Thermo Scientific Dionex ICS-5000+ User manual

Dionex ICS-5000+Ion Chromatography
System Installation Instructions
Document No. 065447
Revision 02
December 2014

© 2014 Thermo Fisher Scientific Inc. All rights reserved.
Chromeleon is a registered trademark of Thermo Fisher Scientific Inc. in the
United States. Microsoft and Windows are registered trademarks of Microsoft
Corporation in the United States and other countries.
The following are registered trademarks in the United States and possibly
other countries: KIMWIPES is a registered trademark of Kimberly-Clark
Corporation. Ultem is a registered trademark of General Electric Company.
PEEK is a trademark of Victrex PLC.
All other trademarks are the property of Thermo Fisher Scientific Inc. and its
subsidiaries.
Thermo Fisher Scientific Inc. provides this document to its customers with a
product purchase to use in the product operation. This document is copyright
protected and 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.
Revision history: Revision 01 released November 2012; initial release of
instrument
Revision 02 released December 2014; support for low-temperature Dionex
ICS-5000+Detector/Chromatography Module
Software versions: Chromeleon 7.1 SR2 (or later) or Chromeleon 6.8 SR12
(or later) for a system including a standard DC; Chromeleon 7.2 SR2 (or later)
for a system including a low-temperature DC
For Research Use Only. Not for use in diagnostic procedures.

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1 • Introduction
1.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.3 Safety Messages and Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.4 Facility Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.5 Configurations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.6 Fitting and Tube Connection Guidelines . . . . . . . . . . . . . . . . . . . . . . . 9
1.6.1 Connecting High-Pressure Tube Fittings . . . . . . . . . . . . . . . 10
1.6.2 Tightening High-Pressure Fittings . . . . . . . . . . . . . . . . . . . . 11
1.6.3 Cutting Non-Capillary Tubing . . . . . . . . . . . . . . . . . . . . . . . 11
2 • Unpacking Instructions
2.1 Unpacking Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.2 Unpacking the Dionex AS-AP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.3 Unpacking the Dionex ICS-5000+Modules . . . . . . . . . . . . . . . . . . . 19
2.4 Installing the Safety Support Bracket . . . . . . . . . . . . . . . . . . . . . . . . 21
2.5 Removing the Pump Shipping Screws (Optional) . . . . . . . . . . . . . . . 23
2.6 Unpacking the Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2.7 Installing the Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
2.8 Unpacking Consumable Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Contents

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3 • System Setup
3.1 System Setup Checklist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
3.2 Connecting the Power Cords . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .28
3.3 Plugging in the Dionex EGC and CR-TC (RFIC-EG System Only) .29
3.4 Setting Up the DC for Capillary IC Applications . . . . . . . . . . . . . . . .32
3.4.1 Installing the IC Cube Component Cartridges . . . . . . . . . . .33
3.4.2 Installing the EG Degas, CRD, or CES Cartridge . . . . . . . . .34
3.4.3 Installing the Detector in the DC . . . . . . . . . . . . . . . . . . . . . .34
3.5 Setting Up the DC for Analytical IC Applications . . . . . . . . . . . . . . .36
3.5.1 Installing the CD or ED . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36
3.5.2 Installing the Suppressor in the DC . . . . . . . . . . . . . . . . . . . .37
3.6 Setting Up the TC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .38
3.6.1 Installing the Temperature Stabilizer in the TC (Optional) . .38
3.6.2 Installing the Columns in the TC . . . . . . . . . . . . . . . . . . . . . .40
3.6.3 Installing the TC Column ID (Identification) System . . . . . .41
3.7 Connecting the Autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42
3.7.1 Connecting the Autosampler Sample Transfer Line . . . . . . .42
3.7.2 Connecting the Injection Valve Waste Line . . . . . . . . . . . . .43
3.8 Connecting Modules to the Computer . . . . . . . . . . . . . . . . . . . . . . . .45
3.8.1 USB Cables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45
3.8.2 USB Compatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .46
3.8.3 USB Connection Examples . . . . . . . . . . . . . . . . . . . . . . . . . .47
3.9 Setting Up the Chromatography Software . . . . . . . . . . . . . . . . . . . . .49
3.9.1 Installing the Software and License . . . . . . . . . . . . . . . . . . .49

Contents
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3.9.2 Starting the Instrument Controller Service or Server . . . . . . 49
3.9.3 Installing the USB Device Drivers . . . . . . . . . . . . . . . . . . . . 50
3.9.4 Configuring the Modules in Chromeleon . . . . . . . . . . . . . . . 51
3.9.5 Selecting Configuration Properties . . . . . . . . . . . . . . . . . . . 52
3.9.6 Starting the Chromeleon Client . . . . . . . . . . . . . . . . . . . . . . 58
3.10 Connecting Drain Lines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
3.11 Degassing the Water . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
3.12 Setting Up the Reservoirs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
3.13 Setting Up the Piston Seal Wash System . . . . . . . . . . . . . . . . . . . . . 67
3.13.1 Setting Up the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
3.13.2 Activating the Piston Seal Wash Function . . . . . . . . . . . . . . 68
3.14 Priming the Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
3.15 Checking the Conductivity of the Water . . . . . . . . . . . . . . . . . . . . . . 70
4 • System Plumbing
4.1 Plumbing a Capillary IC System . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
4.1.1 Tubing and Fittings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
4.1.2 System Plumbing Checklists . . . . . . . . . . . . . . . . . . . . . . . . 73
4.1.3 Installing the Trap Column for KOH-Based Separations . . 74
4.1.4 Connecting the Pump Outlet . . . . . . . . . . . . . . . . . . . . . . . . 75
4.1.5 Filling and Flushing the CD Regenerant Path . . . . . . . . . . . 75
4.1.6 Checking the Background Conductivity . . . . . . . . . . . . . . . 77
4.1.7 Completing the Installation Qualification . . . . . . . . . . . . . . 77
4.1.8 Completing the Operational Qualification . . . . . . . . . . . . . . 78

Dionex ICS-5000+Installation Instructions
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4.1.9 Filling and Flushing the ED Liquid Path . . . . . . . . . . . . . . . .78
4.1.10 Flushing and Conditioning the Electrolytic Devices . . . . . . .79
4.1.11 Flushing and Installing the Columns . . . . . . . . . . . . . . . . . . .84
4.1.12 Completing the Plumbing for Conductivity Detection . . . . .90
4.1.13 Completing the Plumbing for Electrochemical Detection . . .92
4.1.14 Routing the IC Cube Tubing . . . . . . . . . . . . . . . . . . . . . . . . .93
4.2 Plumbing an Analytical IC System . . . . . . . . . . . . . . . . . . . . . . . . . .95
4.2.1 Tubing and Fittings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .95
4.2.2 System Plumbing Checklists . . . . . . . . . . . . . . . . . . . . . . . . .96
4.2.3 Plumbing the Static Mixer or Trap Column . . . . . . . . . . . . .96
4.2.4 Completing the IQ Checklist . . . . . . . . . . . . . . . . . . . . . . . . .98
4.2.5 Performing the System Function Test . . . . . . . . . . . . . . . . . .99
4.2.6 Completing the Operational Qualification . . . . . . . . . . . . . .99
4.2.7 Plumbing the EG for Analytical IC Applications . . . . . . . . .99
4.2.8 Plumbing the DC for Analytical IC Applications . . . . . . . .110
4.2.9 Plumbing the TC for Analytical IC Applications . . . . . . . .114
4.3 Connecting Waste Lines to the Gas Separator Waste Tube . . . . . . .116
4.4 Equilibrating the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .118
4.4.1 Installing a Backpressure Coil . . . . . . . . . . . . . . . . . . . . . . .120
A • Installing Pump Options
A.1 Pressurizing Eluent Reservoirs . . . . . . . . . . . . . . . . . . . . . . . . . . . . .121
A.1.1 Installing the TC/VWD/PDA Regulator Bracket . . . . . . . .122
A.1.2 Connecting the Gas Source . . . . . . . . . . . . . . . . . . . . . . . . .122

Contents
Doc. 065447-02 12/14 v
A.1.3 Pressurizing the Eluent Reservoir . . . . . . . . . . . . . . . . . . . 124
A.2 Replumbing the Seal Wash System (DP only) . . . . . . . . . . . . . . . . 125
B • Installing DC Options
B.1 Installing the ED Amperometry Cell . . . . . . . . . . . . . . . . . . . . . . . . 127
B.1.1 Unpacking and Disassembling the Cell . . . . . . . . . . . . . . . 127
B.1.2 Installing a Disposable Working Electrode . . . . . . . . . . . . 130
B.1.3 Installing a Conventional Working Electrode . . . . . . . . . . 130
B.1.4 Installing the pH-Ag/AgCl Reference Electrode . . . . . . . . 133
B.1.5 Installing the PdH Reference Electrode in a Capillary IC
System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
B.2 Installing Low-Pressure Valves in the DC . . . . . . . . . . . . . . . . . . . 141
B.2.1 Installing a Low-Pressure Valve on the DC Rear Panel . . 141
B.2.2 Installing a Low-Pressure Valve Inside the DC . . . . . . . . . 142
B.3 Installing the Injection Valve Panel in the DC . . . . . . . . . . . . . . . . 143
B.4 Installing the Automation Manager (AM) in the DC . . . . . . . . . . . 146
B.4.1 Installing a High-Pressure Valve on the AM . . . . . . . . . . . 148
B.4.2 Installing a Low-Pressure Valve on the AM . . . . . . . . . . . 149
B.4.3 Installing the RCH-1 Reaction Coil Heater on the AM . . . 149
B.4.4 Installing the Temperature Stabilizer on the AM . . . . . . . . 150
B.4.5 Installing the AM in the DC Upper Compartment . . . . . . . 150
B.5 Installing an IC Cube in the DC . . . . . . . . . . . . . . . . . . . . . . . . . . . 152

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C • Networking Chromeleon 6.8 Computers
C.1 Setting Up a Shared Datasource . . . . . . . . . . . . . . . . . . . . . . . . . . . .158
C.1.1 Setting Up a Shared Datasource on a Workgroup . . . . . . . .158
C.1.2 Setting Up a Shared Datasource on a Domain . . . . . . . . . .159
C.2 Connecting a Client to a Remote Datasource . . . . . . . . . . . . . . . . . .162
C.2.1 Connecting a Server to a Remote Datasource . . . . . . . . . . .163
C.3 Connecting a Client and Server Through a Network . . . . . . . . . . . .163

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1 • Introduction
1.1 Overview
The modular design of the Thermo Scientific Dionex™ICS-5000+Ion
Chromatography System lets you configure and customize components for a
wide range of applications. This manual provides instructions for initial
installation of the components that make up typical ion chromatography (IC)
systems and Reagent-Free™IC (RFIC™) systems with eluent generation
(RFIC-EG™). Configurations for both capillary IC and analytical IC
applications are described. Analytical IC applications can be configured with
either standard bore or microbore plumbing.
Installation instructions for the following Thermo Scientific modules and
components are included:
•Dionex ICS-5000+Dual Pump (DP)
•Dionex ICS-5000+Single Pump (SP)
•Dionex ICS-5000+Eluent Generator (EG)
•Dionex ICS-5000+Detector/Chromatography Module (DC)
•Dionex ICS-5000+Conductivity Detector (CD)
•Dionex ICS-5000+Electrochemical Detector (ED)
•Dionex ICS-5000+IC Cube™(IC Cube)
•Dionex ICS-5000+Automation Manager (AM)
•Dionex ICS-5000+Thermal Compartment (TC)
•Dionex ICS Series AS-AP Autosampler
•Dionex AS-DV Autosampler

Dionex ICS-5000+Installation Instructions
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1.2 Related Documentation
In addition to this manual, the following documents are provided on the
Thermo Scientific Reference Library DVD (P/N 053891).
•Dionex ICS-5000+Ion Chromatography System Operator’s Manual
(Document No. 065447)
•Dionex ICS Series Photodiode Array Detector Operator’s Manual
(Document No. 065147)
•Dionex ICS Series Variable Wavelength Detector Operator’s Manual
(Document No. 065141)
•Dionex AS-AP Autosampler Operator’s Manual (Document No. 065361)
•Dionex AS-DV Autosampler Operator’s Manual (Document No. 065259)
•Manuals for consumable products (columns, suppressors, CR-TC, EGC,
CRD)
•Chromeleon 7 Installation Guide (Document No. 7229.0003)
•Installing Chromeleon 6.8 with a Dionex Ion Chromatograph (Document
No. 031883)
1.3 Safety Messages and Notes
This manual contains warnings and precautionary statements that can prevent
personal injury and/or damage to the system when properly followed. Safety
messages appear in bold type and are accompanied by icons, as shown below.
Indicates an imminently hazardous situation which, if not avoided, will
result in death or serious injury.
Indicates a potentially hazardous situation which, if not avoided, may
result in death or serious injury.
Indicates a potentially hazardous situation which, if not avoided, may
result in minor or moderate injury.