DCMS Link 2.10 for Compass / HyStar

DCMS Link 2.10 for Compass / HyStar DCMS Link Panel (Chromeleon Xpress) Window Compass / HyStar Window DCMS Link Event Log Window Switch between the Windows using the Taskbar Document version: 1.4 March 2011 Dionex

Table of Contents 1 ABBREVIATIONS / GLOSSARY... 4 2 INTRODUCTION... 5 2.1 Scope... 5 2.2 Document Conventions... 6 2.3 Other Resources... 6 2.4 What is DCMS Link?... 7 2.4.1 Instrument Control... 7 2.4.2 Data Acquisition and Storage... 8 2.4.3 Data Processing and Reporting... 8 2.4.4 DCMS Link and Chromeleon... 8 3 HOW TO... 9 3.1 Starting the Software... 9 3.2 Equilibrating the System... 11 3.2.1 Manual Equilibration/Operation via Panels... 11 3.2.2 Manual Equilibration/Operation via Control Commands... 17 3.2.3 Manual Equilibration/Operation via the HyStar Instrument Status bar... 18 3.2.4 Semi-automatic Equilibration by Injecting Eluent... 18 3.3 Creating an Instrument Method... 19 3.3.1 Creating a New HyStar Method... 19 3.3.2 Creating the LC Control Part of the Method (Program)... 20 3.3.3 Autosampler Settings... 24 3.3.4 Adding MS Control and other Parts to the Method... 24 3.3.5 Saving the Method... 24 3.4 Editing an Instrument Method... 25 3.4.1 Opening a HyStar Method... 25 3.4.2 Opening the LC Control Part of the Method (Program)... 26 3.4.3 Editing Specific Program Lines in Commands View... 27 3.4.4 Editing Parameters for a Certain Device in Device Views... 28 3.4.5 Replacing the Entire LC Method Part (Program) Using the Wizard... 28 3.4.6 Importing a Program from Chromeleon... 29 3.4.7 Exporting a Program to Chromeleon... 29 3.4.8 Checking the Program... 29 3.4.9 Saving the Changes... 30 3.5 Creating / Editing a Standby or Shutdown Method... 31 3.6 Creating / Editing a Sample Table (Sequence)... 32 3.6.1 Creating a New Sample Table... 32 3.6.2 Editing the Sample Table... 33 3.6.3 Adding Samples / Copying Parameters... 34 3.6.4 Assigning a Different Method (or Method Part) to a Sample... 35 3.6.5 Saving the Changes / Starting an Acquisition Directly... 35 3.7 Starting, Monitoring, and Stopping an Acquisition (Analysis)... 36 3.7.1 Opening a Sample Table... 36 2

3.7.2 The HyStar Acquisition Module... 38 3.7.3 Starting the Acquisition (Analysis)... 39 3.7.4 Monitoring the Acquisition (Analysis)... 40 3.7.5 Stopping the Acquisition (Analysis)... 41 3.8 The Dionex Area of the Instrument Statusbar... 42 3.8.1 Meaning of the Background Color... 42 3.8.2 The DCMS Link Context Menu... 42 3.8.3 Using the Properties Window... 44 3.9 Viewing Recorded Chromatography Data... 45 3

1 Abbreviations / Glossary Below is a list of abbreviations and terms that are used throughout the document and which may need explanation. Abbreviation / Term Acquisition Module Chromeleon (CM) Chromeleon Server Chromeleon Xpress DCMS Link Method MS Panel / Software Panel Panel Tabset Program (PGM) PDA Sample Table Sequence Server Configuration Timebase (TB) Description This is the module of HyStar, where an analysis can be started and monitored. To start an Acquisition a Sample Table must be loaded. Dionex Chromeleon Chromatography Management System a full featured chromatography data system. DCMS Link is based on Chromeleon technology, i.e., it installs and uses certain portions of Chromeleon. This is the portion of DCMS Link that handles the data acquisition and communication with the connected chromatography modules. A limited version of Chromeleon that allows instrument control and monitoring via software Panel Tabsets. Dionex Chromatography Mass Spectrometry Link An interface software for controlling a wide range of Dionex chromatography instruments from various MS software, e.g. from Compass / HyStar. A HyStar Method has several Method Parts, such as LC control, Autosampler, and MS control. The LC Method Part contains the instrument commands for controlling the LC front-end. The corresponding terminology in DCMS Link / Chromeleon is Program (PGM). Mass Spectrometry or Mass Spectrometer DCMS Link / Chromeleon use this graphical user interface for direct control of instruments and monitoring the running sample. Not to be confused with the physical control panels on the instruments. A collection of Panels that is suitable for a given combination of chromatography modules. A file that contains instrument commands this is the DCMS Link terminology for the LC part of the HyStar Method. Photo Diode Array (detector) A set of samples to be analyzed. Sample Table is the term used in Compass / HyStar. Sequence is used both in HyStar and DCMS Link / Chromeleon. This is the DCMS Link / Chromeleon window where the Timebase (instrument system) can be configured. Also referred to as Device Configuration. Analogous with the Compass / HyStar Hardware Setup Module. This is the DCMS Link term for a set of chromatography modules that share the same system time. Often this means a complete LC system. A Timebase must be created and configured during the installation of DCMS Link. 4

2 Introduction 2.1 Scope The gives an overview of what DCMS Link for Compass / HyStar is, and provides step-by-step instructions about how to control and acquire data from Dionex instruments via the Compass / HyStar software. The guide is designed to provide quick reference for the basic operation. Note: Note: The screen captures and the step-by-step instructions in this guide were created using version 2.0 of DCMS Link and Compass 1.2 SR1 / HyStar 3.2.44. They are however applicable to current versions of DCMS Link and Compass 1.3 / HyStar 3.2 SR2. Small deviations are possible, nevertheless. This guide provides basic information about how to use the Compass / HyStar software with focus on controlling the LC front-end from Dionex. For using DCMS Link with Compass / HyStar efficiently and for controlling the MS, the user must be familiar with the operation of Compass / HyStar and the MS. The information contained in this guide is subject to change without notice and should not be construed as a commitment by Dionex. Dionex assumes no responsibility for any errors that may appear in this document. This document is believed to be complete and accurate at the time of publication. In no event shall Dionex be liable for incidental or consequential damages in connection with or arising from the use of this document. Dionex cannot be held liable for any damage, material or otherwise, resulting from inappropriate or improper use of the software. If there is any question regarding appropriate usage, contact Dionex before proceeding. CHROMELEON and UltiMate are registered trademarks of Dionex. All other trade or company names mentioned are subject to the copyright and the property and trademark rights of the respective companies. All rights reserved, including those for photomechanical reproduction and storage on electronic media. No part of this publication may be copied or distributed, transmitted, transcribed, stored in a retrieval system, or transmitted into any human or computer language, in any form or by any means, electronic, mechanical, magnetic, manual, or otherwise, or disclosed to third parties without the express written permission of Dionex. 5

2.2 Document Conventions At various points throughout the manual, messages of particular importance are indicated by certain symbols: Indicates general information, as well as information intended to optimize performance. Important: Indicates that failure to take note of the accompanying information could cause wrong results or may result in damage to the controlled instruments. 2.3 Other Resources The following documents provide further details about installing, configuring and using the software. Document Installation Guide Troubleshooting Guide Release Notes Migration of Methods Online Help Description - Describes all the requirements for installing DCMS Link (e.g. PC and operating system requirements). - Lists the supported instruments. - Gives step-by-step instructions for installing and configuring DCMS Link for HyStar. Provides reference information about: - Status indicators - Known issues and limitations - DOs and DON Ts for preventing problems Lists and provides remedies for: - Error messages - Typical problems Describes how to collect data for troubleshooting by Dionex. Describes what is new in this DCMS Link for Compass / HyStar release Describes how to modify instrument methods (Programs, PGM files), which were created in Chromeleon before they can be used with DCMS Link for HyStar and vice versa. Provides general information and context sensitive help about the various options available in DCMS Link. After installing DCMS Link, the above resources and this can be easily accessed at any time from the Start menu: Start > All Programs > Dionex > DCMSLink > Documentation. (The documents are installed in the Documentation folder in the DCMS Link installation folder, i.e. in C:\DCMSLink. They are also available on the installation CD in the Additional Documents folder.) For consulting, training, and implementation services, contact your local Dionex support and service center. 6

2.4 What is DCMS Link? Dionex Chromatography Mass Spectrometry Link (DCMS Link ) for Compass / HyStar provides an interface for controlling selected Dionex chromatography instruments from the Compass / HyStar software (from Bruker). Fig. 1 shows a schematic view of the communication between the hardware and software components in an LC-MS system controlled by HyStar via DCMS Link. Fig. 1: Communication between the hardware and software components in an LC-MS system controlled by HyStar via DCMS Link. HyStar controls both the MS and the LC front-end (via DCMS Link ). The acquired data is stored in HyStar. The MS receives the start signal upon injection from the LC system via software synchronization. No cable connection is needed. The sections below provide a short overview of the features available after installing DCMS Link. Section 3 provides step-by-step instructions for using the features. 2.4.1 Instrument Control When DCMS Link is installed (Compass / HyStar must be installed first), control of the connected Dionex instruments becomes possible from HyStar (see Installation Guide for the complete list of supported instruments). There are several ways of controlling the LC system: Direct (manual) control and monitoring this is useful for example during startup. There are three ways of this: via Software Panels this is the recommended way, as the Panels provide a comprehensive, yet easy to use user interface for monitoring and control of the LC modules (section 3.2.1) via Control Commands this provides access for every parameter of the LC modules in a compact dialog. Recommended for advanced use only (section 3.2.2) via the Dionex area of the Instrument Status bar and the DCMS Link Context Menu in the HyStar Acquisition Module these provide an overview and control possibility for the most important LC parameters (e.g. flow, gradient composition, lamp status) directly from HyStar (section 3.8) 7

Automated control via HyStar Methods this is the way of analyzing a single sample or a sequence of samples (sections 3.3-3.7). Creation of the instrument control programs (i.e. the LC part of the HyStar Method) is supported by the DCMS Link Program Wizard. The control programs are stored as the LC part of the HyStar Method. 2.4.2 Data Acquisition and Storage Detector signals (including UV absorbance, or 3D field from PDA detectors) and other channel data (such as pump pressure and column oven temperature) are digitally transferred to HyStar where they are stored. A (temporary) copy of the data is stored inside a Chromeleon Datasource. The user can decide to automatically purge this data after 1 day, 30 days or leave it there. 2.4.3 Data Processing and Reporting HyStar is used for processing and reporting the data / results. 2.4.4 DCMS Link and Chromeleon DCMS Link 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 tool, Control Panels, and the Program Editor. Installation qualification is also managed via Chromeleon tools. If the use of other Chromeleon features is desired, the corresponding Chromeleon licenses have to be purchased and applied. The Troubleshooting Guide contains hints about working with Chromeleon and DCMS Link. 8

3 How To The sections below provide step-by-step instructions on how to perform common tasks such as equilibrating the system, creating an instrument Program (i.e. the LC Method Part of a HyStar Method), creating a sequence (i.e. a HyStar Sample Table), and acquiring and reviewing the chromatography data. 3.1 Starting the Software Important: Compass / HyStar software, DCMS Link, the chromatography instruments, and the mass spectrometer must be properly installed and configured first. In particular, a Dionex System must be added to the HyStar Hardware Setup and the instrument drivers must be added to the Chromeleon Server Configuration. The Hardware Setup containing the Dionex System must be active. The steps for installing and configuring DCMS Link and the chromatography instruments are described in the Installation Guide and the hardware manuals. Important: If a mass spectrometer is used, it is recommended to start the respective control software prior to HyStar. Otherwise, HyStar launches the software and shuts it down on leaving the Acquisition Module. To start the Compass / HyStar software and DCMS Link : 1. Start the Compass / HyStar software using the shortcut icon on the Desktop (or by choosing: Start > All Programs > Bruker Daltonics > HyStar > HyStar). The Compass / HyStar window allows launching the different modules of the software, i.e. Hardware Setup, Method, Sample Table, Acquisition, and Processing (Fig. 2, Fig. 3a). 2. The DCMS Link Event Log may open automatically in a separate window, Fig. 3b. Other portions of DCMS Link (such as the Server Configuration and the Program Wizard) are opened automatically as needed during the work with HyStar. There is a setting in the DCMS Link Context Menu that determines whether the DCMS Link Event Log opens or not, see section 3.8.2. 3. Use the Chromeleon shortcut icon on the Desktop (or choose Start > All Programs > Dionex > DCMSLink > Chromeleon) to open the Chromeleon Xpress window, Fig. 3c. This window contains a Panel Tabset for direct control and monitoring the Dionex frontend (section 3.2.1). It is possible to open the Panel Tabset before starting HyStar. However, this works only, if the Start Server at System Start option had been enabled as described in the Installation Guide. The Panels can also be opened from the DCMS Link Context Menu (3.8.2) from the HyStar Acquisition Module. 9

4. Use the Windows Taskbar to switch between the applications, Fig. 3d. The Show Desktop button (Fig. 3e) in the Windows Quick Launch toolbar and the Windows logo key + D keyboard shortcut provide easy access to the Desktop icons in case several windows cover them. Launch the different modules of Compass / HyStar from here Fig. 2: The Compass / HyStar window is the starting point for launching the different software modules, i.e. Hardware Setup, Method, Sample Table, Acquisition, and Processing. c. DCMS Link Panel (Chromeleon Xpress) Window a. Compass / HyStar Window b. DCMSLink Event Log Window e d Fig. 3: DCMS Link Event Log (b) may open in a separate window as soon as Compass / HyStar (a) has been started. The Panel Tabset (Chromeleon Xpress) is best viewed as a maximized window (c). Click on the buttons in the Windows Taskbar (d) to switch between the windows. The Show Desktop button (e) in the Windows Quick Launch toolbar provides easy access to the Desktop in case several windows cover it. 10

3.2 Equilibrating the System Important: Before you start up your system, you should be familiar with the related recommendations for your MS and LC modules! There are several ways of equilibrating the LC system: Manually setting and monitoring the desired parameters There are three ways of this: via Chromeleon Software Panels this is the recommended way, as the Panels provide a comprehensive, yet easy to use user interface for monitoring and control of the LC modules (section 3.2.1) via Chromeleon Control Commands this provides access for every parameter of the LC modules in a compact dialog. Recommended only for advanced use, or when the required parameter is not available from the Panels (section 3.2.2) via the Dionex area of the Instrument Status bar and the DCMS Link Context Menu in the HyStar Acquisition Module (3.2.3) For this, a HyStar Method with LC part and a Sample Table must be created first. Semi-automatic equilibration by injecting eluent (section 3.2.4) For this, a HyStar Method with LC part and a Sample Table must be created first. Important: When DCMS Link is connected to the chromatography instruments, their (physical) control panels are disabled. Control the instruments via the software Panels or Device Commands provided by DCMS Link! 3.2.1 Manual Equilibration/Operation via Panels provides easy to use Panel Tabsets (collection of software Panels) for direct interaction with the connected Dionex instruments, Fig. 4. The Panels allow easy monitoring of the system (e.g. to see the current UV signal, flow rate and pressure) and provide easy means to control all the common instrument properties (e.g. flow on/off, purge, pressure limits, detector wavelength, etc.). DCMS Link The actual instrument configuration will determine which Panels and controls are included in the Panel Tabset. Older instruments and rare combination of modules may not be (fully) supported. In this case use: - the Control Commands (section 3.2.2), - the Dionex area of the Instrument Status bar and the DCMS Link Context Menu (section 3.8). 11

Basic Operation of the Panels: 1. Double-click the Chromeleon shortcut icon on the Desktop, or choose Start > All Programs > Dionex > DCMSLink > Chromeleon, or in the HyStar Acquisition Module, choose Panels from the DCMS Link Context Menu (section 3.8.2). 2. A Panel Tabset opens in a maximized window, Fig. 4. Panels are best viewed in a maximized window. This ensures that all the controls on the panels are visible. 3. A dialog box may appear asking whether you want to take over the control of the Timebase. Answer Yes. This is necessary, because the HyStar software has control over the Timebase most of the time. In order to perform manual actions through the Panels the control must be taken explicitly. HyStar may take the control back automatically, when it needs it. In this case, some controls on the panel become inactive (grayed out). To take the control back press the Take Control button on the Home Panel of UltiMate 3000 systems, Fig. 4a. It is possible to use the panels (i.e. for monitoring the front-end) during an ongoing data acquisition started from HyStar. However, it is not recommended to take the control and interfere with the ongoing run. 4. To access module specific properties use the tabs in the top row of the screen, Fig. 5a. 5. Use the controls on the Panels to make the necessary settings, Fig. 4b. 6. Advanced properties of the modules, such as Qualification data, can be reached via Sub- Panels, Fig. 5b and Fig. 6. 12

The Home tab provides an overview of the most important system properties a. Should some controls became inactive, press Take Control b. Use the various controls to set the desired parameters Fig. 4: Panels allow easy monitoring and control of the common parameters of the connected chromatography modules. The Home Panel provides an overview of the most important parameters. a. Click on the various tabs to switch between the corresponding Panels The module specific Panels (here the Pump panel) show more details and provide more control for the corresponding device b. Advanced properties of the modules can be reached via sub-panels Fig. 5: Module specific tabs provide further details and provide access to sub-panels with advanced properties, see Fig. 6 13

Fig. 6: Sub-Panels provide access to advanced properties of the modules, such as Wellness and Qualification details Viewing Detector Signals during Equilibration (Manual Data Acquisition): 1. To view the detector signals and other channels (like pressure and temperature data) during equilibration, you must start a manual data acquisition. To start, select the detector s panel (e.g. VWD or DAD), Fig. 7a. 2. Click on the Acq. On (Fig. 7b) or Monitor Baseline - On button. For some systems, the Home Panel or the Detector Panel contains Monitor Baseline On / Off buttons for starting / stopping manual data acquisition. If you do not have a detector in your front-end system and the Home Panel does not offer Monitor Baseline, you can use the Chromeleon Control Commands to start a manual data acquisition: Right-click in a Panel and select Command (or press F8 on the keyboard). In the Commands dialog expand the System node, select AcqOn / AcqOff and click Execute. 3. The Data Acquisition dialog opens. Select the channels that you want to acquire, (note, that not all of these are automatically displayed, see next step) then click OK, Fig. 7c. 4. The On-line Plot emerges on the screen with a predefined set of channels. To select which channels are displayed, double-click in the On-line Plot and use the Add / Remove buttons in the dialog that opens, Fig. 8. 5. When the system is equilibrated, stop the manual data acquisition. Click on the Acq. Off (Fig. 9a) or Monitor Baseline - Off button. Make sure that the Save to sequence option is not selected (Fig. 9b), and acknowledge stopping the manual acquisition by clicking Yes, Fig. 9c. 14

6. Once you are finished, use the Windows Taskbar to switch between the Chromeleon Xpress window (with the Panels) and Compass / HyStar. You can close and re-open the Chromeleon Xpress window (with the Panels) at any time without adverse affects. a. Select the detector tab. b. Click Acq. On to start a manual data acquisition for monitoring the baseline. c. Select the channels that you want to acquire then click OK. Fig. 7: Starting a manual data acquisition for monitoring the baseline Fig. 8: Selecting the channels to be displayed 15

a. Click Acq. Off when you have seen enough of the baseline. b. Deselect the Save to sequence option. c. Acknowledge stopping the manual acquisition. Fig. 9: Stopping the manual data acquisition 16

3.2.2 Manual Equilibration/Operation via Control Commands While Panels provide an easy to use interface for setting the most common instrument properties, Device Commands provide access for all the (numerous!) properties of the modules via a compact dialog, Fig. 10. This way of manual operation is only recommended for advanced use, i.e. when advanced parameters are not available via Panels. 1. There are two ways to open the Commands dialog: - In the HyStar Acquisition Module, choose Commands from the DCMS Link Context Menu (section 3.8.2) - In a Panel, right-click and choose Command from the context menu or press the F8 key on your keyboard. 2. The Commands dialog box opens allowing you to monitor and control all properties of your instruments. 3. In the selection area use the tree control to select the module and the property you want set or check, Fig. 10a. Right clicking in the selection area shows a context menu where Normal, Advanced, and Expert view modes can be selected. Normal mode displays only the frequently used properties, while Expert mode displays all the properties. To find a certain command quickly on the list you can press the starting letter of the command repeatedly on the keyboard. This will toggle through all the commands starting with that letter. The Help area of the dialog provides hints about each property. 4. To set the property enter the desired value or choose from the available values in the drop down list, Fig. 10b. (Some properties are read only, i.e. cannot be set.) 5. Click Execute to send the command to the instrument, Fig. 10c HyStar can take control over the Timebase while the Commands dialog is open and in this case, the commands are not executed. To resolve this situation just close the Commands dialog and open it again. b. Enter the desired value a. Select Module and Property The Help text provides hints about the property c. Click Execute Fig. 10: Control Commands provide access to all the instrument properties in a compact dialog. 17

6. Repeat steps 3-5 for each parameter you want to set. For example: MicroPump.Flow = 0.3 [µl/min], MicroPump.%B = 10.0 [%], UV_VIS_1.Wavelength = 214 [nm], etc. 7. Once you are ready click Close. 3.2.3 Manual Equilibration/Operation via the HyStar Instrument Status bar The advantage of using the Dionex area of the Instrument Status bar and the DCMS Link Context Menu (section 3.8) is that they provide an overview and control possibility for the most important LC parameters (e.g. flow, lamp status) directly from the HyStar Acquisition Module. However, for entering the Acquisition Module a HyStar Method (section 3.3) and a Sample Table (section 3.6) must exist. 3.2.4 Semi-automatic Equilibration by Injecting Eluent The system can also be equilibrated in a semi-automated fashion for running a certain Method. For this, the Method must be created first (section 3.3). Create or edit then a Sample Table (section 3.6) and, at the beginning, include lines referring to the desired Method and injecting eluent. 18

3.3 Creating an Instrument Method A HyStar instrument method ( Method ) has several Method Parts, such as LC control, Autosampler, and MS control. This document focuses on the LC part of the Method. The MS part must be created / edited in Compass MS control software, as usual. When a Dionex front-end is controlled, the LC Method Part is created / edited in a Method editor offered by DCMS Link. The DCMS Link terminology for the instrument method is Program or PGM. Important: To acquire a data channel in HyStar, the channel has to be enabled in the Chromeleon Server Configuration (see Installation Guide), and data acquisition of the channel has to be turned on (and off) in the LC part of the method (see further down). Important: The parameters for a 3D acquisition (such as minimum and maximum wavelength, reference wavelength and bandwidth) must not be changed during a Method. (However, it is possible to assign different Methods for different samples in the same Sample Table (Sequence)). Besides ordinary Methods for analyzing samples (see sub-sections below), it is possible to create special Methods for routine maintenance of the system, such as putting the system stand-by or shutting down. Editing these Methods requires some special considerations, as described in section 3.5. 3.3.1 Creating a New HyStar Method 1. In the Compass / HyStar window click Method and choose Method from the context menu that appears (Fig. 11). Click Method then choose Method from the menu Fig. 11: Creating a new HyStar Method - I. 2. In the Open Method dialog, enter a new name as Method name (Fig. 12a). Click Open (Fig. 12b). 19

3. In the dialog that appears, click Yes to confirm the creation of the new method file (Fig. 12c). 4. The HyStar Method Editor opens (Fig. 13). a. To create a new Method, enter a new name as Method name b. Click Open c. Confirm creation of the new Method Fig. 12: Creating a new HyStar Method - II. 3.3.2 Creating the LC Control Part of the Method (Program) 1. In the LC control part of the HyStar Method Editor click Edit (Fig. 13a) 2. In the following two dialogs, acknowledge adding an LC Method Part to the Method (Fig. 13b.-c.) a. Click Edit b. c. Confirm the two dialogs that appear Fig. 13: Editing the LC Method Part I. 20

3. The DCMS Link Method editor opens. Click on the Wizard button (Fig. 14a). 4. The DCMS Link Program Wizard appears. Go through the Wizard pages to generate the LC part of the instrument method (Fig. 14 shows a few of the Wizard pages). a. Click Wizard to open the DCMS Link Program Wizard b. Go through the Wizard pages and enter the parameters as appropriate for your method c. Select all the acquisition channels that you want to store in HyStar! Fig. 14: Editing the LC Method Part II. 5. Make sure you select all the channels that you want to acquire and store in HyStar, but not more (Fig. 14c). If you have a PDA detector and acquire the 3-D field, make sure that you also acquire at least the first UV channel (UV_VIS_1). This ensures that you can see a chromatogram in the Panels and in the HyStar Acquisition Module during the analysis. You cannot acquire temperature channels (such as the Column Compartment temperature) in HyStar. However, you can see temperature channels in the Panels during data acquisition. 6. At the end, click Finish. 7. The LC part of the Method appears in the DCMS Link Method editor in the so-called Commands View (Fig. 15a). In this view, all the instrument commands are displayed in the order of their execution. (Clicking on the Device Buttons on the left changes the view to Device Views (section 3.4.4) which are similar to the Wizard pages.) 8. Depending on your instrument configuration and application, there might be some commands that have to be added manually to the Method. In some cases, a message will notify you about this before the analysis starts. The table below shows the most common ones. To modify an existing line, make sure that the cursor is somewhere in the line and press the F8 key. 21

To add a new line, place the cursor at the end of the previous line, press the Enter key and then the F8 key. For more information about editing existing Methods, see the section 3.4. Message / Problem Cause / Scenario Line to be added or modified Can't use device 'Pump' as a source of the column pressure. Please check the property "SystemPressure" for a valid device name. A dual gradient pump is used and it is not obvious from where the SystemPressure should be taken for recording the correct pressure on the column chipcard(s) Type in the following line to the Program before the time stamp 0.000: SystemPressure = <device name> Replace <device name> with the name of the pump to be used, usually MicroPump, LoadingPump, PumpLeft, or PumpRight.(keep the double quotation marks) 9. Click on the Check button (Fig. 15b) to check the Program for syntax and semantic (logical) errors. DCMS Link reports any potential problem and provides a short explanation (Fig. 15c.-d.). Take note of any issues and correct them as/if necessary. Section 3.4.8 provides further details about checking the Program. 10. Once you are finished click Close (Fig. 15e). (The DCMS Link program file check runs again.) 11. The HyStar LC Method Part Editor opens with the LC Parameters tab being active (Fig. 16a). Note, that the Runtime is imported to HyStar (read only, Fig. 16c). Important: The overall Runtime of the Method must not be zero (this can be an issue, for example if you are creating a shutdown Program, section 3.5). If it is zero, press the Parameters button to return to the DCMS Link Method editor and change the Program so that it has a (short) runtime. Important: The LC-Timetable tab (Fig. 16b) is not in use when a Dionex frontend is controlled. The Parameters button (Fig. 16d) re-opens the DCMS Link Method editor. 12. Close the LC Method Part Editor and confirm saving the changes to the LC Method Part by answering Yes in the dialog that appears (Fig. 16e-f). Note that the file name for the Method and the LC Method Part are the same by default. 22

e. b. Click Check a. The LC part of the Method opens in Commands view c. DCMS Link reports possible problems with the Program d. Note the problems and click OK Fig. 15: Editing the LC Method Part III. a. The HyStar LC Method Part Editor opens with the LC Parameters tab being active b. Note that the LC Timetable tab is NOT used when a Dionex system is controlled c. The Runtime is imported to HyStar (read only) d. The Parameters button reopens the DCMS Link Method editor e. To save the changes click Close f. then click Yes Fig. 16: Editing the LC Method Part IV 23

3.3.3 Autosampler Settings In the HyStar Method Editor window, select Autosampler method: Standard (Fig. 17a). This tells HyStar, that the Injection Method from the LC Method Part is used. a. select Autosampler method Standard b. Save the changes c. then Close the HyStar Method Editor Fig. 17: Editing the LC Method Part V. 3.3.4 Adding MS Control and other Parts to the Method Add MS control and other parts to the Method as desired (not covered by this document). It can be useful to keep the LC Control and the MS Control Parts separated and use the sample table to specify the MS method (Fig. 29d). As the Method and LC Method Part have the same name, confusion could arise when the same LC method is used with different MS methods. If there is no MS in the system, make sure that the HyStar Hardware Configuration does not contain an MS and that the Method does not contain an MS Method Part. 3.3.5 Saving the Method Save the Method and Close the HyStar Method Editor (Fig. 17b-c). 24

3.4 Editing an Instrument Method This section describes how to open an existing Method and provides details about the editing options available in the DCMS Link Method editor. 3.4.1 Opening a HyStar Method 1. In the Compass / HyStar window click Method and choose Method from the context menu that appears (Fig. 18). 2. In the Open Method dialog, select the Method you want to open (Fig. 19a). Click Open (Fig. 19b). 3. The HyStar Method Editor opens (Fig. 20). Click Method then choose Method from the menu Fig. 18: Opening a HyStar Method - I. a. Select the Method that you want to edit b. then click Open Fig. 19: Opening a HyStar Method - II. 25

3.4.2 Opening the LC Control Part of the Method (Program) 1. In the LC control area of the HyStar Method Editor click Edit (Fig. 20a) 2. The HyStar LC Method Part Editor opens (Fig. 21) 3. Click Parameters (Fig. 21a). 4. The DCMS Link Method editor opens in Commands view i.e. as a chronological list of instrument commands (Fig. 22). a. Click Edit Fig. 20: Opening the LC Method Part I. a. Click Parameters Fig. 21: Opening the LC Method Part II. The DCMS Link Method editor offers various means of editing the Program. These include: Editing specific program lines in Commands view Editing parameters for a certain device in Device views Replacing the entire Program using the Wizard Importing a Program from Chromeleon These, and the other options available in the DCMS Link Method editor, are described in the following sections. 26

3.4.3 Editing Specific Program Lines in Commands View 1. Select the program line you want to edit by placing the cursor anywhere in the line. Right-click and choose Command from the context menu, or use the keyboard shortcut F8, Fig. 22b. 2. The Commands dialog opens with the selected property highlighted, Fig. 23a. The Help area of the dialog provides useful information, Fig. 23b. 3. Make the necessary changes (Fig. 23c) and click OK (Fig. 23d). This updates the program line and closes the Commands dialog. To add a new line, position the cursor at the end of the previous line and press Enter. The Commands view offers usual text editing possibilities (e.g. Copy and Paste) that are accessible from the context menu (Right-click). a. The Program opens in Commands view c. b. Right-click in the line you want to edit and choose Command or press the F8 key Fig. 22: Single parameters can be easily edited in Commands view. c. Enter the desired value a. The Commands dialog opens with the selected command highlighted d. Click OK b. The Help area provides hints about the selected property Fig. 23: Using the Commands dialog 27

3.4.4 Editing Parameters for a Certain Device in Device Views Compared to the Commands view (Fig. 22), Device views (Fig. 24) provide a different user interface: Instead of a chronological list of commands, only the parameters for the selected device are displayed as dialogs/tables on various tab pages. Device views are similar to the Wizard pages that were used for creating the Method, 3.3.1. 1. Use the device buttons on the left side of the Method / Program tab to select a device, such as the pump or the detector, Fig. 24a. 2. The view changes from Commands view to Device view, Fig. 24b. 3. Make the necessary changes, Fig. 24c. Important: Changing the timing for one device will NOT automatically change the timing for other devices. For example shortening the gradient will not automatically shorten the acquisition times. d. b. The view changes to Device view. In this view only the parameters for the selected device are displayed, as they were shown in the Wizard when the Method was generated. c. Edit the parameters as needed a. Choose one of the Device Buttons Fig. 24: Editing parameters for a certain module (the Pump in this example) in Device views 3.4.5 Replacing the Entire LC Method Part (Program) Using the Wizard Occasionally (e.g. if the instrument configuration has been changed considerably) it can be necessary to replace the currently stored LC Method Part (Program) with a completely new one. It is possible then to use the Wizard for this. 1. Click on the Wizard button 2. A dialog warns you that the currently open Program will be overwritten. Acknowledge this by clicking Yes. 3. The DCMS Link Program Wizard opens and guides you through the Program generation, as it did during initial process (3.3.1). 28

3.4.6 Importing a Program from Chromeleon This option is useful if Chromeleon has been previously used for controlling the LC front-end or there are Programs available that you want to use now with DCMS Link. Note, that you must adjust the imported Programs before you can use them in DCMS Link. (Synchronization commands must be added this can be triggered by switching to Device views and changing any parameter after the import). For more information, refer to the DCMSLink for HyStar Migration of Methods document. 3.4.7 Exporting a Program to Chromeleon This option is useful if DCMS Link has been previously used for controlling the LC front-end and there are Programs available that you want to use now with Chromeleon. Note, that you must adjust the exported programs (the synchronization commands have to be removed) before you can use them in Chromeleon. For more information, refer to the DCMSLink for HyStar Migration of Methods document. 3.4.8 Checking the Program 1. Once you have finished editing the Program you should check it for syntax and semantic (logical) errors. Use the Check button to initiate this. DCMS Link checks the Program for possible problems and reports them, including short explanations. The report has two parts. The results of the Chromeleon program file check are categorized as Errors and Warnings according to their severity: - Errors must be fixed, before the Method can be used. - Warnings can be acknowledged without fixing the cause. The HyStar limitation check is provided for information purposes only, normally no action has to be taken. The results are displayed in the DCMS Link Event Log (C:\DCMSLink\Logfiles\DCMSLink_for_HyStar_Dump_<YYYY-MM-DD>). Important: There are error conditions which cannot be detected at this early stage, only later, when the acquisition is about to start. The Troubleshooting Guide provides hints about the most common error messages and problems. The check is automatically performed upon closing the DCMS Link Method editor. 2. Take note of any issues and click OK. You can copy the Result of the program file check by using the standard Windows keyboard shortcut for copying, i.e. Ctrl + C, while the dialog is open. This can be useful for correcting the issues or when asking for support. 29

3. Correct the issues as/if necessary. For more information about editing existing Methods (Programs), see sections above. 3.4.9 Saving the Changes Once you have edited and checked the Program, follow the steps below to save the changes and return to the Compass / HyStar window. 1. Close the DCMS Link Method editor, (Fig. 22c and Fig. 24d), Acknowledge the Result of the program file check 2. Close the HyStar LC Method Part Editor, Answer Yes to save the changes to the LC Method Part 3. Close the HyStar Method Editor 30

3.5 Creating / Editing a Standby or Shutdown Method Important: Before you shut down your system or set it to standby, you should be familiar with the related recommendations for your MS and LC modules! At the start of an Acquisition (analysis), HyStar offers a few Shutdown Settings. These settings take effect at the end of the analysis sequence. The available options are for example: turning off the pump(s) and the detector lamp(s), Fig. 33. For a more sophisticated shutdown or standby process for the front-end (e.g. gradually cooling down the column compartment and decreasing the flow to zero or leaving the system under a low flow) you can generate a dedicated Method, and run this by assigning it to a blank injection (injecting eluent) at the end of the Sample Table (section 3.6). Important: The overall Runtime of the Method must not be zero. Therefore, make sure that the Program has at least a short runtime; 5-10 min is recommended to allow gradual depressurization of the column/system. Important: The LC part of a standby / shutdown Method usually needs customizations in Commands View. Some of these customizations may not be properly handled in Device Views. Therefore, you should not use the Device Views later for maintaining such a Program. You can prevent editing a Program in Device Views by entering the following comment as the first line of the Program: ;##DISABLE_DEVICE_VIEWS The change takes effect after saving, closing, and reopening the Program. Below are the major steps of generating a standby / shutdown Method: 1. Create a new HyStar Method (section 3.3.1). Create the LC part using the DCMS Link Program Wizard (section 3.3.2). 2. Remove any unwanted command lines (in Commands View). 3. Add the necessary extra commands such as Lamp off, etc (in Commands View). To enter a new line: - Press the Enter key. - Right-click and choose Command or use the keyboard shortcut F8 to open the Commands dialog. For tips about the Commands dialog and about editing Programs in Commands view, see sections 3.2.2 and 3.4.3, respectively. 4. Make sure, that the program ends with an End command. 5. Enter the following comment in the very first line of the Program: ;##DISABLE_DEVICE_VIEWS This prevents future editing of the Program in Device Views. 6. Save the changes (section 3.3.5). 7. To run the Program, assign the Method to a blank injection (injecting from a vial that contains the eluent) at the end of the Sample Table (section 3.6) 31

3.6 Creating / Editing a Sample Table (Sequence) A HyStar Sample Table represents a list of samples that can be analyzed as a sequence. HyStar has an editor for editing the Sample Table (Fig. 27). To start an analysis the Sample Table must be loaded to the HyStar Acquisition Module (section 3.7.2-3.7.3). 3.6.1 Creating a New Sample Table 1. In the Compass / HyStar window, click Sample Table (Fig. 25). 2. In the Open Sample Table dialog, enter a new file name (Fig. 26a). Click Open (Fig. 26b). 3. A dialog opens. Click Yes to confirm the creation of the new Sample Table (Fig. 26c). 4. Ignore the warning about Autosamlermethod by clicking Yes (Fig. 26d). 5. The HyStar Sample Table Editor opens with a single sample line. Note, that by default, it uses to the last edited Method (Fig. 27a). Click Sample Table Fig. 25: Creating a new Sample Table - I. a. To create a new Sample Table, enter a new file name b. Click Open c. Confirm creation of the new Sample Table Fig. 26: Creating a new Sample Table - II. d. Ignore this warning by answering Yes 32

3.6.2 Editing the Sample Table You must use the lower area of the HyStar Sample Table Editor to enter the sample properties, which in turn appear in the table, (Fig. 27b) 1. On the General tab of the editor enter the name (Sample Identifier) and the Vial Position of your sample (Fig. 27c-d). The Select in Tray button opens the Position selection dialog. This offers an easy alternative for entering the Vial Position (Fig. 27e). 2. Enter the injection volume on the General tab as needed (Fig. 27f). Important: HyStar will by default specify an injection volume of 5 µl, regardless of the size of the sample loop or the injection mode. 3. Enter other sample parameters on the General tab as needed. 4. To organize your results, specify the folder where the data should be stored (Fig. 27g). Important: The General tab offers the possibility to enter a Prerun time to equilibrate the system before injection. Avoid using Prerun time when operating HyStar with DCMS Link. Instead, include the necessary equilibration time in the Program. a. The Sample Table Editor opens with the last edited Method b. The values entered in the lower area of the editor are immediately reflected in the table c. d. Enter sample name and Vial Position f. Enter injection volume g. Specify path for the results e. The Select in Tray button opens a dialog as an easy alternative for entering the Vial Position Fig. 27: Editing a Sample Table 33

3.6.3 Adding Samples / Copying Parameters 1. From the menu choose: - Edit > Add New Samples -OR- - Edit > Add Samples from Tray, (Fig. 28a). 2. In the dialog that appears: - enter the number of samples you want to add -OR- - click on the vial positions where your samples are, (Fig. 28b). You can copy a sample parameter from one row to all the other rows: - Select (highlight) the parameter column(s) that you want to copy - Select the sample (if necessary edit the parameter) - Choose Edit > Apply to All. a. To add more samples, from the Edit menu choose Add New Samples - OR- Add Samples from Tray b. Click on the vial positions where your samples are -OR- Enter the number of samples you want to add Fig. 28: Adding samples to a Sample Table 34

3.6.4 Assigning a Different Method (or Method Part) to a Sample The Methods tab of the editor allows assigning a different Method (or Method Part) to a sample, (Fig. 29a) 1. Select the sample for which you want to change the assigned Method. 2. The following options are available: - Selecting a different Method, (Fig. 29b) - Editing the selected Method, (Fig. 29c) - Switching to a mode where individual Method Parts can be selected, (Fig. 29d). The last option provides flexibility in combining LC and MS Method Parts. See also section 3.3.4. a. Use the Method tab to assign a different Method or Method Part to a sample b. Click to select another Method c. Click to edit the selected Method d. Unselect to switch to a mode where individual Method Parts can be selected Fig. 29: Assigning a different method to a sample 3.6.5 Saving the Changes / Starting an Acquisition Directly To save the changes choose File > Save and confirm this by clicking Yes in the dialog that appears. You can now close the editor. If you directly want to start an acquisition with the newly created Sample Table, you can choose File > Save and Apply. or click on the corresponding icon on the toolbar. Note, that the acquisition will start with the row of the Sample Table that was highlighted. 35

3.7 Starting, Monitoring, and Stopping an Acquisition (Analysis) To start an analysis (an Acquisition ), the sample(s) must be first entered in a Sample Table (section 3.6). The Sample Table must then be loaded to the HyStar Acquisition Module. From here the analysis of a single sample or the entire sequence can be started. If a mass spectrometer is used, it is recommended to start the respective control software prior to HyStar. Otherwise, HyStar launches the software and shuts it down on leaving the Acquisition Module. 3.7.1 Opening a Sample Table 1. In the Compass / HyStar window click Acquisition and choose Acquisition from the context menu that appears (Fig. 30). The Select Sample Table and initial Sample dialog opens with the last edited Sample Table selected (Fig. 31a). Of course, you can select any another Sample Table, as long as it contains at least one sample that has not been analyzed yet. If you want to start an Acquisition directly with the last edited Sample Table, you can choose File > Save and Apply. or click on the corresponding Acquisition icon in the Sample Table Editor. Click Acquisition then choose Acquisition from the menu Fig. 30: Starting an Acquisition I 36

2. By default, HyStar starts the acquisition with the first non-processed and check-marked row of the Sample Table (Fig. 31b-d). However, you can select the sample to start with (Fig. 31e). 3. Click Open (Fig. 31f). Note, that the Start LC Pump after loading method option is ignored (Fig. 31g). Dionex recommends instead to start equilibrating the system earlier, as described in section 3.2). 4. The HyStar Acquisition Module opens (Fig. 32). When all the instruments are ready for an acquisition the background color of the Instrument Statusbar (Fig. 32c turns green. a. The last used Sample Table is selected by default, but you can select another one from the list b. This sample has already been analyzed c. and this one is unchecked d. so this sample would be started by default e. but you can select (highlight) another sample to start with g. This setting is ignored f. Click Open Fig. 31: Starting an Acquisition II 37

3.7.2 The HyStar Acquisition Module The HyStar Acquisition window has the following parts (beyond the usual Title bar - Fig. 32a, Menu bar - Fig. 32b, Tool bar - Fig. 32e, and Status bar - Fig. 32g) The Instrument Statusbar (Fig. 32c) shows the status of HyStar (the first block of the Instrument Statusbar, Fig. 32c1) and the connected instruments. When HyStar is used with DCMS Link, the Dionex area (Fig. 32c2) shows some of the key parameters of the connected Dionex instruments. (If an MS was connected, it had its own block.) The Instrument Statusbar is also used to control the hardware. This is done via context menus. For example, right-clicking in the Dionex area opens the DCMS Link context menu (described in section 3.8.2). Section 3.8 provides further details about the Instrument Statusbar, for example it explains the meaning of the background color. The Info Line (Fig. 32d) shows information about the sample being (or to be) analyzed. It can also be used to jump from the Acquisition Module to other HyStar modules: - Click the Sample Table button (Fig. 32d1) to edit the currently loaded Sample Table (only lines that are not yet processed can be edited). - Click the Edit button (Fig. 32d3) to edit the current Method - Click the Reload button (Fig. 32d2) to re-send the current method parameters to the instruments. This can help HyStar to become Ready. The Chromatogram / Spectrum Windows (Fig. 32f)show the acquired data a. Title bar b. Menu bar c. Instrument Statusbar c1. HyStar area c2. Dionex area d. Info Line d1 d2 d3 e. Toolbar h. Check that the correct sample is selected i. then click Start to start the Acquisition f. Chromatogram / Spectrum Windows g. Status bar Fig. 32: The HyStar Acquisition Module 38