Thermo Scientific Dionex ICS-1100 User manual

Dionex ICS-1100 Ion Chromatography
System Operator’s Manual
Document No. 065289
Revision 03
October 2012

© 2012 by Thermo Fisher Scientific Inc. All rights reserved.
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any reproduction of the whole or any part of this document is strictly prohibited,
except with the written authorization of Thermo Fisher Scientific Inc.
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.
Thermo Fisher Scientific Inc. makes no representations that this document is
complete, accurate or error-free and assumes no responsibility and will not be
liable for any errors, omissions, damage or loss that might result from any use of
this document, even if the information in the document is followed properly.
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Conditions of Sale, which Terms and Conditions of Sale shall govern all conflicting
information between the two documents.
Revision history: Revision 01 released March 2009; initial release of system
Revision 02 released December 2011; Thermo Fisher Scientific transition
Revision 03 released October 2012; new part numbers assigned
For Research Use Only. Not for use in diagnostic procedures.

Doc. 065289-03 10/12 i
1 • Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1 Introduction to Ion Chromatography (IC) . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Overview of the Dionex ICS-1100 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3 About This Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.3.1 Safety Messages and Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.4 Safety and Regulatory Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.4.1 Safety Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2 • Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.1 Operating Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.1.1 Front Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.1.2 Top Cover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.1.3 Component Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.1.4 Right-Side Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.1.5 Rear Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.2 Flow Schematics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.3 Chromeleon and Chromeleon Xpress . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2.3.1 The Panel Tabset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2.3.2 Software Control Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.3.3 System Wellness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Contents

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2.4 System Component Details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .26
2.4.1 Vacuum Degas Assembly (Optional) . . . . . . . . . . . . . . . . . . . .26
2.4.2 Eluent Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .28
2.4.3 Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .28
2.4.4 Injection Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .30
2.4.5 Auxiliary Valve (Optional) . . . . . . . . . . . . . . . . . . . . . . . . . . . .32
2.4.6 Column Heater (Optional) . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
2.4.7 Suppressor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .34
2.4.8 DS6 Heated Conductivity Cell . . . . . . . . . . . . . . . . . . . . . . . . .34
2.4.9 ER Controller . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35
3 • Operation and Maintenance . . . . . . . . . . . . . . . . . . . . . . . .37
3.1 Operation Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37
3.2 Turning On the System Power . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .39
3.3 Connecting to Chromeleon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .40
3.4 Set Up the Eluent Reservoir . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
3.4.1 Prepare the Eluent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
3.4.2 Degas the Eluent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
3.4.3 Filter the Eluent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43
3.4.4 Fill the Reservoir . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43
3.4.5 Set the Eluent Level . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43
3.4.6 Connect the Reservoir . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .44
3.5 Check All Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .44
3.6 Prime the Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45

Contents
Doc. 065289-03 10/12 iii
3.7 Set System Operating Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
3.8 Equilibrate the System and Verify Operational Status . . . . . . . . . . . . . 46
3.9 Prepare Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
3.9.1 Collecting and Storing Samples . . . . . . . . . . . . . . . . . . . . . . . . 47
3.9.2 Pretreating Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
3.9.3 Diluting Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
3.10 Loading and Injecting Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
3.10.1 Loading Samples with a Syringe . . . . . . . . . . . . . . . . . . . . . . . 50
3.10.2 Loading Samples with a Vacuum Syringe . . . . . . . . . . . . . . . . 51
3.10.3 Loading Samples with an Autosampler . . . . . . . . . . . . . . . . . . 51
3.10.4 Injecting Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
3.11 Processing Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
3.11.1 Manual Sample Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
3.11.2 Automatic (Batch) Sample Processing . . . . . . . . . . . . . . . . . . . 53
3.12 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
4 • Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
4.1 Error Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
4.2 Troubleshooting Error Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
4.3 Liquid Leaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
4.4 Pump Difficult to Prime or Loses Prime . . . . . . . . . . . . . . . . . . . . . . . . 70
4.5 Pump Does Not Start . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
4.6 No Flow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
4.7 Erratic Flow/Pressure Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

Dionex ICS-1100 Ion Chromatography System
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4.8 Excessive System Backpressure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
4.9 Peak “Ghosting” . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .74
4.10 Nonreproducible Peak Height or Retention Time . . . . . . . . . . . . . . . . .75
4.11 Abnormal Retention Time or Selectivity . . . . . . . . . . . . . . . . . . . . . . . .75
4.12 No Cell Response . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .76
4.13 High Cell Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .76
4.14 Baseline Noise or Drift . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .78
4.15 Vacuum Degas Assembly Does Not Run . . . . . . . . . . . . . . . . . . . . . . . .79
5•Service. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .81
5.1 Diagnostic and Calibration Procedures . . . . . . . . . . . . . . . . . . . . . . . . .81
5.1.1 Chromeleon Wellness Panel Overview . . . . . . . . . . . . . . . . . . .82
5.1.2 Calibrating the Conductivity Cell . . . . . . . . . . . . . . . . . . . . . . .84
5.1.3 Calibrating the Flow Rate . . . . . . . . . . . . . . . . . . . . . . . . . . . . .86
5.1.4 Calibrating the Vacuum Degas Assembly . . . . . . . . . . . . . . . . .87
5.2 Isolating a Restriction in the Liquid Lines . . . . . . . . . . . . . . . . . . . . . . .87
5.3 Replacing Tubing and Fittings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .90
5.4 Rebuilding the Injection Valve or Auxiliary Valve . . . . . . . . . . . . . . . .91
5.5 Replacing an Auxiliary Valve Pod . . . . . . . . . . . . . . . . . . . . . . . . . . . . .92
5.6 Cleaning and Replacing the Pump Check Valves . . . . . . . . . . . . . . . . .95
5.7 Replacing a Pump Piston Seal and Piston Rinse Seal . . . . . . . . . . . . . .97
5.8 Replacing a Pump Piston . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .101
5.9 Replacing the Waste Valve or Priming Valve O-Ring . . . . . . . . . . . . .102
5.10 Replacing the Conductivity Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .104

Contents
Doc. 065289-03 10/12 v
5.11 Replacing the Suppressor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
5.12 Replacing the Column Heater . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
5.13 Replacing the Column Heater Heat Exchanger . . . . . . . . . . . . . . . . . . 109
5.14 Replacing the Eluent Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
5.15 Replacing the Leak Sensor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
5.16 Priming the Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
5.16.1 Priming the Eluent Lines with a Syringe . . . . . . . . . . . . . . . . 113
5.16.2 Priming with the Prime Button . . . . . . . . . . . . . . . . . . . . . . . . 115
5.17 Priming the Pump with Isopropyl Alcohol . . . . . . . . . . . . . . . . . . . . . 116
5.18 Changing Main Power Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
A • Specifications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
A.1 Electrical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
A.2 Physical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
A.3 Environmental . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
A.4 Front Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
A.5 Analytical Pump and Fluidics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
A.6 Eluent Regeneration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
A.7 Detector Electronics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
A.8 Conductivity Cell with Heat Exchanger . . . . . . . . . . . . . . . . . . . . . . . 123
A.9 Injection Valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
A.10 Auxiliary Valve (Optional) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
A.11 Vacuum Degas Assembly (Optional) . . . . . . . . . . . . . . . . . . . . . . . . . 124
A.12 Column Heater (Optional) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124

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A.13 Suppressors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .125
A.14 Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .126
A.15 System Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .126
B • TTL and Relay Control. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .129
B.1 TTL and Relay Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .129
B.1.1 Selecting TTL Input Functions and Control Types . . . . . . . . .132
B.2 Controlling TTL and Relay Outputs . . . . . . . . . . . . . . . . . . . . . . . . . . .134
C • Reordering Information. . . . . . . . . . . . . . . . . . . . . . . . . . . . .135
D•FAQ. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .139
D.1 How do I hook up an autosampler? . . . . . . . . . . . . . . . . . . . . . . . . . . .139
D.2 How do I print? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .139
D.3 Why are the retention times moving? . . . . . . . . . . . . . . . . . . . . . . . . . .139
D.4 How do I adjust retention times? . . . . . . . . . . . . . . . . . . . . . . . . . . . . .139
D.5 When should I remake standards? . . . . . . . . . . . . . . . . . . . . . . . . . . . .139
D.6 When should I remake eluents? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .140
D.7 How do I start Chromeleon? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .140
D.8 How do I delete data? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .140
D.9 How do I back up data? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .140
D.10 How do I shut off the system? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .140
D.11 How do I store columns? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .140
D.12 How do I know when a column is dirty? . . . . . . . . . . . . . . . . . . . . . . .140

Contents
Doc. 065289-03 10/12 vii
D.13 How do I clean a column? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
D.14 Why is the conductivity high? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
D.15 How do I configure and operate the auxiliary valve? . . . . . . . . . . . . . 141
E • Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Index

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viii Doc. 065289-03 10/12