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Installation Guide DCMSLink for Analyst

Version 2.0

Revision: 2.0 August 2007

© Dionex

DCMSLink for Analyst Installation Guide

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Table of Contents

1 Definitions........................................................................................................................ 1

2 Abbreviations .................................................................................................................. 1

3 Overview .......................................................................................................................... 2

4 System Requirements / Compatibility........................................................................... 3 4.1 Supported Mass Spectrometry Software ................................................................... 3 4.2 Supported Mass Spectrometers ................................................................................ 3 4.3 Supported Chromatography Instruments and Drivers ............................................... 3 4.4 Compatible Firmware ................................................................................................. 5 4.5 PC Requirements....................................................................................................... 5 4.6 Supported Operating Systems................................................................................... 5

4.6.1 Microsoft® Windows® XP................................................................................... 5 4.6.2 Microsoft® Windows® 2000™............................................................................ 6 4.6.3 Windows Security Updates................................................................................. 6

4.7 Miscellaneous Requirements..................................................................................... 6 4.7.1 Regional Settings................................................................................................ 6 4.7.2 PC Power Management...................................................................................... 7 4.7.3 Firewall Exemptions Needed in Windows XP SP2............................................. 7 4.7.4 Required MDAC Versions................................................................................... 7 4.7.5 Microsoft .NET Framework ................................................................................. 7 4.7.6 Microsoft MSXML................................................................................................ 7

5 Installation and Configuration ....................................................................................... 8 5.1 Analyst: Tray Type Support for Certain Autosamplers .............................................. 8 5.2 Installing DCMSLink..................................................................................................... 8

5.2.1 Upgrading from a Previous Version of DCMSLink ............................................... 8 5.2.2 First Installation of DCMSLink .............................................................................. 9 5.2.3 Chromeleon Installation Qualification (IQ) ........................................................ 10 5.2.4 Enabling Automatic Server Start....................................................................... 11

5.3 Hardware Installation ............................................................................................... 12 5.3.1 Connecting the WPS-3000 Autosampler to the Mass Spectrometer ............... 12 5.3.2 Connecting the FAMOS Autosampler to the Mass Spectrometer .................... 13 5.3.3 Connecting the ICS3000 System to the API2000 Mass Spectrometer ............ 13

5.4 Instrument Configuration in Analyst and DCMSLink ................................................. 14 5.4.1 DCMSLink: Device Configuration ....................................................................... 15 5.4.2 Analyst: Adding DCMSLink to the Hardware Profile .......................................... 19

5.5 WPS-3000 Autosampler Settings ............................................................................ 22 5.6 Before You Start Working ….................................................................................... 23


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1 Definitions Chromeleon (CM) Server: This is the portion of DCMSLink that handles the data acquisition and communication with the connected instruments. Timebase (TB): This is the DCMSLink terminology for an instrument system. A timebase is a complete set of modules that share the same system time.

2 Abbreviations The following abbreviations are used throughout this document. CM (6.80) CHROMELEON® (Release 6.80) IC Ion Chromatograph(y)

IQ Installation Qualification

LAN Local Area Network

MDAC Microsoft® Data Access Components

MS Mass Spectrometer

n.a. Not Applicable

ODBC Open Database Connectivity

OQ Operational Qualification

PDF Portable Document Format

PQ Performance Qualification

SP Service Pack

USB Universal Serial Bus


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3 Overview Dionex Chromatography Mass Spectrometry Link (DCMSLink) for Analyst provides an interface for controlling a wide range of Dionex chromatography instruments with the Analyst® software (from Applied Biosystems/MDS Sciex). DCMSLink is based on Chromeleon® technology, i.e., it installs and uses certain portions of the Dionex Chromeleon Chromatography Management System such as the Chromeleon Server, the Chromeleon Server Configuration, Control Panels, and the Program Editor. This guide describes how to install and configure DCMSLink with the Analyst software.

Tips: For a list of Dionex instruments that can be controlled from Analyst via DCMSLink, refer to page 3.

Before you install the software, read the Readme.html file that is available on the DCMSLink software CD. The file contains last-minute product information and updates this documentation.

The DCMSLink Online Help can be found in the start menu (All Programs > Dionex > DCMSLink > Documentation).


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4 System Requirements / Compatibility

4.1 Supported Mass Spectrometry Software

This release of DCMSLink is designed for and has been tested with specific versions and HotFixes of the Analyst software from Applied Biosystems/MDS Sciex (also referred to as "MS software" throughout this document) as described below.

Analyst 1.4.2 The installation of the following Analyst HotFixes is required: - Hotfixes to November 2006

Analyst QS 2.0 Analyst QS 2.0 is supported with some limitations (digital data acquisition is not supported). For details see the Release Notes.

Tip: Newer versions / Hotfixes may also be compatible with this version of DCMSLink, but this has to be tested by the customer. At a minimum an instrument run with data acquisition should be performed after the upgrade.

4.2 Supported Mass Spectrometers

The type of mass spectrometers that can be used with DCMSLink depends entirely on the MS software. Please refer to the documentation of the MS software.

4.3 Supported Chromatography Instruments and Drivers

DCMSLink facilitates the control of a wide range of Dionex chromatography instruments and drivers with Analyst. This release supports the following instruments/drivers (including all micro, biocompatible and thermostatted variants): UltiMate 3000 LPG-3300, LPG-3400, DGP-3600 (formerly LPG-3600),

HPG-3200, HPG-3400, and ISO-3100 pumps

FLM-3x00 flow managers and thermostatted column compartments

TCC-3x00 thermostatted column compartments

WPS-3000 and WPS-3000SL autosamplers

UVD-3000, VWD-3x00, and PDA-3000 detectors

Probot™ micro fraction collector


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UltiMate (Plus) UltiMate capillary/nano HPLC system (including pump and detector)

Switchos capillary/nano HPLC switching device

FAMOS capillary/nano HPLC autosampler

Summit P680 pump

TCC-100 thermostated column compartment

ASI-100 autosampler

UVD 170U and UVD 340U detectors

PDA-100 and PDA-100U detectors

RI-101 refraction index detector

RF2000 fluorescence detector

IC IP20, IP25, and IS25 isocratic pumps

GP40, GP50, GS50, ICS-3000 DP and ICS-3000 SP gradient pumps

AXP pump

EG40, EG50, and ICS-3000 EG eluent generators

AS50 and AS-3000 autosamplers

ED40, ED50, ED50A, and ICS-3000 ED electrochemical detectors

CD20, CD25, CD25A, and ICS-3000 CD conductivity detectors

AD20 and AD25 UV detectors

IC20, IC25, and IC25A IC systems

DX-120 IC system

ICS-90(A), ICS-1000, ICS-1500, ICS-2000, and ICS-3000 IC systems

ICS-3000 DC detector/chromatography module

UI20 universal interface

Miscellaneous External MSV Motorized Switching Valve

ELS 2100 detector

TSP AS3500 autosampler

Fraction Collection (Generic driver)

Integrator (Generic driver)

Remote Inject (Generic driver)

Virtual Channel Driver (Generic driver)


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4.4 Compatible Firmware

To ensure proper operation, Dionex IC instruments should be equipped with the most current firmware. A table of validated firmware versions is provided in the "IC Firmware Compatibility Matrix…" document in the "Additional Documents" folder on the distribution CD. If you have instruments with firmware versions older than those listed, please contact your local Dionex office for assistance. For other Dionex instruments, such as the Summit and UltiMate 3000 modules, the recommended firmware versions are included in DCMSLink. You can check the version and update the firmware from within CM Server Configuration. Details about new firmware versions are available in the Chromeleon Release Notes in the "Additional Documents" folder on the distribution CD.

Caution: During firmware download all operations on the computer should be stopped! Never switch off the module during the firmware update and reset process!

4.5 PC Requirements

The PC hardware that is needed for DCMSLink for Analyst is basically determined by the requirements of the Analyst software. For details, please refer to the Analyst documentation. In addition DCMSLink has the following requirements for the PC:

• USB port / PCI slot (for connecting Dionex chromatography devices see the documentation of the device to be connected)

• 2 GHz processor • 1024 MB RAM (total)

Tip: Dionex can only guarantee the correct operation of DCMSLink if both the above requirements and the hardware and software requirements of the Analyst software are met.

4.6 Supported Operating Systems

The operating systems that DCMSLink for Analyst supports depends on both the requirements of the Analyst software (including HotFixes) and the requirements of the Chromeleon components on which DCMSLink is based on. Below is the list of operating systems that fulfill all these requirements.

4.6.1 Microsoft® Windows® XP

The required version of Windows XP is SP2. (Windows XP and SP1 are not supported by the Analyst HotFixes to November 2006.)


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4.6.2 Microsoft® Windows® 2000™

The recommended version of Windows 2000 is SP4. Windows 2000 SP3 is still accepted, but the Chromeleon Setup and IQ will issue a Warning. DCMSLink will NOT install on SP2 or earlier versions of Windows 2000.

4.6.3 Windows Security Updates

For optimum security, Dionex recommends that you keep your systems up to date with the latest security updates. Security updates rarely affect correctly functioning programs or change the specified behavior of the system. Most security updates affect only the handling of invalid input to operating system routines, e.g. so-called buffer overflows. The risk that a security update affects the correct operation of DCMSLink is generally low. Since security updates should generally be installed as soon as possible to keep the "window of vulnerability" small, it would make no sense for the users to wait until Dionex performs an exhaustive formal validation, which tests various combinations of systems and procedures. Instead, we recommend that users test the security updates briefly in the context of their own installation and operating procedures. Dionex recommends the following test procedure at minimum: – Install the security update and DCMSLink on a test PC – Run Chromeleon IQ (as described in the Chromeleon online Help). – If desired, also perform further PQ tests according to your needs.

Tips: Dionex will not formally validate Windows security updates. Installation and testing of security updates is the user’s own responsibility.

Should you find any compatibility problem during testing a Windows Security Update, please contact your Dionex support and service center for support. Although we will make reasonable efforts to solve such problems, we can not guarantee compatibility with every security update.

4.7 Miscellaneous Requirements

4.7.1 Regional Settings

Caution: Make sure the decimal point (".") is used as a decimal symbol. Otherwise, operation may fail.

(If in doubt, open the Windows Control Panel and select Regional and Language Options. Click Customize… .On the Numbers tab page, verify that the decimal point is specified under Decimal symbol.)


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4.7.2 PC Power Management

Verify that the PC Power Management features are disabled in the BIOS. If they are enabled, problems may occur when controlling instruments.

4.7.3 Firewall Exemptions Needed in Windows XP SP2

The Dionex IP Utility is used to assign IP addresses to certain Dionex devices that are connected via LAN (P680, UVD 340U, and UVD 170U). With the Windows Firewall of WinXP SP2 enabled, the Chromeleon IP Utility does not operate properly unless it is added to the Windows Firewall Exemption List. Same is true for the Chromeleon Server. These services are automatically added to the List during installation. If required for some reason, these exemptions can easily be added by selecting <Unblock> in the message box displayed by Windows XP the first time they are launched.

4.7.4 Required MDAC Versions

DCMSLink requires specific database interfaces that are provided with the Microsoft Data Access Components (MDAC, part of the supported Windows versions). The validated versions are:

Operating System MDAC Version

Windows 2000 SP4 2.5 SP3

Windows XP SP2 2.8 SP1

Tip: The MDAC check for DCMSLink includes all MDAC versions from 2.5 (RTM - SP3), 2.6 (RTM - SP2), 2.7 (RTM - SP1) and MDAC 2.8 (RTM and SP1). Future MDAC versions may not be recognized correctly. If in doubt, check for the newest version of Microsoft's 'Component Checker' tool on the Microsoft homepage. A version of this tool is also available on the CD: Other Tools\ODBC\Component_Check.exe.

4.7.5 Microsoft .NET Framework

DCMSLink 2.0 requires the Microsoft .NET Framework, Version 2.0. The necessary files are automatically installed during the installation if not already present on the target computer. In this case the installation events are logged in a file called DotNetInstall20.log in the \DCMSLink\IQ folder. CM IQ checks whether .NET is properly installed. If not, an Error is issued.

4.7.6 Microsoft MSXML

DCMSLink 2.0 requires the Microsoft MSXML Version 4 SP2. The necessary files are automatically installed during the installation if not already present on the target computer. In this case the installation events are logged in a file called msxmlsetup.log in the \DCMSLink\IQ folder. CM IQ checks whether MSXML is properly installed. If not, an Error is issued.


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5 Installation and Configuration

5.1 Analyst: Tray Type Support for Certain Autosamplers

This applies for AS, AS50, WPS-3000 and TSP AS3500 autosamplers only! To enable control of certain autosampler tray types, you need to add the autosampler to the Analyst sampler database manually:

1. Close the Analyst window and stop the AnalystService.exe service. To do so, open the Windows Control Panel and select Administrative Tools -> Services. Right-click AnalystService and select Stop.

2. Copy the DionexTrayTypeSupport.adb file from the Additional Files folder on the software CD to the Analyst\bin folder on your computer (normally, the path is C:\Program Files\Analyst\ bin).

3. In the same folder (Analyst\bin), double click AutosamplerAddIn.exe.

4. Click Merge User Autosampler DB and double-click the DionexTrayTypeSupport.adb file.

5. Exit the Autosampler Add-in program. Either restart the AnalystService or reboot the PC.

5.2 Installing DCMSLink

Caution: Make sure that the person performing the installation has full local administrator privileges. Otherwise, the installation will fail or be incomplete. After reboot, the administrator running the setup must login again so that the installation process can be completed correctly.

5.2.1 Upgrading from a Previous Version of DCMSLink

Possible upgrade paths: - It is possible to install DCMSLink 2.0 on a PC running any former version of

DCMSLink. - To install DCMSLink 2.0 on a PC running a version of Chromeleon earlier than

6.70 SP1, you first need to upgrade to this or a higher version of Chromeleon. - DCMSLink 2.0 cannot be installed over Chromeleon 6.80 SP3 or higher.


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To install an update:

1. Check section 4 of this document to verify that all requirements are met. For example, you may have to upgrade your Analyst installation before you can proceed.

2. Stop all Chromeleon programs including the Server Monitor. Ensure that no Analyst and DCMSLink services are running Click Start -> Settings -> Control Panel -> Administrative Tools -> Services and stop the following services if necessary:

Analyst Service

Chromeleon Driver

Chromeleon Server

3. Install Dionex Chromatography Mass Spectrometry Link from the DCMSLink software CD:

The Master Setup starts automatically when you insert the software CD into the respective drive if CD Autostart is active on your PC. (If CD Autostart is not active, start autorun.exe from the Autorun folder.) To install DCMSLink, select Install DCMSLink X.X (with X.X = version number).

By default, the software is installed to the DCMSLink directory (C:\DCMSLink).

4. When asked, reboot the PC (again, with local Administrator privileges). The installation will be completed and an Installation Qualification report will be created, see section 5.2.3.

5.2.2 First Installation of DCMSLink

1. Check that all requirements in section 4 of this document are met, for example, ensure that Analyst 1.4.2 or Analyst 2.0 QS has already been installed.

2. Install Dionex Chromatography Mass Spectrometry Link from the DCMSLink software CD:

The Master Setup starts automatically when you insert the software CD into the respective drive if CD Autostart is active on your PC. (If CD Autostart is not active, start autorun.exe from the Autorun folder.) To install DCMSLink, select Install DCMSLink X.X (with X.X = version number).

By default, the software is installed to the DCMSLink directory (C:\DCMSLink).

Note: After DCMSLink is installed, the MS Software Integration license is automatically selected on the License page in the Server Configuration program.

3. When asked, reboot the PC (again, with local Administrator privileges). The installation will be completed and an Installation Qualification report will be created, see section 5.2.3.


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5.2.3 Chromeleon Installation Qualification (IQ)

At the end of the installation process, Chromeleon Installation Qualification (IQ) runs automatically, checking the current installation. A report is generated that can be read using the Windows Notepad or any other word processor. Current information about the installed files is compared with a reference list supplied by Dionex during the setup. If the information is identical, successful installation of the software is confirmed. When there are differences, a note, warning, or error message appears indicating the following: Note: No action is required. The file date is different. The note appears only

because the file was compared to the file in the list supplied with the setup. The difference should not impair DCMSLink functionality.

Warning: Usually, no action is required. If a problem occurs nevertheless, contact Dionex Service. A warning appears when the file size or the version differs from the expected size or version. For example, this may happen if newer versions of system files have been installed during the installation of other programs and if DCMSLink uses these files as well. It is unlikely that such an update impairs DCMSLink functionality. The warning appears to facilitate troubleshooting just in case a problem occurs.

Error: A vital file is missing. Please contact your Dionex representative.


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5.2.4 Enabling Automatic Server Start

To enhance performance, we recommend starting the Chromeleon Server every time the computer is started. To do so:

1. Start the Server Monitor in the DCMSLink program group (Start > All Programs > Dionex > DCMSLink).

2. Click the Config… button.

3. On the Server tab page, select the Start Server at System Start check box.

Note: The above dialog shows “Mass Spectrometry support is disabled”. This is normal, as it does not refer to the MS support provided by DCMSLink, but another type of MS support provided by Chromeleon.

4. Confirm the dialog with OK.

5. Start the Server using the Start button in the Server Monitor.

6. Close the Server Monitor.


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5.3 Hardware Installation

Connect all Dionex instruments via USB to your PC as described in the Operating Instructions of the instrument(s).

Note: Do not connect new Dionex instruments via USB to your PC until DCMSLink installation is finished, i.e., until the PC is rebooted and Chromeleon Installation Qualification (IQ) is completed and passed.

In order to start MS data acquisition, the MS start input must be connected to a relay output on one of your Dionex modules (e.g., the sampler or the pump). As the connections vary depending on the instruments, this chapter can only give a few examples. If your combination of instruments is not described in this chapter, please contact your Dionex representative.

5.3.1 Connecting the WPS-3000 Autosampler to the Mass Spectrometer

The accessories kit for the WPS-3000 includes a 6-pin Mini-DIN signal cable (P/N 6000.1004). Connect the AB/MDS Sciex Aux I/O cable (P/N 014474) and the Mini-DIN signal cable as shown to establish communication between the autosampler and the mass spectrometer.

• On the free end of the Aux I/O cable, short together wire 9 (red with black

stripe) and wire 10 (orange with black stripe). Isolate these wires (wrap with electrician’s tape) to prevent them from contacting any other wire or metal.

• Connect the AUX I/O wire 22 (white/black stripes) to the brown core of the Mini-DIN signal cable. Isolate these wires as well.

• Connect the AUX I/O wire 21 (green/black stripes) to the white core of the Mini-DIN signal cable and isolate the connection.

• Insert the Mini-DIN connector into the WPS-3000 Autosampler relay 4 connector.

• Insert the other end of the AUX I/O cable into the Mass Spectrometer AUX I/O connector.


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5.3.2 Connecting the FAMOS Autosampler to the Mass Spectrometer

Connect the AB/MDS Sciex Aux I/O cable (P/N 014474) as shown to establish communication between the autosampler and the mass spectrometer. Use a DB15 male (available at any electronics store that sells cables).

• On the free end of the Aux I/O cable, short together wire 9 (red with black stripe) and wire 10 (orange with black stripe). Isolate these wires (wrap with electrician’s tape) to prevent them from contacting any other wire or metal.

• Connect the AUX I/O wire 22 (white/black stripes) to pin 1 of the DB15 male. • Connect the AUX I/O wire 21 (green/black stripes) to pin 13 of the DB15

male connector. • Insert the DB15 male connector into the FAMOS Autosampler P2 connector. • Insert the other end of the AUX I/O cable into the Mass Spectrometer AUX

I/O connector.

5.3.3 Connecting the ICS3000 System to the API2000 Mass Spectrometer

Use the AB/MDS Sciex contract closure cable (ID 017971B) to establish the connection between the API 2000 (AUX I/O, rear, green and grey/black wires) and Relay_1 on the pump module.

• Short together the wires, orange with black stripes and red with black stripes. • Attach the green wire to pin 5 and the grey/black wire to pin 3 of the

connector to the AUX I/O. To activate Relay_1, include the Pump_Relay_1.Closed Duration = 2.00 command in the program.


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5.4 Instrument Configuration in Analyst and DCMSLink

After you have installed Analyst and DCMSLink, check that the mass spectrometer has been configured as described in the Analyst documentation.

Afterward, follow the description below to configure DCMSLink and activate the Hardware Profile in Analyst. DCMSLink will appear in the Analyst Navigation bar as a "Companion Software". During the configuration procedure, you may have to switch between the Analyst window and the DCMSLink window. There are several ways to make the DCMSLink window active on the screen:

• Double-click Dionex Chromatography MS Link on the Analyst navigation pane • Click the button on the Taskbar • Use Alt + Tab to switch between the two windows

Double-click Dionex Chromatography MS Link on the navigation pane, or click the button on the Taskbar.


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5.4.1 DCMSLink: Device Configuration

To control instruments by Analyst via DCMSLink, the corresponding drivers must be added to the Chromeleon Server Configuration:

1. Double-click Dionex Chromatography MS Link on the Analyst navigation pane to open DCMSLink.

2. Go to the Options tab page in DCMSLink. Click Device Configuration.

Tip: If you want to change something in the configuration at a later time, the Device Configuration button may be disabled. In this case, deactivate the Analyst Hardware Profile.


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3. In the Server Configuration window, right-click on the Server name and select Add Timebase.

When you choose a name for the timebase, remember that the name should be unique within the computer network (we recommend including the computer name e.g., choose UltiMate_on_<Computer Name>).


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4. Now you must add your Dionex devices to the timebase. Right-click the new timebase and select Add Device… to open the related dialog box.

5. Under Dionex, select DCMSLink and add the DCMSLink for Analyst driver to the timebase. This driver is required to link Analyst and Chromeleon.

6. In the Dionex DCMSLink for Analyst dialog, accept the default settings by

clicking OK.


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7. Add all the Dionex devices that you want to control in the same way. The image below shows how to add a WPS-3000 Autosampler:

Tips: Accept the default device and signal names on any of the configuration pages.

Do not add any devices that are not supported by DCMSLink. For a list of supported instruments, refer to page 3.

8. If you use a WPS-3000, ensure that Relay_4 is enabled in the autosampler configuration (on the Relays tab page).


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9. If you want to record UV signals or other digital data channels, make sure the channels you want to record are activated in the instrument configuration.

10. Click File and Save Installation, and then close the Server Configuration.

11. DCMSLink is closed. To continue, you must activate the Analyst Hardware Profile including DCMSLink (see next section).

5.4.2 Analyst: Adding DCMSLink to the Hardware Profile

To establish the link between Analyst and the previously installed Dionex instruments, DCMSLink must be added to the Analyst Hardware Profile:

1. On the Analyst navigation pane, double-click Hardware Configuration under Configure. The Hardware Configuration Editor dialog box opens.

2. Select the hardware profile with your MS and deactivate it, if necessary.

Tip: You may want to leave your current Hardware Profile (with a mass spectrometer only) intact and create a new one including both the mass spectrometer and the LC front end. In this example the default Hardware Profile will be modified.

3. Click Edit Profile to open the Edit Hardware Profile dialog box.

4. Click Add Device… to open the Available Devices dialog box.


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5. From the Device Type drop-down list, select Software Application and click OK.

6. Click Setup Device to open the Software Application Settings dialog box:

7. Select Dionex Chromatography MS Link from the Software applications list. In the Alias name field, type a name, e.g., DCMSLink. Click OK.

8. Click OK to close the Edit Hardware Profile dialog box and return to the Hardware Configuration Editor dialog box.


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9. Click Activate Profile (this will start DCMSLink). Close the Hardware Configuration Editor dialog box.

10. The Connect to Timebase dialog opens.

11. Click the Plus sign (+) beside the My Computer icon to display the items underneath. The configured timebase is listed if the Chromeleon Server is running.

12. Select a timebase and click OK to confirm your selection. DCMSLink is now connected to the selected timebase.


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5.5 WPS-3000 Autosampler Settings

Set up the WPS-3000 to output the inject response to relay 4:

1. On the Main tab page in DCMSLink, click Commands… to open the Commands dialog box.

2. Right-click into the command list and select Expert.

3. Double-click Sampler and select Relay4Enabled.

Tip: If you press the letter "R", the program will jump to the next command that starts with the letter "R". Press the letter a couple of times until you have found the Relay4Enabled command.

4. Select 10sec_InjectOut and click Execute

5. Close the dialog box.

The WPS will remember the setting even if it is disconnected from the power supply.


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5.6 Before You Start Working …

Caution: Before you start working, make sure the decimal point (".") is used as a decimal symbol. Otherwise, operation may fail.

(If in doubt, open the Windows Control Panel and select Regional and Language Options. Click Customize… .On the Numbers tab page, verify that the decimal point is specified under Decimal symbol.)

For information about how to start working with Analyst and DCMSLink, refer to the Quick Start Guide (Start > All Programs > Dionex > DCMSLink > Documentation > Quick Start Guide).