RFIC Eluent Degasser . . . . . . . . . . . . . . . . . . . . . . . . 355
9.17 Installing a Backpressure Coil . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 355
9.18 Changing the EG Main Power Fuses . . . . . . . . . . . . . . . . . . . . . . . . 357
DC Service . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 359
9.19 Replacing Tubing and Fittings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 359
9.19.1 Tubing and Fittings for Capillary IC Systems . . . . . . . . . . 359
9.19.2 Tubing and Fittings for Analytical IC Systems . . . . . . . . . 362
9.20 Connecting a Sample Loading Port to the Injection Valve . . . . . . . 363
9.21 Replacing the Leak Sensor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 364
9.22 Rebuilding a High-Pressure (Injection) Valve . . . . . . . . . . . . . . . . . 366
9.23 Replacing a High-Pressure (Injection) Valve Pod . . . . . . . . . . . . . . 367
9.24 Installing or Replacing an I/O Option Board . . . . . . . . . . . . . . . . . . 369
9.25 Changing the DC Main Power Fuses . . . . . . . . . . . . . . . . . . . . . . . . 371
9.26 IC Cube Service Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 372
9.26.1 Replacing an IC Cube Cartridge . . . . . . . . . . . . . . . . . . . . . 372
9.26.2 Replacing Capillary Columns . . . . . . . . . . . . . . . . . . . . . . . 374
9.27 CD Service Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 379
9.27.1 Calibrating the CD Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . 379
9.27.2 Replacing an Analytical Suppressor . . . . . . . . . . . . . . . . . . 381
9.27.3 Replacing a CD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 382
9.27.4 Removing Trapped Air from the Conductivity Cell . . . . . . 383
9.28 ED Service Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 385

Contents
Doc. 065342-06 12/11 xiii
9.28.1 Disconnecting the ED Cell . . . . . . . . . . . . . . . . . . . . . . . . . 385
9.28.2 Replacing an ED Cell Disposable Working Electrode
Gasket . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 386
9.28.3 Replacing an ED Cell Conventional Working Electrode
Gasket . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 386
9.28.4 Polishing an ED Cell Conventional Working Electrode . . . 389
9.28.5 Replacing a pH-Ag/AgCl Reference Electrode . . . . . . . . . 392
9.28.6 Calibrating the pH-Ag/AgCl Reference Electrode . . . . . . . 394
9.28.7 Replacing the pH-Ag/AgCl Reference Electrode O-Ring . 399
9.28.8 Replacing a PdH Reference Electrode . . . . . . . . . . . . . . . . 400
9.28.9 Replacing an ED Detector . . . . . . . . . . . . . . . . . . . . . . . . . 404
TC Service. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 407
9.29 Replacing Tubing and Fittings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 407
9.30 Setting Up the Column ID System . . . . . . . . . . . . . . . . . . . . . . . . . . 408
9.31 Rebuilding an Injection Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 410
9.32 Replacing an Injection Valve Pod . . . . . . . . . . . . . . . . . . . . . . . . . . 411
9.33 Changing the Main Power Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . 413
A • Specifications
DP/SP Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 415
EG Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 419
DC Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 423
TC Specifications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 433

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B • Reordering Information
DP/SP Reordering Information . . . . . . . . . . . . . . . . . . . . . . . . . . . 435
EG Reordering Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 439
DC Reordering Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 441
TC Reordering Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 445

Doc. 065342-06 12/11 1
1 • Introduction
1.1 Thermo Scientific Dionex ICS-5000 System
Overview
The Thermo Scientific Dionex ICS-5000 Ion Chromatography System offers
a full range of Reagent-Free™IC (RFIC™) components. RFIC-EG combines
automated eluent generation and self-regenerating suppression to make IC
easier and more powerful than ever before. It is no longer necessary to spend
time preparing eluents and regenerants. All you need is deionized water—the
IC system automatically generates eluent in the exact amount and
concentration needed for your application, ensuring superior analytical
Figure 1-1. Dual Dionex ICS-5000 System with RFIC-EG™
Dionex ICS-5000
Detector/Chromatography Module
Dionex ICS-5000 Dual Pump (DP)
Dionex ICS-5000 Eluent Generator
(EG)
1
2
3
1
2
3

Dionex ICS-5000 Operator’s Manual
2Doc. 065342-06 12/11
results. In combination with capillary columns at flow rates of 0.010 mL/min,
the Dionex ICS-5000 system can be used for long periods of continuous
operation and minimal eluent consumption.
The dual-analysis capabilities (both simultaneous and sequential) of the
Dionex ICS-5000 system let you maximize efficiency and throughput and
minimize downtime. The modular system design lets you quickly configure
and customize hardware.
The single-channel Dionex ICS-5000 can be configured to run either capillary
IC applications or microbore or standard bore IC applications.
•Capillary IC applications use 0.4 mm diameter columns with flow rates
typically from 0.005 to 0.02 mL/min.
•Microbore IC applications use 2 mm diameter columns and with flow
rates typically from 0.2 to 0.5 mL/min.
•Standard bore IC applications use 4 mm diameter columns with flow rates
typically from 1.0 to 2.0 mL/min.
A dual Dionex ICS-5000 system can be configured with any combination of
the above application types (for example, one capillary IC channel and one
microbore IC channel, or two capillary IC channels, or one microbore IC
channel and one standard bore IC channel).
1.1.1 Dionex ICS-5000 System Components
The table below identifies modules in the Dionex ICS-5000 product line, as
well as additional products that can be added to a Dionex ICS-5000 system.
Refer to the page number indicated here for a brief product overview.
Product Type Product Name Page
Pump Dionex ICS-5000 Dual Pump page 3
Dionex ICS-5000 Single Pump page 3
Eluent Generator Dionex ICS-5000 Eluent Generator page 5
Eluent Organizer Dionex ICS-5000 Eluent Organizer page 6
Detector/Chromatography
Compartment
Dionex ICS-5000
Detector/Chromatography Module
page 7
IC Cube™(inside DC) Dionex IC Cube page 7

1 • Introduction
Doc. 065342-06 12/11 3
Dionex ICS-5000 Dual Pump (DP) and Dionex ICS-5000 Single Pump (SP)
Each Dionex ICS-5000 pump can be configured for either capillary IC
applications or analytical (standard bore and microbore) IC applications.
Capillary IC pumps are always isocratic (they deliver one eluent). Analytical
IC pumps can be either isocratic or low pressure proportioned gradient.
Gradient pumps deliver gradient mixtures of up to four eluent components.
The eluent composition selected for a gradient pump can be delivered as
isocratic, isocratic proportioned, linear ramp, step, curved, or any
combination of these.
The SP contains one of the following pump types:
•Isocratic capillary IC pump
•Isocratic analytical IC pump
•Gradient analytical IC pump
The DP contains two pumps in any combination of the three types listed
above (for example, two isocratic capillary IC pumps, or two isocratic
analytical IC pumps, or one isocratic capillary IC pump and one gradient
analytical IC pump).
Detector (inside DC) Dionex ICS-5000 Conductivity
Detector
page 7
Dionex ICS-5000 Electrochemical
Detector
page 7
Accessory (inside DC) Dionex ICS-5000 Automation
Manager
page 8
Detector (outside DC) ICS Series Photodiode Array
Detector
page 9
ICS Series Variable Wavelength
Detector
page 10
Thermal Compartment Dionex ICS-5000 Thermal
Compartment
page 8
Autosampler Dionex AS Autosampler page 9
Dionex AS-DV Autosampler page 9
Mass Spectrometer MSQ Plus™page 10
Product Type Product Name Page

Dionex ICS-5000 Operator’s Manual
4Doc. 065342-06 12/11
The second pump in the DP can be operated as a second-channel
chromatography pump, an auxiliary dependent pump, or an auxiliary
independent pump.
Capillary IC pumps operate at flow rates ranging from 0.001 to 3.0 mL/min
and operating pressures up to 41 MPa (6000 psi) (without RFIC) and up to
35 MPa (5000 psi) (with RFIC).
IMPORTANT
Capillary IC pumps shipped before February 17, 2011 were rated for lower
operating pressures than the pumps currently being shipped. The older
pumps can be operated at pressures up to 35 MPa (5000 psi) (without
RFIC) and up to 21 MPa (3000 psi) (with RFIC). Before operating at
pressures above these limits, verify that you have the appropriate pump.
•HPC is stamped on the secondary
pump heads of the older (lower
pressure rated) capillary IC pumps.
•HPC-2 is stamped on the secondary
pump heads of the newer (higher
pressure rated) capillary IC pumps.
A Capillary Pump High-Pressure Upgrade Kit (P/N 075994) is available
for converting a lower pressure rated capillary IC pump to a higher
pressure rated pump. The kit includes the HPC-2 secondary pump head and
high-pressure pump seals.
NOTE A high-pressure EG degas (capillary) cartridge (P/N 074459) is
also required when operating a capillary RFIC system at pressures
up to 35 MPa (5000 psi). For details, see page 5.
Capillary
IC