Thermo Scientific Dionex ICS Series User manual

Dionex ICS Series Photodiode Array
Detector Operator’s Manual
Document No. 065378
Revision 01
January 2012

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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.
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,
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information in the document is followed properly.
Revision history: Revision 01 released January 2012
For Research Use Only. Not for use in diagnostic procedures.

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1 • Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1 Detector Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Theory of Photodiode Array Detection . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2.1 Advantages of Photodiode Array Detection . . . . . . . . . . . . . . . . 3
1.3 Operator’s Manual Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.4 Safety and Regulatory Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.4.1 Safety Messages and Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.4.2 Safety Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
1.4.3 Declaration of Conformity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2•Description. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.1 Front Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.2 Inside Front Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.3 Optical System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.3.1 Flow Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.4 Electronics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.5 Rear Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
2.6 Operating Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.6.1 Mobile Phases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.6.2 Solvent Delivery System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Contents

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2.7 Chromatography Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
2.7.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
2.7.2 3D Data Acquisition License . . . . . . . . . . . . . . . . . . . . . . . . . . .30
2.7.3 System Wellness and Predictive Performance . . . . . . . . . . . . .30
3 • Operation and Maintenance . . . . . . . . . . . . . . . . . . . . . . . .33
3.1 Getting Started . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
3.1.1 Initial Startup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33
3.1.2 Connect to the Chromeleon 7 Client . . . . . . . . . . . . . . . . . . . . .34
3.1.3 Connect to the Chromeleon 6.8 Client . . . . . . . . . . . . . . . . . . .35
3.1.4 Turn On the Lamps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37
3.2 System Equilibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37
3.3 Routine Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .38
3.3.1 Direct Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .38
3.3.2 Automated Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .41
3.3.3 Stand-Alone Analog Operation . . . . . . . . . . . . . . . . . . . . . . . . .41
3.4 Optimizing Detector Performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43
3.5 Shutdown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55
3.6 Routine Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55
4 • Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .59
4.1 Alarms and Error Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .59
4.2 ALARM LED Is Lighted . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73
4.3 Lamp Does Not Light/Lamp LED Is Flashing Rapidly . . . . . . . . . . . . .73

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4.4 No Detector Response . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
4.5 Noisy Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
4.6 Drifting Baseline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
4.7 Deuterium Lamp Intensity Reading Too Low . . . . . . . . . . . . . . . . . . . . 79
4.8 Wavelength Calibration Fails . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
4.9 Wavelength Verification Fails . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
4.10 No Spectra Collected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
4.11 Low Spectral Resolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
4.12 Peaks Too Large or Small . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
4.13 Poor Peak Shape . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
4.14 Faulty USB Communication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
4.14.1 Moduleware Run-Time Diagnostics . . . . . . . . . . . . . . . . . . . . 87
4.14.2 Software Diagnostics and Calibration . . . . . . . . . . . . . . . . . . . 87
5•Service. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
5.1 Liquid Leaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
5.2 Cleaning the Flow Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
5.3 Removing Trapped Air from the Flow Cell . . . . . . . . . . . . . . . . . . . . . 93
5.4 Removing the Flow Cell from the Optical Bench . . . . . . . . . . . . . . . . . 94
5.5 Replacing the Flow Cell Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
5.6 Replacing the Flow Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
5.7 Replacing the Deuterium Lamp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
5.8 Replacing the Tungsten Lamp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
5.9 Replacing the Main Power Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

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A • Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .105
A.1 Electrical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .105
A.2 Physical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .105
A.3 Environmental . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .105
A.4 Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .106
A.5 Flow Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .107
A.5.1 Standard Flow Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .107
A.5.2 Semi-Micro Flow Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .107
A.5.3 Semi-Preparative Flow Cell . . . . . . . . . . . . . . . . . . . . . . . . . .108
A.6 Heat Exchangers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .108
B • Installation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .111
B.1 Facilities Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .111
B.2 Unpacking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .112
B.3 Installing the Flow Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .113
B.4 Connecting the Waste Line . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .116
B.5 Connecting the Analog Outputs (Optional) . . . . . . . . . . . . . . . . . . . . .116
B.6 Connecting the Relays/TTLs (Optional) . . . . . . . . . . . . . . . . . . . . . . .117
B.7 Connecting to the Chromeleon PC . . . . . . . . . . . . . . . . . . . . . . . . . . . .118
B.7.1 Before You Begin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .118
B.7.2 Chromeleon 7: Starting the Instrument Controller Service . . .119
B.7.3 Chromeleon 6.8: Starting the Server . . . . . . . . . . . . . . . . . . . .119
B.7.4 Connecting the USB Cable . . . . . . . . . . . . . . . . . . . . . . . . . . .120
B.8 Connecting the Power Cord . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .123

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B.9 Installing the USB Device Drivers . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
B.10 Configuring the Dionex PDA in Chromeleon . . . . . . . . . . . . . . . . . . . 125
B.10.1 Using the USB Auto Configuration Wizard . . . . . . . . . . . . . . 125
B.10.2 Selecting Configuration Properties . . . . . . . . . . . . . . . . . . . . 127
B.11 Starting the Chromeleon Client . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
C • Reordering Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131

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1 • Introduction
1.1 Detector Overview
The Thermo Scientific Dionex™ICS Series Photodiode Array Detector (Dionex
PDA) (P/N 074114) is an optical chromatography detector capable of measuring
absorbance signals and absorbance spectra from 190 to 800 nm. The Dionex PDA
can be used with the following Thermo Scientific Dionex systems: the ICS-5000
(analytical systems only), ICS-2100, ICS-1600, ICS-1100, and ICS-900 (as well
as some legacy systems). The Dionex PDA can be used in numerous laboratory
environments for routine analysis, as well as for sophisticated research tasks.
A deuterium lamp optimizes the UV range (190 to 380 nm) and a tungsten lamp
optimizes the visible range (380 to 800 nm). When using the Dionex PDA, up to
five single wavelengths (2D chromatograms) can be collected without the
necessity for collecting 3D data. Collecting individual wavelengths instead of the
spectra offers two advantages: it eliminates the need to perform signal extractions
for analyses that do not require spectral data and it conserves disk space.
Figure 1-1. Thermo Scientific Dionex ICS Series Photodiode Array Detector

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Key features of the Dionex PDA include:
•The deuterium and tungsten lamps ensure low baseline noise, high signal
intensity, and applications flexibility in the wavelength range from 190 to
800 nm.
•The 1024-element photodiode array optimizes spectral resolution.
•The built-in holmium oxide filter verifies wavelength calibration accuracy.
•Five flow cells are available for standard, semi-micro, and semi-preparative
applications.
•LEDs on the front cover provide detector status at a glance.
•Four analog outputs support data collection on alternate data collection
systems.
•The detector is controlled with a PC (personal computer) running Microsoft®
Windows Vista® or Windows®XP and either the Chromeleon®7
Chromatography Data System or the Chromeleon®6.8 Chromatography Data
System. Chromeleon 7 and Chromeleon 6.8 also provide data acquisition and
data processing functions.
NOTE Thermo Scientific Dionex Chromeleon® Xpress software
can provide real-time control and monitoring of the
detector, but does not include data management
capabilities.
1.2 Theory of Photodiode Array Detection
Monochromatic variable wavelength detectors monitor eluting components of the
sample at a single wavelength (ideally, the wavelength of maximum absorbance).
Photodiode array detectors scan a range of wavelengths every few milliseconds
and continually generate spectral information. Wavelength, time, and absorbance
can all be plotted.
Photodiode array detectors provide three-dimensional information that allows an
accurate assessment of peak identity, purity, and quantitation in a single analysis.
Software support for photodiode array detectors includes peak purity and spectral
library search functions to help determine peak homogeneity and identity.

1•Introduction
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1.2.1 Advantages of Photodiode Array Detection
Photodiode array detectors are useful in both research and quality
assurance laboratories. In the research laboratory, the photodiode array
detector provides the analyst with a variety of approaches to the analysis.
In the quality assurance laboratory, the photodiode array detector provides
several results from a single analysis, thereby increasing the throughput
of the HPLC.
Photodiode array detection offers the following advantages:
•Peak measurement at all wavelengths
In methods development, detailed information about the detector
conditions required for the analysis may not be known. When a
variable wavelength detector is used, a sample must often be injected
several times, with varying wavelengths, to ensure that all peaks are
detected. When a photodiode array detector is used, a wavelength
range can be programmed and all compounds that absorb within this
range can be detected in a single analysis.
•Determination of the correct wavelengths in one analysis
After all peaks have been detected, the maximum absorbance
wavelength for each peak can be determined. A photodiode array
detector can collect spectra of each peak, after which the detector
software can calculate the absorbance maximum.
•Detection of multiple wavelengths
A photodiode array detector can monitor a sample at more than one
wavelength. This is especially useful when the wavelength maxima of
the analytes are different. Wavelengths can be selected to analyze
each compound at its highest sensitivity.
•Peak purity analysis
It is difficult to determine component purity from a chromatogram.
However, a photodiode array detector can analyze peak purity by
comparing spectra within a peak. The better the spectra match, the
higher the possibility that the peak is pure.
•Positive peak identification
In liquid chromatography, peak identification is usually based on
relative retention times. When a photodiode array detector is used,

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spectra are automatically collected as each peak elutes. The detector
software compares the spectra with those stored in a library to
determine the best fit matches; this method increases the likelihood of
correctly identifying peaks.
For example, Figure 1-2 shows an overlay of pyrene and an impurity
obtained from two consecutive chromatographic analyses. Based on
2D data, or if the analyses had been performed with a conventional
variable wavelength detector, the peaks might have been
misidentified as the same component.
The Dionex PDA, under the control of Chromeleon 6.8 with the 3D
Data Acquisition license, correctly identified and differentiated the
components. The spectra of pyrene and the impurity (see Figure 1-3)
clearly indicate that the two peaks are different components.
Figure 1-2. Overlay of Pyrene and an Impurity
Impurity
Pyrene

1•Introduction
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Figure 1-3. Spectra of Pyrene and an Impurity
Impurity
Pyrene

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1.3 Operator’s Manual Overview
The electronic version (i.e., the PDF file) of this manual contains numerous
hypertext links that can quickly take you to other locations within the file. These
links include:
•Table of contents entries
•Index entries
•Cross-references (underlined in blue) to sections, figures, tables, etc.
If you are not familiar with how to navigate PDF files, refer to the Help system for
Adobe®Acrobat®or Adobe Reader®for assistance.
Chapter 1
Introduction
An introduction to the Dionex PDA and the theory of
photodiode array detection; includes an explanation of
conventions used in this manual.
Chapter 2
Description
An overview of Dionex PDA operating features; includes
an introduction to the chromatography software
(Chromeleon) required for detector control.
Chapter 3
Operation and
Maintenance
Instructions for routine Dionex PDA operation with
Chromeleon and guidelines for optimizing Dionex PDA
performance. Preventive maintenance procedures.
Chapter 4
Troubleshooting
Minor problems that may occur during operation, with
step-by-step procedures for how to isolate and eliminate
the cause of each problem. A list of Chromeleon Audit
Trail error messages, with an explanation of the possible
cause of each message and the corrective action to take.
Chapter 5
Service
Step-by-step instructions for routine service and parts
replacement procedures the user can perform for the
Dionex PDA.
Appendix A
Specifications
Specifications and installation site requirements for the
Dionex PDA.
Appendix B
Installation
Installation instructions for the Dionex PDA.
Appendix C
Reordering
Information
Spare parts for the Dionex PDA.

1•Introduction
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1.4 Safety and Regulatory Information
The Dionex PDA was manufactured by Thermo Fisher Scientific at the following
location: 527 Lakeside Drive, Sunnyvale, CA 94088-3603 U.S.A. The Dionex
PDA is designed for use with IC (ion chromatography), BioLC® (biocompatible
liquid chromatography), and HPLC (high-performance liquid chromatography)
systems and should not be used for any other purpose. Operation of the Dionex
PDA in a manner not specified by Thermo Fisher Scientific may result in personal
injury.
If there is a question regarding appropriate usage, contact Technical Support for
Dionex products. In the U.S. and Canada, call 1-800-346-6390. Outside the U.S.
and Canada, call the nearest Thermo Fisher Scientific office.
1.4.1 Safety Messages and Notes
This manual contains warnings and precautionary statements that can
prevent personal injury and/or damage to the Dionex PDA when properly
followed. Safety messages appear in bold type and are accompanied by
icons, as shown below.
Messages d’avertissement en français
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.
Indicates that the function or process of the instrument may be
impaired. Operation does not constitute a hazard.
Signale une situation de danger immédiat qui, si elle n'est pas évitée,
entraînera des blessures graves à mortelles.

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Warnhinweise in Deutsch
Informational messages also appear throughout this manual. These are
labeled NOTE and are in bold type:
NOTE NOTES call attention to certain information. They alert
users to an unexpected result of an action, suggest how
to optimize instrument performance, etc.
Signale une situation de danger potentiel qui, si elle n'est pas évitée,
pourrait entraîner des blessures graves à mortelles.
Signale une situation de danger potentiel qui, si elle n'est pas évitée,
pourrait entraîner des blessures mineures à modérées. Également
utilisé pour signaler une situation ou une pratique qui pourrait
gravement endommager l'instrument mais qui n'entraînera pas de
blessures.
Bedeutet unmittelbare Gefahr. Mißachtung kann zum Tod oder
schwerwiegenden Verletzungen führen.
Bedeutet eine mögliche Gefährdung. Mißachtung kann zum Tod oder
schwerwiegenden Verletzungen führen.
Bedeutet eine mögliche Gefährdung. Mißachtung kann zu kleineren
oder mittelschweren Verletzungen führen. Wird auch verwendet, wenn
eine Situation zu schweren Schäden am Gerät führen kann, jedoch
keine Verletzungsgefahr besteht.

1•Introduction
Doc. 065378-01 1/12 9
1.4.2 Safety Labels
These symbols appear on the Dionex PDA or on Dionex PDA labels.
1.4.3 Declaration of Conformity
The TUV GS, C, US Mark safety label and the CE Mark label on the
Dionex PDA indicate that the Dionex PDA is in compliance with the
following standards: EN 61010-1:2001 (safety), CAN/CSA-C22.2 No.
1010.1-92+A2:97 (safety), UL 61010C-1:2002 R8.02 (safety), and EN
61326:1997+A1:1998 (EMC susceptibility and immunity).
Alternating current
Primary protective conductor terminal
Secondary protective conductor terminal
Power supply is on
Power supply is off
Indicates a potential hazard. Refer to this operator’s
manual for an explanation of the hazard and how to
proceed.

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2•Description
2.1 Front Features
Figure 2-1 illustrates the features on the front of the Thermo Scientific Dionex
ICS Series Photodiode Array Detector (Dionex PDA).
•The status bar provides LEDs (light emitting diodes) that indicate the status of
several Dionex PDA components and functions (see Figure 2-2).
•Use the power button for routine on/off control of the Dionex PDA.
NOTE The main power switch is on the Dionex PDA rear panel
(see Figure 2-8). Always leave the main power switch on
unless instructed to turn it off (for example, before
performing a service procedure).
•The front cover provides access to the components inside the Dionex PDA. To
remove the cover, grasp the cover by the sides and pull it straight off.
Figure 2-1. Dionex PDA Front Features
Status Bar
Power Button Front Cover

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Figure 2-2. Dionex PDA Status Bar
LED Label LED Status Function
CONNECTED Lighted The Dionex PDA is connected to a Chromeleon 7
instrument or a Chromeleon 6.8 timebase.
Off The Dionex PDA is not connected to a
Chromeleon 7 instrument or a Chromeleon 6.8
timebase.
ALARM Lighted A problem has occurred (a leak, for example).
Check the Chromeleon Audit Trail for the cause.
Off No problems have been detected.
DEUTERIUM – UV Lighted The deuterium lamp is on.
Flashing The LED flashes once every second while the
deuterium lamp is firing.
The LED flashes every 0.5 second if a command
is issued to turn on the lamp, but the lamp fails to
turn on (see Section 4.3). If a subsequent attempt
to turn on the lamp is successful, the LED will
automatically stop flashing.
Off The deuterium lamp is off.
TUNGSTEN – VIS Lighted The tungsten lamp is on.
Flashing The LED flashes once every second while the
tungsten lamp is firing.
The LED flashes every 0.5 second if a command
was issued to turn on the lamp, but the lamp failed
to turn on (see Section 4.3). If a subsequent
attempt to turn on the lamp is successful, the LED
will automatically stop flashing.
Off The tungsten lamp is off.
POWER Lighted The Dionex PDA power is on.
Off The Dionex PDA power is off.
CONNECTED ALARM
DEUTERIUM - UV POWERTUNGSTEN - VIS