dcmslink 2.11 for xcalibur

DCMSLink 2.11 for Xcalibur Quick Start Guide

Switch between Xcalibur and DCMSLink windows using the Taskbar

Xcalibur Home Page

DCMSLink Panels for easy control of the Dionex front-end

Click here to see the DCMSLink Pane in the

Xcalibur Information View

Document version: 1.6

June 2011 © Dionex


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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 DCMSLink? .................................................................................................. 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 DCMSLink and Chromeleon ............................................................................ 8

3 How To… ........................................................................................................................... 9

3.1 Starting the Software ............................................................................................... 9

3.2 Equilibrating the System ....................................................................................... 12 3.2.1 Manual Equilibration/Operation – via Panels .............................................. 12 3.2.2 Manual Equilibration/Operation – via Control Commands ......................... 17 3.2.3 Semi-automatic Equilibration by Injecting Eluent ...................................... 18

3.3 Creating an Instrument Method .......................................................................... 19 3.3.1 Opening the Method Editor / Creating a new Instrument Method .............. 19 3.3.2 Creating the LC part of the Instrument Method (Program) ......................... 20 3.3.3 Creating the MS part of the Instrument Method .......................................... 22 3.3.4 Checking the Program and Saving the Instrument Method ......................... 22

3.4 Editing an Instrument Method ............................................................................. 24 3.4.1 Opening the LC part of an Instrument Method (Program) .......................... 24 3.4.2 Editing Specific Program Lines in Commands View .................................. 24 3.4.3 Editing Parameters for a Certain Device in Device Views .......................... 25 3.4.4 Replacing the Entire LC Method Part (Program) Using the Wizard ........... 26 3.4.5 Importing a Program from Chromeleon ...................................................... 27 3.4.6 Exporting a Program to Chromeleon ........................................................... 27 3.4.7 Checking the Program and Saving the Changes .......................................... 27

3.5 Creating / Editing “On”, “Off”, and “Standby” Programs ............................... 28

3.6 Creating / Editing a Sequence .............................................................................. 32 3.6.1 Creating a new Sequence ............................................................................. 32 3.6.2 Editing a Sequence ....................................................................................... 34

3.7 Running a Sequence or a Sample – The Acquisition Queue .............................. 35 3.7.1 Starting a Sequence or a Sample .................................................................. 35 3.7.2 The Acquisition Queue ................................................................................ 37 3.7.3 Deleting a Sample / Sequence from the Acquisition Queue ........................ 37 3.7.4 Stopping, Pausing, and Resuming the Acquisition Queue .......................... 37

3.8 Monitoring the Running Samples ........................................................................ 39 3.8.1 Monitoring Signals in the Xcalibur Real Time Plot View ........................... 39 3.8.2 Monitoring Selected System Properties in the DCMSLink Pane of the

Information View ......................................................................................... 40


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3.9 Initiating Standby / Shut Down ............................................................................ 42 3.9.1 Automatic Standby / Shut Down after a Run............................................... 42 3.9.2 Manually Initiating Standby / Shutdown ..................................................... 43

3.10 Viewing Chromatography Data – The Xcalibur Qual Browser ........................ 44 3.10.1 Opening a Raw Data File or a Sequence ..................................................... 44 3.10.2 Working with Cells, Views, and Ranges ..................................................... 45


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1 Abbreviations / Glossary Below is a list of abbreviations and terms that are used throughout the document and which may need explanation.

Abbreviation / Term Description

Acquisition Queue The Xcalibur Acquisition Queue is the list of the samples that has been submitted (waiting for) analysis. (Analogous with the Chromeleon Batch.)

Chromeleon (CM) Dionex Chromeleon Chromatography Management System – a fully featured chromatography data system.

DCMSLink is based on Chromeleon technology, i.e. it installs and uses certain portions of Chromeleon.

Chromeleon Server This is the portion of DCMSLink that handles the data acquisition and communication with the connected chromatography modules.

Chromeleon Xpress A limited version of Chromeleon that allows instrument control and monitoring via software Panel Tabsets.

DCMSLink Dionex Chromatography Mass Spectrometry Link – An interface software for controlling a wide range of Dionex chromatography instruments from various MS software, e.g. from Xcalibur.

Instrument Method A file that contains instrument commands. An Xcalibur Instrument Method for LC-MS (or IC-MS) contains an MS part (settings for the mass spectrometer) and an LC part (settings for the IC or LC front end – also referred to as Program)

MS Mass Spectrometry or Mass Spectrometer

Panel / Software Panel DCMSLink / 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.

Panel Tabset A collection of Panels that is suitable for a given combination of chromatography modules.

PDA Photo Diode Array (detector)

Program (PGM) A file that contains instrument commands – This is the DCMSLink terminology for the LC part of the Xcalibur Instrument Method.

Queue See Acquisition Queue.

Sequence A set of samples to be analyzed. Once a Sequence (or selected samples from it) is started, they are submitted to the Acquisition Queue.

Server Configuration This is the DCMSLink window where the Timebase (instrument system) can be configured. Similar to the Xcalibur Instrument Configuration application.

Timebase (TB) A complete set of chromatography modules that share the same system time. Analogous with the Xcalibur Configuration (created in Instrument Configuration.).

A Timebase must be created and configured during the installation of DCMSLink.


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2 Introduction

2.1 Scope

The Quick Start Guide gives an overview of what DCMSLink for Xcalibur is, and provides step-by-step instructions about how to control and acquire data from Dionex instruments via the Xcalibur™ software. This guide is designed to provide a quick reference for the basic operation.

Note: The screen captures and the step-by-step instructions in this guide were created using version 2.0 of DCMSLink and version 2.0.7 of the Xcalibur software. However, they are applicable, with small deviations, to current versions of DCMSLink and Xcalibur. For example, some windows have been renamed in Xcalibur 2.1.

Note: This guide provides some basic information about how to use the Xcalibur software with focus on controlling the LC (or IC) front-end. For using DCMSLink with Xcalibur efficiently and for controlling the MS, the user must be familiar with the operation of Xcalibur 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.


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2.2 Document Conventions

At various points throughout the manual, messages of particular importance are indicated by certain symbols:

Tip: 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 Description

Installation Guide - Describes all the requirements for installing DCMSLink (e.g. PC and operating system requirements)

- Lists the supported instruments - Gives step-by-step instructions for installing and configuring DCMSLink for

Xcalibur Troubleshooting Guide 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.

Release Notes Describes what is new in each DCMSLink for Xcalibur release Migration of Methods Describes how to modify instrument methods (Program scripts, PGM files)

that were created in Chromeleon before they can be used with DCMSLink for Xcalibur and vice versa

Online Help Provides general information and context sensitive help about the various options available in DCMSLink

Tip: After installing DCMSLink, the above resources and this Quick Start Guide 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 DCMSLink installation folder, i.e. in C:\DCMSLink. They are also available on the installation CD in the “Additional Documents” folder.)

Tip: For consulting, training, and implementation services, contact your local Dionex support and service center.


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2.4 What is DCMSLink?

Dionex Chromatography Mass Spectrometry Link (DCMSLink) for Xcalibur provides an interface for controlling a wide range of Dionex chromatography instruments (IC as well as LC modules) from the Xcalibur software (from Thermo Scientific). Fig. 1 shows a schematic view of the communication between the hardware and software components in an IC/LC-MS system controlled by Xcalibur via DCMSLink.

Xcalibur Software

Mass Spectrometer from Thermo

IC / LC systemfrom Dionex

Start signal cable

Control

Data

DCMSLink (LC Driver)Control

Data

MS Driver

Fig. 1: Communication between the hardware and software components in an LC-MS system controlled by

Xcalibur via DCMSLink. Xcalibur controls both the MS and the LC front end (via DCMSLink). The acquired data is stored in Xcalibur. The MS receives the start signal upon injection from the LC system via a cable.

The sections below provide a short overview of the features available in DCMSLink. Section 3 provides step-by-step instructions for using the features.

2.4.1 Instrument Control

When DCMSLink is installed (Xcalibur must be installed first), control of the connected Dionex instruments becomes possible from Xcalibur (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 two ways to do this:

♦ via Software Panels – this is the recommended way, as the Panels provide a comprehensive, yet easy to use 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)

• Automated control via Xcalibur Instrument Methods – this is the way to analyze a single sample or a sequence of samples (sections 3.3, 3.6-3.7).

Creation of the instrument control programs (i.e. the LC part of the Xcalibur Instrument Method) is supported by the DCMSLink Program Wizard. The control programs are stored inside the Xcalibur Instrument Method.


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2.4.2 Data Acquisition and Storage

Detector signals (including conductivity, UV absorbance, and 3D field from PDA detectors) and other channel data (such as pump pressure and column oven temperature) are digitally transferred to Xcalibur where they are stored.

A (temporary) copy of the data is stored inside a Chromeleon Datasource. DCMSLink generates three kinds of temporary data:

- Chromeleon sequences - saved under a local Datasource

- Chromeleon Audit Trail - also saved under the local Datasource

- DCMSLink daily log files - saved under "C:\DCMSLink\Logfiles\" folder

DCMSLink can automatically delete this temporary data after some time. The following choices are available:

- Older than 1 day: This option keeps the temporary files at minimum. However, troubleshooting is only possible for the current and the previous calendar day.

- Older than 30 days: This is the recommended choice. It allows trouble shooting for the last 30 days. The temporary files are then automatically deleted.

- Never (do not delete): Choose this option only if you use DCMSLink and Chromeleon in parallel. In this case, you will have to manually manage the samples/sequences in Chromeleon and delete superfluous Audit Trail and DCMSLink log files.

2.4.3 Data Processing and Reporting

Xcalibur is used for processing and reporting the data / results.

2.4.4 DCMSLink and Chromeleon

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 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 DCMSLink.


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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 Method, creating and running a Sequence and reviewing the chromatography data.

3.1 Starting the Software

Important: Xcalibur software, DCMSLink, the chromatography instruments and the mass spectrometer must be properly installed and configured first. In particular, DCMSLink must be added to the Xcalibur Instrument Configuration and the instrument drivers must be added to the Chromeleon Server Configuration.

Tip: The steps for installing and configuring DCMSLink and the chromatography instruments are described in the Installation Guide and the hardware manuals.

To start the Xcalibur software and DCMSLink:

1. Start the Xcalibur software, for example by choosing: Start > All Programs > (Thermo) Xcalibur > Xcalibur. Note that the Xcalibur window has two main areas as described in Fig. 2 and Fig. 3.

a. Use these tools to switch between views (Roadmap, Sequence Setup, Real Time Plot) in the right side of the “Home Page” window

b. The right side of the “Home Page” window showing the “Roadmap View”

Fig. 2: The Xcalibur Home Page window is divided into a left and a right area. (a.) The first three tools in the “View” toolbar is used to switch between the “Roadmap”, “Sequence Setup”, and “Real Time Plot” views.

(b) The right side currently shows the “Roadmap” view.


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a. Click on the “Information View” tool to display the corresponding view on the

left side of the “Home Page”

b. The left side of the “Home Page” window

showing the “Information View”

Fig. 3: The 4th tool in the “View” toolbar enables/disables the “Information View” on the left.

2. The DCMSLink Event Log window (Fig. 4a) may open automatically (depending on a setting in the Xcalibur Instrument Configuration). This window lists all the communication events between Xcalibur, DCMSLink, and the connected LC modules.

Fig. 4: DCMSLink starts automatically with Xcalibur.

a. You can close the DCMS

e

Link

Event Log window.The same information can b

displayed in the Link Panin the Xcalibur Information View.

b. Switch between Xcalibur and DCMSLink using the Windows Taskbar

c.

d


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Tip: You can keep the DCMSLink Event Log window closed as it is mainly used for troubleshooting. The same information can also be displayed in the DCMSLink Pane of the Xcalibur Information View (see Fig. 5). The same and additional communication details are also stored in daily log files in the DCMSLink installation directory, e.g. C:\DCMSLink\Logfiles.

3. Use the Windows Taskbar to switch between the Xcalibur and DCMSLink windows as needed, Fig. 4b.

4. To display the DCMSLink Pane in the Xcalibur Home Page, click on the “Dionex Chromatography MS Link” node in the “Information View” area, Fig. 5a.

5. The “Panels…” button in the DCMSLink Pane tab (Fig. 5c) opens a separate Panel Tabset window for direct control and monitoring the front-end, see section 3.2.1.

Tip: The Panels can also be opened before Xcalibur, using the “Chromeleon” shortcut icon on the desktop, Fig. 4d. Note that this only works if the “Start Server at System Start” option has been enabled as described in the Installation Guide.

Tip: The “Show Desktop” button (Fig. 4c) 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.

a. Click on “Dionex Chromatography MS Link” to display the DCMSLink pane

b. The DCMSLink Pane

c. Buttons to open the DCMSLink

Panels and Commands windows

Fig. 5: To show the DCMSLink Pane, click on the “Dionex Chromatography MS Link” node in the “Information

View” area. Buttons in the DCMSLink pane can be used to open the Panels and the Commands dialog.


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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/IC modules!

There are several ways of equilibrating the LC system

• Manually setting and monitoring the desired parameters. There are two options for 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 (see 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 (see section 3.2.2);

• Semi-automatic equilibration by injecting eluent (see section 3.2.3). For this, an Instrument Method (with LC part) and a Sequence must be created first.

Important: When DCMSLink is connected to the chromatography instruments, their (physical) control panels are disabled. Control the instruments via the software Panels or Device Commands provided by DCMSLink.

Important: Xcalibur offers the possibility to select a “Start Up Instrument Method” when a Sequence is submitted to the Acquisition Queue (see section 3.7). This option is NOT supported by DCMSLink (Fig. 31c).

3.2.1 Manual Equilibration/Operation – via Panels

DCMSLink provides easy to use Panel Tabsets (collection of software Panels) for direct interaction with the connected Dionex instruments, Fig. 6. The Panels allow easy monitoring of the system (e.g. to see the current UV signal, flow rate, background conductivity, and pressure) and provide easy means to control all the common instrument properties (e.g. flow on/off, purge, pressure limits, detector wavelength, EG concentration setpoint, suppressor current, etc.).

Tip: 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 Control Commands for direct control of the modules (section 3.2.2) - use the Status Window to monitor selected properties (section 3.8.2)

Basic Operation of the Panels:

1. To open the Chromeleon Xpress window with the Panel Tabset, do one of the following: - On the DCMSLink Pane (in the Xcalibur Information View) click on the Panels… button (Fig. 5c), or


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- Choose Start > All Programs > Dionex > DCMSLink > Chromeleon, or - Double-click on the “Chromeleon” icon on the Desktop.

2. A Panel Tabset opens in a maximized window, Fig. 6.

Tip: Panels are best viewed in a maximized window. This ensures that all the controls on the panels are visible.

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. 6: 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.

3. A dialog box may appear asking whether you want to take over the control of the Timebase. Answer Yes.

Tip: This is necessary, because the Xcalibur 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. Xcalibur 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. 6a. For IC systems, the corresponding button is called “Local Control – Take”, see Fig. 7a. It is possible to use the panels (i.e. for monitoring the front-end) during an ongoing data acquisition started from Xcalibur. 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. 8a.

5. Use the controls on the Panels to make the necessary settings, Fig. 6b.


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a. Should some controls became inactive for an IC system, press

“Take” (Local Control) on the Home Panel

Fig. 7: Home Panel of an IC system with the Take / Release Local Control buttons.

6. Advanced properties of the modules, such as Qualification data, can be reached via Sub-Panels, Fig. 8b and Fig. 9.

a. Click on the various tabs to switch between the corresponding Panels

b. Advanced properties of the modules can be reached via sub-panels

The module specific Panels (here the “Pump” panel) show more details and provide more

control for the corresponding device

Fig. 8: Module specific tabs provide further details

and provide access to sub-panels with advanced properties, see Fig. 9


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Fig. 9: 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. 10a.

2. Click on the Acq. On (Fig. 10b) button.

Tip: For some systems, the Home Panel or the Detector Panel contains “Monitor Baseline – On / Off” buttons for starting / stopping manual data acquisition.

Tip: 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. 10c.

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. 11.

5. When the system is equilibrated, stop the manual data acquisition. Click on the Acq. Off (Fig. 12a) or Monitor Baseline - Off button,. Make sure that the “Save to sequence” option is not selected (Fig. 12b), and acknowledge stopping the manual acquisition by clicking Yes, Fig. 12c.


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6. Once you are finished, use the Windows Taskbar to switch between the Chromeleon Xpress window (with the Panels) and Xcalibur.

Tip: You can close and re-open the Chromeleon Xpress window (with the Panels) at any time without adverse affects.

b. Click Acq. On to start a manual data acquisition for monitoring the baseline.

a. Select the detector tab.

c. Select the channels that you want to acquire then click OK.

Fig. 10: Starting a manual data acquisition for monitoring the baseline

Fig. 11: Selecting the channels to be displayed


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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. 12: Stopping the manual data acquisition

3.2.2 Manual Equilibration/Operation – via Control Commands

While Panels provide 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. 13. This way of manual operation is only recommended for advanced use, i.e. when advanced parameters are not available via Panels.

Manually equilibrating the system using Control Commands:

1. There are several ways to open the Commands dialog: - In a Panel, right-click and choose Command… from the context menu or - Press the F8 key on your keyboard when a Panel window is active. - On the DCMSLink Pane (in the Xcalibur Information View) click on the Command… button (Fig. 5c). (This option may not work, depending on Xcalibur version and windows user privileges.)

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. 13a.

Tip: 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.


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Tip: 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.

Tip: 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. 13b. (Some properties are read only, i.e. cannot be set.)

5. Click Execute to send the command to the instrument, Fig. 13c

Tip: Xcalibur 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.

6. Repeat steps 3-5 for each parameter you want to set. For example: MicroPump.Flow = 20 [µl/min], MicroPump.%B = 10.0 [%], UV_VIS_1.Wavelength = 254 [nm], DC_Suppressor1_CurrentSet=50[mA], EluentGenerator_EGC-1_Concentration=10[mM], etc.

7. Once you are ready click Close.

b. Enter the desired value

a. Select Module and Property

c. Click Execute

The Help text provides hints about the property

Fig. 13: Control Commands provide access to all the instrument properties in a compact dialog.

3.2.3 Semi-automatic Equilibration by Injecting Eluent

The system can also be equilibrated in a semi-automated fashion for running a certain Instrument Method. For this, the Method must be created first (section 3.3). Create or edit a Sequence (section 3.6) and, at the beginning, include lines referring to the desired Instrument Method. Place a vial with eluent to the referred autosampler position(s).


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3.3 Creating an Instrument Method

An Xcalibur instrument method (“Instrument Setup”) typically contains an MS part (settings for the mass spectrometer) and an LC part (settings for the LC / IC front end). This document focuses on the LC part of the Method. The MS part must be created / edited in the Xcalibur Instrument Setup, as usual. When a Dionex front-end is controlled, the LC part of the method is created / edited in an embedded method editor offered by DCMSLink. The DCMSLink terminology for the instrument method is “Program”; hence, the editor is referred to as the “DCMSLink Program Editor”.

Important: To acquire a data channel in Xcalibur, 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).

Besides ordinary Instrument Methods for analyzing samples (described is sections 3.3 and .3.4 below), Xcalibur offers the possibility of using dedicated “On”, “Off”, and “Standby” programs. The user can define which one of these is executed after a Sequence has been finished. These special programs must be edited separately, as described in section 3.5.

3.3.1 Opening the Method Editor / Creating a new Instrument Method 1. In Xcalibur, activate the Roadmap view, Fig. 14a.

2. Click Instrument Setup, Fig. 14b. This opens the instrument method editor with a new, empty Instrument Method, Fig. 15.

b. Click “Instrument Setup” to launch the instrument

method editora. Activate the

“Roadmap” view

Fig. 14: Starting the Xcalibur Instrument Method editor (“Instrument Setup”).


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3.3.2 Creating the LC part of the Instrument Method (Program) 1. Click on Dionex Chromatography in the left side of the Xcalibur method editor

(Instrument Setup) window, Fig. 15a. This opens the embedded DCMSLink instrument method (program) editor in the main part of the window.

2. Click Wizard in the DCMSLink Program Editor, Fig. 15b.

b. Click “Wizard…” to start the DCMSLink

Program Wizard

a. Ensure that

Dionex Chromatography

is selected

Fig. 15: Starting the DCMSLink Program Wizard.

3. The DCMSLink Program Wizard appears.

4. Go through the Wizard pages (Fig. 16) to generate the LC part of the Instrument Method. Make sure you select the channels that you want to acquire and store in Xcalibur. At the end, click “Finish”.

b. Select all the acquisition channels that you want to

store in Xcalibur

a. Go through the Wizard pages and enter the parameters as appropriate for your method

Fig. 16: A few examples of the Program Wizard pages


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5. The LC part of the Method appears in the DCMSLink Program Editor (embedded in the Xcalibur Instrument Setup window) in the so-called “Commands View” (Fig. 17a). 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 the “Device Views” (section 3.4.3) which are similar to the Wizard pages.)

6. Depending on your instrument configuration and application, there might be some commands that have to be added manually to the Program (instrument 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.

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 Instrument Methods, see sections 3.4.2 and 3.4.3.

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).

The MS data acquisition does not start

If a different sampler to the WPS-3000 is used (or the Relays of the WPS-3000 were configured differently compared to the Installation Guide) the Program must contain a command for sending the start signal.

If, for example, Relay_1 of the Pump is used for the synchronization, then insert lines like these (depending on the pump model): Pump_Relay_1.Closed Duration = 2.00 UM3PUMP_Relay1.On Duration = 2.00 after the Inject command. The Wizard inserts a remark about this at the proper position.


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3.3.3 Creating the MS part of the Instrument Method

This document focuses on the LC part of the Method. Create the MS part of the method in the Xcalibur Instrument Setup, as usual.

Tip: If the Instrument Configuration does not contain an MS, the LC or IC front-end can be operated alone via Xcalibur and DCMSLink.

3.3.4 Checking the Program and Saving the Instrument Method 1. Click on the Check button (Fig. 17b) to check the LC part of the method (Program) for

syntax and semantic (logical) errors.

2. DCMSLink reports any potential problem and provides a short explanation in the “Check Results” dialog (Fig. 17c.). The issues are categorized as Errors and Warnings according to their severity:

- Errors must be fixed, before the Program can be used. - Warnings can be acknowledged without fixing the cause.

Important: There are error conditions which cannot be detected at this early stage, only later, when the acquisition is about to start.

Tip: The Troubleshooting Guide provides hints about the most common error messages and problems.

Tip: Errors and warnings are written to the Error Log, which can be viewed in the Qual Browser, Fig. 41d. Method A

3. Take note of any issues and click OK, Fig. 17d.

Tip: You can copy the content of the “Check Results” window by using the context menu or by using standard Windows keyboard shortcuts, i.e. Ctrl + A (Select All), Ctrl + C (Copy). This can be useful for correcting the issues or when asking for support.

4. Correct the issues as/if necessary. For more information about editing existing Instrument Methods, see sections 3.4.2 and 3.4.3.

5. To save the Instrument Method (including the Program), click “Save” (Fig. 18b). Enter a suitable file name and a comment, Fig. 18c-d.


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a. The LC part of the

Method opens in

“Commands” view

b. Click “Check”

d. Note the problems and click

OK

c. DCMSLink reports possible problems with the Program

Fig. 17: Checking the LC part of the Instrument Method (Program)

a. Note, that the method is not

yet saved

b. Click “Save”

c. Enter a File name and click “Save”

d. Enter a Comment and click “OK”

Fig. 18: Saving the LC part of the Instrument Method (Program)


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3.4 Editing an Instrument Method

The DCMSLink Program Editor, which is integrated into the Xcalibur method editor (Instrument Setup), offers various means of editing the LC part of the instrument method. 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 DCMSLink method editor, are described in the following sections.

Tip: This document focuses on the LC part of the Method. Edit the MS part of the method in the Xcalibur Instrument Setup, as usual.

Tip: If the Instrument Configuration does not contain an MS, the LC or IC front-end can be operated alone via Xcalibur and DCMSLink.

3.4.1 Opening the LC part of an Instrument Method (Program) 1. In Xcalibur, activate the Roadmap view, Fig. 14a.

2. Click Instrument Setup, Fig. 14b. This opens the Xcalibur method editor.

3. Click File > Open… to open the method file you want to edit.

4. Click on Dionex Chromatography in the left side of the Xcalibur instrument method editor (Instrument Setup) window, Fig. 15a. This opens the embedded DCMSLink instrument method (Program) editor in the main part of the window.

5. The LC part of the Method opens in Commands view, i.e. as a chronological list of instrument commands, Fig. 19a.

3.4.2 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. 19b.

2. The “Commands” dialog opens with the selected property highlighted, Fig. 20a. The Help area of the dialog provides useful information, Fig. 20b.

3. Make the necessary changes (Fig. 20c) and click OK (Fig. 20d). This updates the program line and closes the Commands dialog.

Tip: To add a new line, position the cursor at the end of the previous line and press Enter.

Tip: The Commands view offers usual text editing possibilities (e.g. Copy and Paste) that are accessible from the context menu (Right-click).


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a. The method opens in

“Commands” view b. Right click in the line you

want to edit and choose “Command…” or press F8

Fig. 19: Single parameters can be easily edited in Commands view.

c. Enter the desired value

d. Click “OK”

b. The Help area provides hints about the

selected property

a. The “Commands” dialog opens with the selected command highlighted

Fig. 20: Using the Commands dialog

3.4.3 Editing Parameters for a Certain Device in Device Views

Compared to the Commands view (Fig. 19), Device views (Fig. 21) 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, Fig. 16.

1. Use the device buttons on the left side of the embedded DCMSLink Program Editor to select a device, such as the pump or the detector, Fig. 21a.

2. The view changes from Commands view (Fig. 19) to Device view, Fig. 21b.

3. Make the necessary changes, Fig. 21c.


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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.

a. Choose one of the Device Buttons

c. Edit the parameters as needed

b. The view changes to “Device view”:

In this only the parameters for the selected device are

displayed, as they were shown in the Wizard when the Method was generated

Fig. 21: Editing parameters for a certain module (the Pump in this example) in “Device views”

3.4.4 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, Fig. 22a.

2. A dialog warns you that the currently open Program will be overwritten. Acknowledge this by clicking “Yes”.

3. The DCMSLink Program Wizard opens and guides you through the Program generation, as it did during initial process (3.3.2).

ab

c

Fig. 22: Other options in the DCMSLink method editor


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3.4.5 Importing a Program from Chromeleon

This option (Fig. 22b) 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 DCMSLink. Note, that you must adjust the imported Programs before you can use them in DCMSLink. (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 Xcalibur – Migration of Methods document.

3.4.6 Exporting a Program to Chromeleon

This option (Fig. 22c) is useful if DCMSLink 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 Xcalibur – Migration of Methods document.

3.4.7 Checking the Program and Saving the Changes

Once you have finished editing the LC part of the method, you should check it for syntax and semantic (logical) errors as described in section 3.3.4.

To save the changes you made in the LC part of the method, save the Xcalibur Instrument Setup by choosing File > Save. (The LC part of the method is embedded into the Xcalibur Instrument Method).


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3.5 Creating / Editing “On”, “Off”, and “Standby” Programs

Once a Sequence is finished, Xcalibur puts the instruments into one of three states: “On”, “Off”, or “Standby”, based on the “After Sequence Set System…” setting in the Run Sequence dialog, Fig. 31d.

For the MS these states have the following effect:

• On: All power and flows are maintained at operational levels. This allows running another Sequence without waiting.

• Off: The Off state indicates that all power to the instrument, which can be controlled by Xcalibur software, is turned off. This includes power to all heaters and most subassemblies, but in some cases, this may not be all subassemblies. This option is primarily used prior to maintenance.

• Standby: Depending upon the instrument, this state turns gas and liquid flows off, but maintains heaters and other subsystems in an on state so that there is no warm-up time required when changing to the On state. This allows running another Sequence with only a short delay.

Important: The Off state does not guarantee that all voltages are turned off, nor does it indicate that all heated components are at room temperature. To perform maintenance on an instrument, refer to the Hardware Manual for your instrument.

Tip: The “After Sequence Set System…” options have the same effect as choosing Actions > Devices On / Devices Off / Devices Standby from the Xcalibur menu bar. You can use these to manually put the system into one of these states as described in section 3.9.2.

For the LC (or IC) front-end the corresponding special Programs (instrument methods) can be created according to the steps described below. Typically, these methods should do the following:

• On: Do nothing, i.e. keep the flow and the column/autosampler temperatures as they are, keep the detector lamps on.

• Off: Turn off the detector lamps, turn of column and autosampler thermostatting, and gradually decrease the flow to zero.

• Standby: Decrease the flow, keep the column/autosampler temperatures as they are or turn thermostatting off, keep the detector lamps on or turn them off, as desired.

Important: Before you create and use On / Off / Standby Programs, you should be familiar with the related recommendations for your MS and LC/IC modules.


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To edit a special Program

1. In Xcalibur, activate the Roadmap view, Fig. 14a.

2. Click Instrument Setup, Fig. 14b. This opens the Xcalibur method editor.

3. From the Dionex Chromatography MS Link menu choose “Edit Program for…” and select the desired option, Fig. 23a.

a. Use the “Dionex Chromatography MS Link”

menu to start editing a Program for “On”, “Off”, or “Standby”

Fig. 23: Creating / Editing special Programs for “On”, “Off”, and “Standby” I

4. The special Program opens in Commands view, Fig. 24a.

Important: Device views are disabled, as these special Programs must not be edited in Device views. Editing these special Programs in Device views would add commands (e.g. synchronization, injection, and data acquisition commands), which do not make sense in this context.

5. To add new lines, press the Enter key when the cursor is at the end of the previous line, Fig. 24b

a. The special Programs open in Commands

view.

Device views are disabled.

c. Use these buttons to Save / Cancel the special Program

d. Useful hints

b. To add new line(s) – Press “Enter”

To add/edit commands – Press “F8”

Fig. 24: Creating / Editing special Programs for “On”, “Off”, and “Standby” II

6. To add or edit commands, right-click and choose Command… or use the keyboard shortcut F8, Fig. 24b. This opens the Commands dialog, Fig. 20. For tips about the Commands dialog and about editing Programs in Commands view, see section 3.2.2 and 3.4.2, respectively.


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7. Add the necessary commands such as Lamp off, Suppressor current off, CR-TC off, set the Flow to a low value, set the Cartridge Concentration to 0.00 mM, etc.

8. Finish the program with an “End” command.

9. Click the special Save button in the DCMSLink Program Editor to save the changes you made to the special Program, Fig. 24c (the Save button and the File > Save menu item in the Xcalibur Instrument Setup are disabled).

If you do not want to save the changes press Cancel, Fig. 24c.

Example

Fig. 25 shows a typical “Off” Program. Note that programming a ramp (for gradually decreasing the flow) requires two set points with a time stamp and a flow value for each (e.g. at 0 min flow = 1 ml/min, at 5 min Flow = 0 ml/min).

Tip: For UltiMate 3000 systems, this requirement can be worked around and a “smart” “Off” and “Standby” Programs can be written without the need to specify the initial flow. Instead the “MaximumFlowRampDown” command can be used to specify the steepness of the ramp. An example shown in Fig. 26. If, for example, the current flow of the system is 1 ml/min, using MaximumFlowRampDown of 0.2 ml/min2 would result in a gradual decrease of the flow during 5 min.

Typical Program for turning the LC devices OFF

Fig. 25: A typical “Off” Program


31

Smart “Off” Program for decreasing the flow in UltiMate 3000 systems

Fig. 26: A smart “Off” Program for decreasing the flow in an UltiMate 3000 system


32

3.6 Creating / Editing a Sequence

An Xcalibur Sequence is a table that represents a list of samples to be analyzed. It contains the information necessary to identify and run the samples. Once the necessary information is entered, the Sequence (or selected samples from it) can be submitted to the Acquisition Queue to start the analysis, see section 3.7.

3.6.1 Creating a new Sequence 1. In Xcalibur, click Sequence View, Fig. 27a.

The view changes accordingly, Fig. 27b.

2. Choose File > New, or click on the New icon, Fig. 27c. The New Sequence Template dialog opens, Fig. 27d.

3. Enter general data, Fig. 27e: - The Base File Name will be automatically extended with a suffix to produce the File Name in the Sequence, Fig. 28b. Note, that spaces are not allowed in the file name. - Choose the Path where the data will be stored. - Choose an Instrument Method. (For more about creating an Instrument Method see section 3.3.) - Processing Method and Calibration File are only needed for quantitative analysis.

4. Enter sample data, Fig. 27f - Enter the Number of (different) Samples. - Indicate replicate injections using the Injections per Sample field. - Checking the Re-Use Vial Positions option will inject the replicate injections from the same vial. - You can indicate the Initial Vial Position. - The Base Sample ID will be extended with the Vial Position in the Sample ID, in the Sequence, Fig. 28c. - The Tray Type is currently NOT available for Dionex instruments.

5. Bracket Type, Calibration, and QC information (Fig. 27g) is only necessary for quantitative analysis.

6. Click OK when finished, Fig. 27h. A new Sequence table is now created according to your entries, Fig. 28.

7. Enter the Injection Volumes.

Tip: You can use the Fill Down tool to copy a value to several cells below: - Fill in the desired value in the topmost cell of the range; - Select the range where you want to copy including the cell with the new value at the top, Fig. 28e; - Click on the Fill Down tool, Fig. 28f; - The Fill Down dialog appears, Fig. 29 which allows you to copy the content in other columns simultaneously. Make your choice and click OK.

8. To Save the new Sequence, click on the corresponding tool, Fig. 28g. Enter a Comment and click OK, then enter a File name and click Save.


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f. Enter sample data

e. Enter general data (affecting all samples)

g. This information is only needed for

quantitative analysis

h.

a. Click “Sequence View”

c. Click “New”

b. The “Sequence

Setup” View is now displayed

d. The “New Sequence Template” dialog opens

Fig. 27: Creating a Sequence

e. Enter the Injection Volume and select the other cell where this

should be copied

a. The “Information View” is turned off

to gain space f. Click “Fill Down”

b. Xcalibur adds a consecutive suffix to the “Base File

Name” to create the “File Name”

c. Xcalibur adds the Vial Position to the “Base Sample ID”.

You can change the “Sample ID” as you like.

d. As a result of selecting “Re-Use Vial Positions”, duplicate

injections are assigned to the same vial.

g. Click “Save”

Fig. 28: Editing a Sequence


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Fig. 29: The Fill Down dialog

3.6.2 Editing a Sequence

Besides the Fill Down tool (see above), you can use the following usual tools in the Edit menu:

- Copy/Paste, - Insert/Delete Row.

In addition the following useful tools are available in the Change menu: - Transfer Row Info – copy data to rows with the same Sample ID or Position; - Column Arrangement – view / hide and rearrange the columns of the sample table; - User Labels – change the name of the five user definable columns such as Study and Company.


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3.7 Running a Sequence or a Sample – The Acquisition Queue

To start an analysis (to “run” samples) a Sequence must be created first, see section 3.6. The complete Sequence, or selected samples from it, can then be submitted to the Acquisition Queue. The Acquisition Queue is the list of the samples that are actually waiting for analysis. The status of the Queue can be monitored in the Acquisition Queue tab of the Information View.

Tip: You can add several Sequences to the Queue.

3.7.1 Starting a Sequence or a Sample 1. Turn on the Information View and select the Acquisition Queue tab, Fig. 30a.

The Queue (Fig. 32) will be shown here as soon as the analysis starts.

2. Select a sample (the selected sample is shown with blue font), Fig. 30b.

3. Click Run Sample to run the selected sample, or click Run Sequence to run the entire Sequence.

Tip: You can also select a continuous subset of the samples (e.g. rows 2-4) and run only these as a Sequence. The Run Sequence dialog will show, which samples were selected, Fig. 31e.

4. The Run Sequence dialog (Fig. 31) opens. Note the following:

♦ DCMSLink is normally the Start Instrument, Fig. 31a

♦ If the Start When Ready option is enabled (as in Fig. 31b – recommended), the analysis starts immediately (unless the Acquisition Queue is in paused state). If this option is disabled, the samples are placed to the Acquisition Queue, but the analysis only starts after pressing the Start Analysis button (Fig. 33d).

♦ Do NOT specify any Start Up or Shut Down methods, as these are NOT supported by DCMSLink (Fig. 31c). Specifying any of these methods will cause unwanted behavior.

♦ It is important to choose the correct After Sequence Set System option, Fig. 31d. Make sure, that you edited the corresponding special Program as described in section 3.5.

5. Check that the correct samples will be analyzed (Fig. 31e), then click OK.


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a. Turn the “Information View” on and select the

“Acquisition Queue” tab b. Select a single

sample, then click …… “Run Sample”, or …

… “Run Sequence”

You can also select a continuous range of samples and start them as a Sequence

The Queue will be displayed here, as

soon as the Sequence is started

Fig. 30: Starting a Run

b. “Start When Ready” should be enabled

a. DCMSLink should normally be the “Start

Instrument”

d. Choose the option that suits your needs

Make sure you have edited the corresponding special

Program in DCMSLink

c. “Start Up” and “Shut Down” Methods are NOT supported by

DCMSLink

e. Check that the correct samples will be analyzed

Fig. 31: The Xcalibur Run Sequence dialog


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3.7.2 The Acquisition Queue

The Queue (Fig. 32) appears in the Information View (Fig. 30a). - The currently running Sequence and sample are highlighted with green, Fig. 32a, - Samples that have already been analyzed are marked with blue and a cross, Fig. 32b

a. The currently running Sequence and sample are

marked with green

b. A Samples that has already been analyzed are

marked with blue and a cross

c. To delete a sample from the Queue, first select it (check-mark)

then pres the Delete key

d. Deleted samples are marked with a cross and

the text DELETED

Fig. 32: The Xcalibur Acquisition Queue with three Sequences

3.7.3 Deleting a Sample / Sequence from the Acquisition Queue

You can delete Sequences and samples from the Acquisition Queue, as long as the analysis of the given sample has not started:

1. Select the sample or the Sequence in the Acquisition Queue tab of the Information View (Fig. 32c)

2. Press the Delete key on the keyboard.

Deleted samples are marked with a cross and the text “DELETED”, Fig. 32d.

3.7.4 Stopping, Pausing, and Resuming the Acquisition Queue

Xcalibur offers the below described options to stop, pause, and resume the Acquisition Queue. You can reach the related commands using the tools shown in Fig. 33 or via the Actions menu.

b. “Stop Analysis” – immediately

a. “Pause Analysis” – after the current sample

d. “Start Analysis” c. “Resume Analysis”

Fig. 33: Options for stopping, pausing, and resuming the Acquisition Queue.


38

• Use the Pause Analysis tool (Fig. 33a) or the Actions > Pause Analysis menu to pause the Queue after finishing the currently running sample. Xcalibur completes the current sample, creates a raw file for it, and enters the paused state (see below).

• Use the Stop Analysis tool (Fig. 33b) or the Actions > Stop Analysis menu to immediately stop the analysis of the current sample and to pause the Queue. Xcalibur creates a raw file for the sample that contains the raw data acquired to the time of the Stop Analysis command. Xcalibur then enters the paused state (see below).

Tip: If you do not want to continue the analysis at all, then you must delete all the samples/Sequences from the Acquisition Queue, see section 3.7.3 above.

• The paused state of Xcalibur is indicated by: - the pressed Pause tool, Fig. 34, - a check mark to the left of the Pause Analysis command in the Actions menu (not shown), - the text PAUSED to the right of the “Sequence” in the Run Manager node on the Status tab of the Information View, Fig. 34. You can resume from the paused state by clicking on the pressed Pause tool (Fig. 33c) or choosing the Actions > Pause Analysis menu (which is marked with a check mark in paused state). Xcalibur then starts the next sample in the Acquisition Queue.

Important: If DCMSLink encounters a problem, e.g. due to an exceeded pressure limit or a missing vial, it will issue an error message and will put Xcalibur to paused state. After fixing the problem, you will have to resume the Acquisition Queue manually as described above.

Indicators of the paused state

Fig. 34: Xcalibur in paused state.

• The Start Analysis tool (Fig. 33d) or the Actions > Start Analysis menu starts the next run in the Acquisition Queue. They are only effective, when: - an MS Detector contact closure interface is configured, AND - the Start When Ready check box was NOT selected in the Start Options group box of the Run This Sample dialog box or the Run Sequence dialog box, AND - Xcalibur is in the Ready state.


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3.8 Monitoring the Running Samples

There are three ways of viewing detector signals (and other channel data, like temperature and pressure signals) from the running samples:

• Via DCMSLink Panels – this is the recommended way, if the focus is on the front-end signals and system parameters. To open the Panels, click on the “Panels” button in the DCMSLink Pane (Fig. 5), or double-click on the “Chromeleon” desktop shortcut icon. For more information about using the Panels, see section 3.2.1.

• Via the Xcalibur Real Time Plot View – use this method (see below in section 3.8.1), if viewing the MS signal is (also) important.

• Via the Qual Browser – data from the running sample can be opened in the Qual Browser (see section 3.10). This provides more control over the plots.

In addition, there is a possibility to monitor selected system parameters in the DCMSLink Pane in the Xcalibur Information View. This is described below in section 3.8.2.

3.8.1 Monitoring Signals in the Xcalibur Real Time Plot View 1. Click Real Time Plot View in the Xcalibur Home Page, Fig. 35a. The view changes and

shows the available detector signals for the ongoing data acquisition.

2. By default the view is Locked to the instruments (Fig. 35b), i.e. the plot is continuously updated, Fig. 30b.

3. Click the lock button to toggle between Locked and Unlocked mode, Fig. 35c. In Unlocked mode, you can use the menus and the buttons on the Toolbar to review the data, e.g. zoom in, normalize, etc.

Tip: The Real Time Plot View can become quite crowded, especially if you acquire many channels. You can double-click somewhere in a plot to enlarge that plot, Fig. 35d. To return to the original view, double-click in the enlarged plot.

Tip: Due to an interface limitation, all channel data are displayed as “UV” signals, including pressure and temperature channels, and signals from electrochemical detectors. Also the Real Time Plot is not able to display negative signals, these are recorded however.


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a. Click “Real Time Plot View” to see the data during an

ongoing acquisition

b. The view is “Locked” to the instrument, i.e. the plot is being continuously updated

d. Double-click somewhere in a plot to enlarge it

c. Click to toggle to “Unlocked” mode so that you can use the toolbar buttons

and menus to review the data

Fig. 35: Monitoring the ongoing data acquisition in the Xcalibur Real Time Plot View

3.8.2 Monitoring Selected System Properties in the DCMSLink Pane of the Information View

Most properties of the front-end system can be easily monitored via Panels (or sub-panels). In addition, there is an alternative method for monitoring selected system properties in the DCMSLink Pane in the Xcalibur Information View. This can be useful, if:

• You want to record the properties. The selected properties are logged with a 1 sec interval to the Xcalibur Status Log, Fig. 41c;

• You want to monitor a few, rarely used parameters (possibly scattered on various (sub)panels) in a compact view directly from Xcalibur.

• The Panels are not available (older instruments and rare combination of modules may not be (fully) supported by Panels);

Monitoring System Properties in the DCMSLink Pane of the Information View

1. If the DCMSLink Pane is not displayed in the Xcalibur Information View, see Fig. 5 for instructions.

2. On the Property Selection tab, select the properties that you want to monitor / record, Fig. 36a. Note, that the property selection cannot be changed (greyed out) while a sample is running.

Important: To avoid generating huge files and performance issues, do not select more than a few properties. Especially be careful not selecting all the properties for the entire system or a module.

Tip: The bottom area of the Property Selection tab shows a short description of the selected property, Fig. 36b.


41

3. Click on the Properties tab to see the status of the selected properties, Fig. 36c. (A predefined selection of parameters is included by default.)

a. On the “Property Selection” tab Select the (few) properties

that you want to display

c. The “Properties” tab shows now the status/values of the

selected properties

b. Hint about the selected property

Fig. 36: Monitoring system properties in the DCMSLink Pane of the Xcalibur Information View


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3.9 Initiating Standby / Shut Down

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/IC modules!

Tip: For instructions to stop the currently running samples, see section 3.7.4.

When you do not want to use the system for a while, you can put it to Standby mode or shut it down. This can be either done automatically (see section 3.9.1 below) or manually (see section 3.9.2 below). In both cases, you have to consider the procedure for the MS and the front-end modules.

3.9.1 Automatic Standby / Shut Down after a Run

There are two techniques that can be used to automatically put the system to standby mode or shut it down after finished analysis:

• Once a Sequence is finished, Xcalibur puts the instruments into one of three states: “On”, “Off”, or “Standby”, based on the “After Sequence Set System…” setting in the Run Sequence dialog, Fig. 31d. You can utilize this function to automatically put the system to standby mode or shut it down. Section 3.5 describes the effect of choosing these states on the MS and provides step-by-step instructions for creating dedicated Programs for the front-end. The advantage of this approach is its simplicity.

Important: The Run Sequence dialog also offers the possibility to select a “Shut Down Instrument Method”, Fig. 31c. However, this option is NOT supported by DCMSLink.

• Alternatively, or in combination with the above, you can create dedicated Instrument Methods for Standby / Shut Down and add a sample to the Queue that uses this Method. The advantage of this approach is flexibility. With this you can: - create more complex standby / shut down procedures, - create and save different procedures suitable after running different analysis methods.


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3.9.2 Manually Initiating Standby / Shutdown • The instruments can be put to standby state or shut down manually using the Actions >

Devices Standby / Devices Off menus, Fig. 37a. Section 3.5 describes the effect of choosing these states on the MS and provides step by step instructions for creating dedicated Programs for the front-end.

Tip: If you do not want the command to affect all the devices (e.g. both the MS and the front-end), you can right-click on the device (e.g. “Dionex Chromatography MS Link”) in the Status tab of the Information View and choose Turn Device On / Off / Standby, Fig. 37b.

a. The “Devices…” commands issued from the Actions menu

affect all devices

b. The corresponding commands issued by right-clicking on a specific device affect that device only.

(In this example only the Dionex front-end, but not the MS)

Fig. 37: Manually turning all or selected devices on, off, or standby

• In addition, the front-end can be manually set to standby / shut down using Panels, see section 3.2.1 or Control Commands, see section 3.2.2.

Important: When DCMSLink is connected to the chromatography instruments, their (physical) control panels are disabled. Control the instruments via the software Panels or Device Commands provided by DCMSLink.

Tip: It is recommended to allow a gradual depressurization of the column/system

over 5-10 min using a flow gradient.


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3.10 Viewing Chromatography Data – The Xcalibur Qual Browser

This section describes how to view the chromatography data that has been acquired via DCMSLink in Xcalibur.

Tip: Data from the currently running sample can also be viewed in the Qual Browser. Once a file is open, press the F5 key to refresh the screen content (or choose View > Refresh).

Data from the currently running samples can also be viewed in DCMSLink Panels (see section 3.2.1) and via the Xcalibur Real Time Plot View (see section 3.8.1).

3.10.1 Opening a Raw Data File or a Sequence 1. Activate the Roadmap View, Fig. 38a.

2. Click on Qual Browser, Fig. 38b to open the corresponding window.

3. Choose File > Open… or Open Sequence… the Open or the Open Sequence tool (Fig. 39a) to open single raw data files or Sequences, respectively. Browse to the file(s) you want to view.

4. If you opened a Sequence, the sample list appears in the Info Bar, Fig. 39c. Select the sample that you want to view, Fig. 39b. Use the Toggle Info Bar tool to hide the sample list to gain space, Fig. 39i.

b. Click “Qual Browser”

a. Activate the “Roadmap” view

Fig. 38: Opening the Xcalibur Qual Browser


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b. Select the sample

that you want to

view

d. The results are displayed in “Cells”

of a “table”

h. Tools for Modifying the size of single Cells

g. Tools for Adding / Removing cell Rows / Columns

a. Click to open a single file or a Sequence

e. Click to “pin” the Cell that you want to modify

f. Show Previous/Next and zooming tools

c. Info Bar

i. The “Toggle Info Bar” tool

Fig. 39: Opening samples / Sequences in the Qual Browser, and working with “cells”

3.10.2 Working with Cells, Views, and Ranges 1. The results (such as various channels, 3D (PDA) fields, spectra) are displayed in “Cells”

of a table grid, Fig. 39d.

2. To modify the content of a Cell, it must be selected (pinned) first: Click the pin in the top right corner of the Cell, Fig. 39e. The pin turns to green.

3. Use then the tools on the toolbar to zoom, modify the size of the Cell, etc, Fig. 39f-g.

4. The Cells show the data in various Views, such as Chromatogram, Spectrum, (3D) Map, Fig. 40a-c.

5. To change the View in a Cell, use the context menu, Fig. 40d.

a. Map

c. Spectrum

b. Chromatogram

d. Use the context menu

to change View

Fig. 40: Working with Views


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6. There are special Report Views available to display text data, such as Sample Information, Instrument Method, Status Log, and Error Log, Fig. 41a-d. Even these views are available via the context menu, Fig. 41e.

Tip: The Status Log is saved with the first UV channel. If you do not see it, right-click, choose View > Ranges… > Detector = UV. If no UV channel is present, only the very first entry in the log can be viewed.

a. Sample Information

c. Status Log

b. Instrument Method

d. Error Log

e. Use the context menu to select a Report View

Fig. 41: Report Views

7. For most Views a Range can be selected. Fig. 42 shows the Range selection for the Chromatogram view.

8. To change the Range, choose Ranges… from the context menu, Fig. 42a. The Chromatogram Ranges dialog opens.

a. Choose “Ranges” from the context menu

b. Select Detector

c. Select Plot type

Fig. 42: Defining Ranges


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9. Select the Detector that produced the data you want to view, Fig. 42b. (Note, that due to an interface limitation, all channel data are displayed as “UV” signals, including pressure and temperature channels, and signals from electrochemical detectors.)

10. Select the Plot type, Fig. 42c you want to see.

11. You can modify the content of a Cell interactively. Fig. 43 shows for example how to show a Spectrum that belongs to a certain time point in the PDA Map. First pin the Cell with the Spectrum, Fig. 43a. Then click in the PDA Map at the time that you want to show, Fig. 43b. You can use the same technique for example to show an enlarged area of a chromatogram in another Cell.

a. Pin the Cell to be modified

b. You can click/drag in another Cell to influence the

content of the Pinned Cell

Fig. 43: Modifying the content of the Pinned Cell by clicking in another Cell