Quick Start Guide

Quick Start Guide
Chromeleon 7
Thermo Scientific Dionex Chromeleon

Software Version 7.1 SR1
December 2011
Doc. No. 7829.0004, Rev. 2.1
Chromeleon 7
Quick Start Guide

Chromeleon 7
Table of Contents
Table of Contents i
1 Introduction 1
1.1 About this Document 1
1.2 Other Documentation 1
2 How To… 2
2.1 Configure Instruments 2
2.2 Start Chromeleon 2
2.3 Control Your Instrument 3
2.3.1 Connect Modules 3
2.3.2 Control Modules Directly 4
2.3.3 Start up Instrument using Smart Startup 6
2.3.4 Monitor an Ongoing Analysis 7
2.4 Create and Start a Sequence 8
2.4.1 Via eWorkflows 8
2.4.2 Without Using eWorkflows 10
2.5 Process Data 18
2.5.1 Review Chromatograms and Results 18
2.5.2 Adjust Peak Detection 22
2.5.3 Identify Peaks 30
2.5.4 Calibration 37
2.6 Review and Report Results 40
2.6.1 View Results Using Report Templates 40
2.6.2 Customize Report Templates 41
2.6.3 Print Results (Using Report Templates) 43
2.7 Save Changes 47
2.7.1 Save Changes per Object 47
2.7.2 Save All Changes at Once 48
Quick Start Guide Page i

Chromeleon 7
3 Appendix: Chromeleon Overview 49

3.1 Introduction 49
3.2 Instrument Controller Service 50
3.3 Chromeleon Client 51
3.3.1 Chromeleon Console 52
3.3.2 Chromatography Studio 59
Index 68
Page ii Quick Start Guide

Chromeleon 7
Copyright
Copyright © 2011 Thermo Fisher Scientific
The information contained in this document is subject to change without
notice.
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 Thermo Fisher Scientific Inc.
Trademarks
Windows, Windows Vista, SQL Server 2008, SQL Server, and Microsoft are
registered trademarks of Microsoft Corporation.
All other trademarks are property of Thermo Fisher Scientific Inc. and its
subsidiaries
Quick Start Guide Page iii

Chromeleon 7
1 Introduction
1.1 About this Document

The layout of this Quick Start Guide is designed to provide quick
reference to sections of interest. However, we recommend that you
review the Quick Start Guide thoroughly before working with
Chromeleon 7 in order to obtain full understanding of the software. A
general overview of Chromeleon 7.1 is provided in the appendix.
This Quick Start Guide is provided "as is". Every effort has been
made to supply complete and accurate information and all technical
specifications and programs have been developed with the utmost
care. However, Dionex assumes no responsibility and cannot be held
liable for any errors, omissions, damage, or loss that might result
from any use of this manual or the information contained therein. We
appreciate your help in eliminating any errors that may appear in this
document.
At various points throughout this document messages of particular
importance are indicated by the following symbols:
Note: Indicates general information that points out specific items

of interest.
Caution: Indicates areas where operations should be

performed carefully.
1.2 Other Documentation

Chromeleon is provided with other documents that will help you to
learn more about the software. Their scope is described in the
Document Overview, which is delivered in printed form with the
Chromeleon installation media, but also available in electronic form
on the installation disk in the Documents folder.
Quick Start Guide Page 1

Chromeleon 7
2 How To…
2.1 Configure Instruments

The Installation Guide contains instructions to:
• Start the Chromeleon Instrument Controller Service.
• Install and configure instruments.
Please refer to this document for further information.
2.2 Start Chromeleon

There are several ways to start the Chromeleon Client. Below are the
two most common ones:
• Double click the Chromeleon 7 icon on the desktop:
• Use the Windows Start menu:
Select Start, All Programs, Chromeleon 7, Chromeleon 7

The Chromeleon Console window opens. If user management is
active, you will be prompted to log in to the software; enter the
credentials provided by your Chromeleon adminstrator to gain
access to Chromeleon.
Page 2 Quick Start Guide

Chromeleon 7
2.3 Control Your Instrument

Connecting and controlling chromatography instruments is done via
the Instruments category of the Console, using the ePanel tabs in the
Work Area (Figure 72B).
2.3.1 Connect Modules

Before you can control an instrument, communication must first be
established between the Modules and the Chromeleon Instrument
Controller. This is referred to as “Connecting the Modules”.
To connect the chromatography modules, follow these steps:
1. In the Console, choose the Instruments category and click
your instrument’s name in the Navigation Pane.
2. Select the ePanel tab for the required module in the Work
Area.
3. On the ePanel, click Connect (Figure 1A).
Figure 1: Connect your Instrument

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Note: The ePanel sets are generated automatically, based on

ePanel selector files. These files are created to support modules
from a specific instrument series (e.g., UltiMate 3000, ICS-5000).
When combining modules from these instruments, ePanels for
some modules may not be displayed automatically.
To manually add ePanels to a set, follow these steps:

1. Right-click any of the present ePanel tabs. Click Add
ePanels (Figure 2).
Figure 2: Add ePanels

2. Select the required ePanel from the list (Figure 3). Click Add.
Figure 3: Selecting ePanel
2.3.2 Control Modules Directly

Usually, samples are analyzed as part of a sequence using a
predefined set of instrument commands stored in an Instrument

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Method. Sometimes (typically between sequence runs) it is

necessary to issue individual commands to the instrument modules,
such as for starting or stopping the flow, setting eluent composition,
switching on or off the detector lamp, or monitoring the baseline. This
is referred to as Direct Control of the instruments.
To control modules directly, follow these steps:
your instrument’s name in the Navigation Pane (Figure 4A).
2. Select the ePanel tab for the required module in the Work
Area (Figure 4B).
3. Use the controls (buttons, sliders, check boxes, and so forth)

on the ePanel to issue instrument commands (Figure 4C).
4. To monitor the detector signals without starting a Sequence,

click Monitor Baseline on the Instrument Toolbar. Click the
same button again to stop monitoring the baseline (Figure
4D).
B D
A C
Figure 4: Control Modules via ePanel

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Note: Most common commands are available from the ePanels. If

you need to execute a command that is not available there, you
can access all available instrument commands from a dialog that
is accessible via the commands button ( ) in the
Instruments toolbar.
2.3.3 Start up Instrument using Smart Startup

Before starting an analysis, the Instrument must be properly started
up and equilibrated. For many Dionex instruments, the steps involved
in this process can be performed automatically, using Smart Startup.
Note: The settings used during an Instruments Smart Startup are

automatically extracted from the instrument method. If changes
are required, they can be made in the Startup / Shutdown section
of the instrument method in the Chromatography Studio.
To startup an Instrument using SmartStartup, follow these steps:

your instrument’s name in the Navigation Pane (Figure 5A).
2. Click Smart Startup on the Instruments toolbar (Figure 5B).
a. Click using Queue Settings when the sequence to run

is already added to the queue (Figure 5C).
b. Click using Instrument Method when you want to

manually select a specific instrument method (Figure
5D).

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B C
Figure 5: Start up instrument

3. Follow the instructions that appear in the message bar and
click OK to close the message bar (Figure 6).
Figure 6: Message bar
2.3.4 Monitor an Ongoing Analysis

When an analysis is running, it is useful to monitor the signal
(chromatogram(s)) and other instrument parameters (such as
pressure and temperature). This is referred to as monitoring the
instrument or monitoring the analysis.

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To monitor the ongoing analysis, follow these steps:

your instrument’s name in the Navigation Pane.
2. Select the ePanel for the detector in the Work Area.
3. See the chromatogram evolving on the screen.
Note: The settings of all other modules can be monitored on their

respective ePanels.
2.4 Create and Start a Sequence

2.4.1 Via eWorkflows
An eWorkflow is an easy-to-use but powerful tool for creating well-
defined sequences based on pre-defined templates and rules.
Note: If no eWorkflows are available in the eWorkflows category,

contact your laboratory manager, create a new one, or follow the
steps in section 2.4.2.
To create and start a sequence via an eWorkflow, follow these steps:

1. In the Console, choose the eWorkflows category and select
the required eWorkflow from the Navigation Pane (Figure
7A).
2. In the Work Area, select the instrument on which you want to

run the eWorkflow (Figure 7B).
3. Click Launch (Figure 7C).

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A
B
Figure 7: Start run via eWorkflows
4. Fill in the number of samples you want to analyze and the

start position in the autosampler rack and click Next.
5. If necessary, fill in a sequence name and the sequence

location, then click Finish.
The sequence is now created (Figure 8).

6. If necessary, change the injection names (Figure 8A).
Figure 8: Sequence created via eWorkflow: Step 7

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Tip: If no modifications to the sequence are required, you can

immediately start the sequence by selecting the Run sequence
after creation check box ( ).
7. Click Start to start the sequence (Figure 8B). The sequence

is added to the Queue. If the Queue is not running, it is
started automatically (Figure 9).
Tip: It is also possible to start the sequence with Smart Startup, or

to run only Smart Startup, using the split button.
Figure 9: Running Sequence

For instructions on how to monitor the analysis, please refer to
section 2.3.3.
Note: If no methods are defined in the eWorkflow, you will be

asked to browse for an existing method or to create one via the
wizards (directly accessible via the eWorkflows wizard).
2.4.2 Without Using eWorkflows

If a suitable eWorkflow is not available, you can create a sequence
using the Sequence Wizard. To do so, the following files must first be
prepared:
• Instrument Method
• Processing Method
• Report Template
To create a new file, use the Create menu in the Console. Clicking
Create (Figure 10A) expands the complete menu.

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Figure 10: Create Options
2.4.2.1 C reate an Ins trument Method

1. In the Console, on the Create menu, click Instrument
Method (Figure 10).
2. If you have multiple instruments, select the instrument for

which you want to create the Instrument Method (Figure 11)
and click Next.
Figure 11: Instrument Method Wizard, Select Instrument

3. Complete all wizard steps.
4. On the last wizard page, complete additional details and click

Finish (Figure 12).

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Figure 12: Instrument Method Wizard, Complete Details

The created Instrument Method opens in the Chromatography
Studio.
5. Review the Instrument Method by selecting the module views
in the navigation pane (Figure 13A). Edit settings, if
appropriate.
6. Save the Instrument Method using the Save icon in the Quick
Access Toolbar (Figure 13B).
Figure 13: Reviewing the Instrument Method

7. Select a location and enter an object name (Figure 14). Close
the Chromatography Studio.

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Figure 14: Instrument Method Wizard, Save File
The instrument method is now created.
2.4.2.2 C reate a P roc es s ing Method

1. In the Console, on theCreate menu, click Processing
Method (Figure 10).
2. Select one of the predefined layouts and click Next (Figure

15).
Figure 15: Processing Method Wizard, Select layout
3. Enter a name, select a file location and optionally enter a

comment (Figure 16).

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Figure 16: Processing Method Wizard, Save File

The processing method is now created. Steps to update the contents
of the processing method are described in section 2.5.
2.4.2.3 C reate a R eport T emplate

1. In the Console, on theCreate menu, click Report Template
(Figure 10).
2. Select one of the predefined templates and click Next (Figure

17).
Figure 17: Report Template Wizard, Select Template

3. Select a file location and enter a file name (Figure 18).
Figure 18: Report Template Wizard, Save File

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The report template is now created. For instructions on how to use

the report template, please refer to section 2.6.2.
2.4.2.4 C reate a S equenc e via the W izard

1. In the Console, on the Create menu, click Sequence (Figure
10).
2. If you have multiple instruments, select the instrument for

which you want to create the sequence (Figure 19) and click
Next.
Figure 19: Sequence Wizard, Select Instrument

3. Complete the fields for the injections and click Next (Figure
20).
Note: When you are creating a sequence using the wizard, you
can only add injections with type Unknown. Once the sequence is
created, you can modify the Injection Types (see 7).

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Figure 20: Sequence Wizard, Unknown Injections
4. Select methods and reporting preferences and click Next

(Figure 21).
Figure 21: Sequence Wizard, Select Files
5. Enter a comment for the sequence (optional) and click

Finish. This will open the Save dialog.
6. Specify where to save the sequence, enter a file name and

click Save.
The sequence is now created (Figure 22).

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Figure 22: New Sequence
7. If necessary, change the injection names, Injection Types,

and other entries (Figure 22A). For an overview of Injection
Types, please refer to section 3.3.1.2.
2.4.2.5 S tart S equenc e

After a sequence has been created, click Start to start the sequence.
The sequence is added to the Queue. If the Queue is not running, it
will start (Figure 23).
Figure 23: Running Sequence
For instructions on how to monitor the analysis, please refer to

section 2.3.4.

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2.5 Process Data

After chromatographic data has been acquired, it can be processed.
The most common processing steps will be described.
All processing steps are performed in the Studio. To open the Studio
from the Console, double click any object in a sequence, or on the
sequence itself.
Note: After changes are made in a sequence, all results are

dynamically updated. When you make a change in the Processing
Method, the results for all injections in the sequence which use
that Processing Method are recalculated instantaneously. There is
no need to “reprocess” the sequence.
2.5.1 Review Chromatograms and Results

Once your samples are analyzed, you might want to review the
chromatograms (visually check that the chromatograms look like they
should) and their results.
2.5.1.1 C us tomizing Views

Before reviewing results, you may need to customize your view.
Follow the steps below:
1. Open your sequence in the Studio, for example by double-
clicking an injection in the Console.
2. Click the Data Processing category bar.
3. Show the Chromatogram Pane and the Interactive Results

Pane in the Work Area using the corresponding tools in the
Data Processing Home Ribbon tab (Figure 24).
Tip: To improve visibility of the information on the screen, you can

hide other panes.

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4. You can show/hide different elements of the Chromatogram

Pane: Click inside the chromatogram, click the Layout
contextual Ribbon tab, and then click the buttons to
show/hide the various elements.
Figure 24: Panes Group of the Data Processing Home Ribbon tab
Tip: The Presets group (left of the Panes group in the Data
Processing Home Ribbon tab) provides shortcuts to display typical
combination of Panes.
5. You can customize the Interactive Results Pane: Click inside

the table, then click the Summary Table or Integration Table
contextual Ribbon tab. For Summary Tables you can decide
which injection types to include. For Integration Tables you
can show/hide Unidentified Peaks and Undetected
Components.
All settings for the screen layout of the Work Area, including the
interactive results tables, are stored in the View Settings file (visible in
the Navigation Pane). If you want to keep the changes made to this
screen layout, make sure you save this file.
Note: The interactive results tables can be customized in a similar

way as the Report Template. Refer to section 2.6.2 for more
details.

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2.5.1.2 Navigate T hrough Y our Data

Navigating through your data can be done in the Data Processing
category of the Studio. Follow the steps below:

3. There are several ways of navigating between the injections

and channels:
• Use the Previous and Next buttons in the Navigation

group of the Data Processing Home Ribbon tab (Figure
25).
Figure 25: Navigation Group in Data Processing Home Tab
• In the Navigation Pane (Figure 26), select the injection

and/or channel you want to evaluate.

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Figure 26: Data Processing Navigation Pane
• Double-click the component and/or injection you want to

evaluate in the Integration / Summary Table of the
Interactive Results table (Figure 27).
Figure 27: Selection in interactive results table
Note: You can use the pins in the Navigation Pane to overlay
chromatograms from different injections and channels.

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2.5.2 Adjust Peak Detection

For correct quantification or qualification of a chromatogram, it is
important that all peaks are correctly detected. To achieve this, you
might need to:
• Create a new set of Detection Parameters.
• Modify an existing Processing Method.
• Insert a new Detection Parameter.

• Modify existing Detection Parameters.
• Integrate unresolved Peaks.
The following sections describe how to perform these actions.
2.5.2.1 C reating a New S et of Detec tion P arameters

To set up the Detection Parameters in a new Processing Method,
follow these steps:
Tip: For more information about creating Processing Methods,

please refer to section 2.4.2.2.

3. Click in the chromatogram plot.
4. Click the Processing contextual Ribbon tab.
5. To activate the Cobra™ Peak Detection Wizard, select the

Cobra Wizard option in the Detection Parameters group
(Figure 28).

Chromeleon 7
Figure 28: Activate Cobra Wizard
Tip: While using the Cobra wizard, you can zoom in the
chromatogram. Hold the control (Ctrl) key on your keyboard and
zoom using the mouse.
6. Select if Void Peaks need to be considered, and select the

area to be integrated, then click Next (Figure 29).
Figure 29: Select Area to Integrate

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7. If required, enter the baseline range used to determine the

noise, or select the Use Auto Range option, and click Next.
8. Select the narrowest peak in the chromatogram in order to

define the Cobra smoothing width used for peak detection, or
select the Use Auto Smoothing Width option, and click Next.
9. Select the smallest peak in the chromatogram that needs to

be detected and click Next (Figure 30). The minimum area
will be set to 90% of the area of the selected peak.
Figure 30: Select the smallest Peak to Integrate

10. In the final step, you can select the injection type and channel
to which the settings should apply (Figure 31). If necessary,
choose the appropriate injection type and channel and click
Finish.

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Figure 31: Select Injection Type and Channel
The most important settings for peak detection are now configured.
Save the changes that you made.
2.5.2.2 Ins ert a New Detec tion P arameter

To insert a new Detection Parameter, follow these steps:
3. To display the detection parameters in the Chromatogram, in

the Detection Parameters group, click Detection Parameters
(Figure 32).

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Figure 32: Detection Parameters Group in Processing Ribbon

Tab
4. Click Insert (Figure 32).
5. Select the appropriate Detection Parameter from the list.
Tip: The most frequently needed parameters are listed here. If

you need other Detection Parameters, select Other Parameter.
6. Move the mouse pointer to the location in the chromatogram

where you want to insert this parameter. Note that the mouse
pointer changed (Figure 33A).
Figure 33: Move mouse to desired location

7. Click to insert the Detection Parameter. The effect of the
newly inserted parameter is immediately visible in the
chromatogram (Figure 34A).

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Figure 34: Chromatogram with updated Detection Parameters
2.5.2.3 Modify E xis ting Detec tion P arameters

3. To display the detection parameters in the Chromatogram,

select the Detection Parameters option in the Detection
Parameters group (Figure 32).
4. In the Pointer / Zoom group, click the Automatic tool (Figure

35).
Figure 35: Select Automatic Tool
5. To move a Detection Parameter, grab its tag or the detection

parameter line (Figure 36A) and move it to the required
location (Figure 37).

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Figure 36: Grabbing a Detection Parameter to Move
Figure 37: Updated Chromatogram

6. To edit the value of a parameter, double-click its tag (Figure
38A).
Figure 38: Modifying a Detection Parameter Value
2.5.2.4 Integrate Unres olved P eaks

A chromatogram can contain unresolved peaks. The SmartPeaks™
integration assistant helps you to integrate these peaks according to
your requirements. To easily adjust the peak detection parameters
using the SmartPeaks wizard, follow the steps below:

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3. Select the SmartPeaks tool from the Detection Parameters

group (Figure 39).
Figure 39: Selection of SmartPeaks Tool
4. Drag a rectangle around the area that needs adjusted

detection parameters (Figure 40A).
Figure 40: SmartPeaks: Drag a Rectangle
5. Select the preferred peak detection (Figure 41) and click OK.

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Figure 41: SmartPeaks: Select Preferred Peak Detection

6. The Detection Parameters in the Processing Method are now
inserted (Figure 42A).
Figure 42: Adjusted Detection Parameters in Processing Method
Note: You can also manually add/modify detection parameters on

the Detection tab of the Processing Method.
2.5.3 Identify Peaks

For correct peak identification, it is important to have an accurate
Component Table. To achieve this, you might need to:
• Create a Component Table
• Update the expected retention times and windows.
The following sections describe how to perform these actions.

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2.5.3.1 C reate a C omponent T able

The component table is the part of the Processing Method that stores
information about components (analytes) that enables them to be
matched to chromatographic peaks, and can also store information
for quantitative analysis. The three most common ways to create a
component table are described below.
2.5.3.1.1 Via the Component Table Wizard

To create a component table by using the Component Table wizard:
3. Activate the Peak Windows option and the Component

Table Wizard option in the Component Table group (Figure
43).
Figure 43: Component Table Group of the Processing tab
4. Set a time range for peak detection and click Next (Figure
44).

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Figure 44: Time Range for Peak Detection

5. Optionally, set a filter to reduce the number of detected
peaks for identification. Click Next.
6. Review the component table and, if required, modify settings

(Figure 45). Click Finish.
Figure 45: Review Component Table
Tip: The component table wizard can also be used to update

existing component tables. When there are already components
defined in the table, upon running the wizard the following
message appears: The current processing method already
contains components. What do you want to do with these
components? Your choices are to drop (delete) them or to
update them.

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2.5.3.1.2 Interactively in the Chromatogram Pane

To add a component to the component table interactively:
3. Activate the Peak Windows option and the Add Component

option in the Component Table group (Figure 43).
4. Drag a rectangle around the peak you want to add to the

component table (Figure 46A).
Figure 46: Drag Rectangle

5. The peak is now added to the component table and the Peak
Window is visible. Double-click the Peak Window and enter
the component name (Figure 47A).
Figure 47: Enter Component Name
2.5.3.1.3 Via the Component Table (Processing Method)

To create a component table in the processing method:
1. Click the Data Processing Home Ribbon tab.
2. In the Panes group, click Processing Method (Figure 48) to

display the Processing Method.

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Figure 48: Panes Group of the Data Processing Home tab
Tip: To conveniently display the Processing Method, consider

hiding the other panes.
3. In the Processing Method, select the Component Table tab

(Figure 49A). Click below the component table on the line
labeled Click here to add a new component.
Figure 49: Component Table in Processing Method
Note: The Processing Method can have different layouts,

consisting of different tabs and names. Therefore the Processing
Method tables and columns you see may look different from the
ones in these pictures.

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4. Enter the component name in the dialog box and click Create
(Figure 50).
Figure 50: Enter Component Name

5. The new component is added to the component table.
Update the component retention time and Window in the Ret.
Time and/or Window column by selecting the cell and typing
the new retention time and/or window size.
6. Repeat step 3 to 5 for all components that must be added to

the component table.
The components are now added to the Processing Method.
2.5.3.2 Update R etention T imes and W indows

During chromatographic analyses, retention times of components
may shift due to column, temperature, or eluent changes. Therefore,
updating the expected retention times and retention time windows in
the Processing Method is one of the tasks most often performed
when processing data. The two most common ways to do this are
described below.
2.5.3.2.1 Interactively in the Chromatogram Pane

To update a component’s expected retention time window
interactively:

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3. Activate the Peak Windows option in the Component Table

group Figure 43). The expected peak windows are now
graphically represented above the chromatogram (Figure
51A).
4. Drag a Peak Window to the correct location using the left

mouse button (Figure 51B). You can also grab one of the
delimiters to widen or narrow the peak window.
Figure 51: Shift Peak Windows
The peak’s expected retention time/window is simultaneously

updated in the Processing Method.
2.5.3.2.2 Via the Processing Method

To update the component retention times in the Processing Method:
1. Click the Data Processing Home Ribbon tab.
2. In the Panes group, click Processing Method (Figure 48) to

display the Processing Method.
3. In the Processing Method, select the Component Table Tab

(Figure 52).

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4. Update the component retention times and/or Windows in the

Ret. Time and/or Window column by selecting the cell and
typing the new retention time and/or Window size.
The retention times are now updated in the Processing Method.

Tip: Choose the Processing Method layout appropriate for your

application, or define your own layout by selecting individual tabs
via the Processing Method layout dialog ( ).
2.5.4 Calibration
2.5.4.1 S et up C alibration
In Chromeleon 7, calibration levels are defined directly in the injection
list. Any calibration level added in the injection list is automatically
added to the processing method. To set up a calibration:

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1. Click the Injection List Category.
2. Make sure all calibration standards have the injection type

Calibration Standard.
3. Click in the Level cell for the first calibration standard. This
shows the option Create new level (Figure 53).
Figure 53: Create new Calibration Level

4. Click Create new level. The value 01 is added (Figure 54).
Assign this level to all injections of this calibration standard.
Figure 54: Assign Level to Calibration Standard

5. Repeat Step 3 and 4 for all calibration levels.
6. Select the Data Processing Category.
7. Go to the Data Processing Home Ribbon tab.
8. In the Panes group, click Processing Method (Figure 48).
9. In the Processing Method, select the Component Table -

Advanced Tab.

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10. Go to the Calibration Level columns and enter the

concentrations (Figure 55).
11. The calibration is updated immediately (Figure 56) and the

results are visible in the Interactive Results Table or the
Report Template.
Figure 56: Updated Calibration
2.5.4.2 Update C alibration Amounts

Whenever calibration standard solutions are newly made, the
component concentrations should be updated in the Component
Table in the Processing Method.

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Follow the steps below to update the concentrations.

1. Go to the Data Processing Home Ribbon tab.
2. In the Panes group, click Processing Method (Figure 48).
3. In the Processing Method, select the Component Table -

Advanced Tab.
4. Go to the Calibration Level columns and update the amounts

(Figure 55).
5. The results are immediately visible in the Interactive results

tables or the Report Template.
2.6 Review and Report Results

The Report Template is a spreadsheet-like file that defines how data
is displayed, printed or exported. This chapter describes how to use
and customize the Report Templates. The Report Template is
accessible via the Report Designer category in the Studio (Figure
57).
Figure 57: Report Designer Category Bar
2.6.1 View Results Using Report Templates

To access the Report Template, click the Report Designer category
bar.
The Navigation Pane lists the available Report Templates in the
sequence. Click one of them to apply that template to the sequence.
If the sequence contains no Report Template, Chromeleon offers a
gallery of its default templates. Select one of them. When you close
the sequence, you will be asked whether you want to save this
template. It will then be added to the sequence.

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The results can be reviewed by clicking the appropriate sheet of the

Report Template.
Navigating through the injections can be performed in the following
way:
• Use the Previous and Next buttons in the Navigation
group of the Home Ribbon tab.
• In the Navigation pane (Figure 26), select the injection
and/or channel you want to view.
2.6.2 Customize Report Templates

The predefined Report Templates have many Report Formulas and
tables with defined Report Columns available.
Tip: Dynamic Chromeleon objects like Report Tables, Report

Variables, and Chromatograms are indicated with a red triangle
( ). Cells that contain text or a spreadsheet formula are not
marked like this.
Sometimes you may need to change one of these formulas /

columns (for example: Change Plate Number from EP to USP). This
is described in the following steps:
1. Select the Report Column that needs a change (Figure 58A).
Figure 58: Select Report Column

Chromeleon 7
2. Click the Integration Table (or Summary Table) tab and open
the Column Properties dialog by clicking the dialog launcher
of the Column Properties group (Figure 59A).
Figure 59: Open Column Properties
3. Click Parameters to open additional settings (Figure 60A).
Figure 60: Column Properties
4. Select the option USP Formula (Figure 61A).

Chromeleon 7
Figure 61: Resolution Parameters
5. Click OK to close the parameters dialog, then click OK to

close the column properties dialog. The Report Column is
now changed (Figure 62).
Figure 62: Changed Column
2.6.3 Print Results (Using Report Templates)

Once you have acquired and processed your data, you may want to
print the results. Printing can be started via the Studio Menu (Figure
63).

Chromeleon 7
Figure 63: Studio Menu: Print
When printing results, you can:

• Print the currently selected injection only.
• Print the entire sequence.
Both processes will be described in the following sections.
2.6.3.1 P rint R es ults for a S ingle Injec tion

To print the results for the currently selected injection, follow these
steps:
1. Select the Report Designer category bar.
2. Select the Report Template you want to use in the Navigation

Pane.
3. Select the injection you want to print in the Navigation Pane

(refer to section 2.5.1, Figure 26).
4. On the Studio Menu, select Print to open the Print dialog

(Figure 64).

Chromeleon 7
Figure 64: Print Dialog to Print Injection
5. Select Apply to Current Injection (Figure 64A).
6. Select the Printer you want to print on (Figure 64B).
7. Select the Sheets to be printed for the current injection

(Figure 64C).
The results for the current injection are now printed.
2.6.3.2 P rint R es ults for the E ntire S equenc e

To print results for the entire sequence, follow these steps:
1. Click the Report Designer category bar.
2. Select the Report Template you want to use in the Navigation

Pane.
3. On the Studio Menu, select Print to open the Print dialog

(Figure 65).

Chromeleon 7
Figure 65: Print Dialog to Print Sequence
4. Select Apply to Current Sequence (Figure 65A).
5. Select the Printer you want to print on (Figure 65B).
6. Select the Sheets to be printed (Figure 65C).
7. Click the Down Arrow ( ) in the Condition column to apply

print conditions for the selected sheet (Figure 66).
Figure 66: Print Conditions

Chromeleon 7
The results for the sequence are now printed.
Tip: To print several injections from a sequence, first select the

injection row or rows you want to print, right-click, and then click
Print.
2.7 Save Changes

When you make changes to any object in the sequence, it is
important to save these changes. The two ways to do this are
described below.
2.7.1 Save Changes per Object

In the Navigation Pane of the Studio, all files belonging to the
selected category are listed. Whenever changes are made to a file, a
save icon appears to the right of the object name (Figure 67).
Figure 67: Changed Files Indicated with Save Icon

Chromeleon 7
To save changes to an object, click the save icon.
2.7.2 Save All Changes at Once

To save all changes made while working in the Studio follow the
steps below.
1. Click Save, Save All in the Studio Menu (Figure 68).
Figure 68: Save All

2. All changed files will be saved.

Chromeleon 7
3 Appendix: Chromeleon Overview
3.1 Introduction
Chromeleon 7 is a Chromatography Data System that allows you to
control chromatography instruments and to evaluate, process, report,
and backup data.
The software consists of two major parts:

1. Instrument Controller Service: The Instrument Controller
Service handles communication with and data acquisition
from the connected instruments. The Instrument Controller
Service runs as a Windows service.
2. Client: The Client provides a user interface for instrument

control and for accessing, processing, and presenting
chromatography data.
Chromeleon has several other software components that are used

occasionally:
3. Services Manager: Shows the status of the Chromeleon
Instrument Controller Service and provides a user interface to
control this service. The status of all other Chromeleon
services is also displayed.
4. Instrument Configuration Manager: Allows configuration of

Instruments connected to the Instrument PC.
5. Administration Console: Central access point for

administrative tasks, like:
a. License Manager: Provides tools for managing licenses

for Chromeleon stations and users.

Chromeleon 7
b. Scheduler: Provides tools for scheduling data transfer.
c. User Database: Provides tools for managing system

policies, users and groups, access privileges, and
operational privileges.
d. Global Policies: Provides settings for global Chromeleon

policies.
e. Discovery: Central repository with information about the

available Instruments and Data Vaults.
f. Local Machine: Provides tools for managing local

Chromeleon 7 Data Vaults (Create, Mount and
Dismount) and Chromeleon 6 Datasources (Mount and
Dismount) and offers possibility to change the
Chromeleon Domain Controller.
Note: If User Management is enabled, the possibility to execute

steps described in this document might be limited by user
privileges.
3.2 Instrument Controller Service

The Chromeleon Instrument Controller Service handles all real-time
instrument processes (communications, control, and data
acquisition). It runs in the background as a Windows service on PCs
to which instruments are physically connected. Its status is
represented by an icon ( , ) in the Notification Area of the
Windows Taskbar (Figure 69).

Chromeleon 7
A B
Figure 69: Notification Area of Windows Taskbar for Windows

XP (A) and Windows 7 (B)
The instruments can be configured with the Instrument Configuration

Manager.
3.3 Chromeleon Client

The Chromeleon Client provides the user interface for all typical daily
chromatography tasks (instrument operation, data analysis, and data
management).
The Chromeleon Client has two different window types:
1. Chromeleon Console: The main Chromeleon window in
which you can control instruments, navigate through all data
and use or manage eWorkflows.
2. Chromatography Studio: A separate window that is

launched from the Console in which you can work with all
data and objects related to a selected sequence. Here you
can view and optimize all aspects of the data, modify
instrument methods and processing methods, define and
generate reports, and manage spectral libraries.

Chromeleon 7
3.3.1 Chromeleon Console

When you start Chromeleon 7, the Console is the first window to
appear. The Console window has three major parts.
5 7
6
4
2 3
1
8
Figure 70: Chromeleon Console
1. Category Bars: Via the category bars you can switch

between the three categories: Instruments, Data, and
eWorkflows (Figure 71).
Figure 71: Categories
2. Navigation Pane: An area where you can navigate through

the objects related to the selected category.

Chromeleon 7
3. Work Area: The area that shows the content of the object
that was selected in the Navigation Pane, and allows you to
work with that object.
There are three additional parts for user interaction:

4. The Filter Toolbar offers different views of the list in the
Navigation Pane:
a. Local: Items available on the local Chromeleon

station.
b. Global: Items available on the Chromeleon Domain.
c. Custom: Filter based on text input.
5. The Menu Bar is always present.
6. The Sequence Toolbar is available when a Sequence is

selected in the Navigation Pane.
Finally there are two parts for status information:

7. The Sequence Control Bar indicates the sequence status
(New, Running, Complete, Interrupted, Incomplete) and
provides relevant actions for the sequence.
Note: When a sequence is configured to be electronically signed,

additional statuses are available.
8. The Status Bar shows general information such as the

currently logged on user.

Chromeleon 7
3.3.1.1 Ins truments C ategory

The Instruments Category gives access to all instruments on the
network (this might be limited by user privileges).
D E
Figure 72: Instruments Category
The list of instruments is visible in the Navigation Pane (Figure 72A).

In the Work Area you can access the ePanel tabs (Figure 72B) for
direct instrument control, the Instrument Audit Trail (Figure 72C) for
an overview of all actions performed on the selected instrument,
Startup for an overview of the SmartStart process (Figure 72D), and
the Queue (Figure 72E), to start and stop analyses and to manage
the order in which sequences are processed.

Chromeleon 7
3.3.1.2 Data C ategory

The Data Category provides access to all data stored in each
connected Data Vault ( , container for all data).
Note: Chromeleon 6 Datasources ( ) are visible in Chromeleon

7. It is not possible to make changes in these Datasources, but
data can be copied from them to Chromeleon 7 Data Vaults.
A B
Figure 73: Data Category
All chromatography data is visible in the Navigation Pane (Figure

73A) in a Windows Explorer-like structure and can be accessed and
organized from there. The Work Area (Figure 73B) shows the content
of the selected object and allows you to edit the object.

Chromeleon 7
A Data Vault can contain the following objects:
1. Folder: A container for objects. Folders are useful for

organizing data in a Data Vault.
2. Sequence: Collection of injections that belong together.
3. Instrument Method: Set of timed commands for an

instrument to perform during a chromatographic analysis.
4. Processing Method: Collection of parameters that are

used for evaluating a chromatogram. Includes parameters for
peak detection and calibration.
5. Report Template: Spreadsheet-like file that defines how

data is printed or exported. When the template is applied to a
sequence (to view, print, or export the results) the outcome is
referred to as the Report.
6. Electronic Report: Electronic printout copy of the results

of a sequence.
7. View Settings: Definition of how data is presented on the

screen. Includes settings for the chromatogram, interactive
result tables, the calibration curve, etc.
8. Spectral Library: Collection of spectra used for peak

identification.
9. Query: Data Vault Search function for finding data that

match specific criteria.
A typical sequence contains an Instrument Method, a Processing

Method, a Report Template, and a View Settings file. When a diode
array detector is used, Spectral Libraries may also be present.

Chromeleon 7
The sequence is a collection of injections that are analyzed and

processed together in series. Each injection is represented by a row
in the sequence (replicate injections are represented with multiple
rows). Injections can have one of the following Injection Types:
1. Unknown: A sample for which the quantity, presence, or

absence of components is to be determined during the
analysis.
2. Calibration Standard: A sample with known

concentrations of components. Calibration Standards are
used to construct a calibration curve that establishes a
relationship between the amounts of components in the
sample and the corresponding detector responses.
3. Check Standard: A sample with known component

concentration(s). Check Standards are used to verify a
calibration.
4. Blank: An injection used to characterize the background

signal (baseline), and/or to ensure that components are not
detected when they should not be present. Blank “injections”
can be made without an actual injection taking place.
5. Matrix: The sample matrix can influence the analysis

results. A Matrix Injection can be used to compensate for
this. The peak areas in the Matrix are subtracted from the
corresponding peak areas in all the other injections in the
sequence. The resulting areas are then used for further
calculations; for example, for calibration.
6. Unspiked: An Unknown sample to be analyzed with the

Standard Addition method.
7. Spiked: An Unknown sample to be analyzed with the

Standard Addition method, with known amounts of
components added.

Chromeleon 7
Note: Chromeleon sequences are complete packages containing

all raw data and associated files that are needed to generate,
process, and report the data.
3.3.1.3 eW orkflows C ategory

eWorkflows are electronic procedures for automating all laboratory
processes related to a chromatographic analysis.
An eWorkflow contains a set of templates (such as Instrument
Methods, Processing Methods, Report Templates, View Settings,
and/or Spectral Libraries) and a set of rules. The rules define, for
example, the sequence layout (such as the maximum number of
Unknown injections allowed between Calibration Standards), and the
list of instruments in the network that are suitable for the analysis.
When you start an eWorkflow, it will create a sequence with
predefined associated files and a well-defined structure.
A B
Figure 74: eWorkflows Category
The list of available eWorkflows is visible in the Navigation Pane

(Figure 74A). In the Work Area (Figure 74B) you find an overview of
the instruments (including their status) that can be used with the
selected eWorkflow. You can start an eWorkflow from here. This will
guide you to create an appropriate sequence.

Chromeleon 7
3.3.2 Chromatography Studio

When you open a sequence from the Console, the Chromatography
Studio (Figure 75) is opened. In the Studio you can edit all objects
related to the selected sequence: the Injection List, Instrument
Methods, Processing Methods, View Settings, Report Templates,
Electronic Reports, and Spectral Libraries.
Note: When you open an object outside the context of a

sequence, only the corresponding category of the Studio will be
available.
5 4
2 3
Figure 75: Chromatography Studio

Chromeleon 7
The Chromatography Studio is structured similarly to the Chromeleon

Console, and consists of the following major parts:
1. Category Bars: These switch the display between the five
categories (Figure 76): Injection List, Instrument Method,
Data Processing, Report Designer and Spectral Library.
Figure 76: Categories
2. Navigation Pane: An area in which you can navigate through

the objects available in the selected category.
3. Work Area: The content changes according to the selected

category.
There are two additional parts for user interaction:

4. Ribbon: The menu tool for main actions in the Studio.
Depending on the category or the selected pane, different
Ribbon tabs are available.
5. Studio Menu: The location for commands related to general

tasks, like printing, exporting, saving, etc.
3.3.2.1 Injec tion L is t C ategory

In the Injection List category, you can edit the Injection List (Figure
77B), and output the injection list as a printed document or as an
exported file.

Chromeleon 7
A B
Figure 77: Injection List Category
The Navigation Pane (Figure 77A) gives an overview of all files used
in this sequence.
Note: You can also edit the Injection List directly in the Console. If
a Sequence is open in both the Console and the Studio, changes
made in either window are automatically made in the other, such
that the copies of the Sequence stay synchronized.
3.3.2.2 Ins trument Method C ategory

The Instrument Method category lets you edit Instrument Methods.
The Navigation Pane lists the Instrument Methods in the sequence
(Figure 78A), and provides an overview of the instrument’s modules
(Figure 78B). The Work Area lets you edit the Instrument Method
(Figure 78C) via the Module Views or Script Editor.

Chromeleon 7
A C
Figure 78: Instrument Method Category
3.3.2.3 Data P roc es s ing C ategory

In the Data Processing category, you can view chromatography
results, edit the Processing Method, and manually integrate
chromatograms.
The Navigation Pane (Figure 79A) gives an overview of all injections,
channels, processing methods and view settings used in the
sequence. In the Work Area (Figure 79B), chromatographic results
are shown.

Chromeleon 7
A B
Figure 79: Data Processing Category
Via the Panes group of the Data Processing Home tab of the
Ribbon (Figure 80) you can show or hide various panes (such as
Chromatogram, Interactive Results, Calibration Plot, and Processing
Method).
Figure 80: Pane Selection in Ribbon

Chromeleon 7
Tip: The Presets group (left of the Panes group in the Data
Processing Home Ribbon tab) provides shortcuts to display typical
combination of Panes.
3.3.2.4 R eport Des igner C ategory

In the Report Designer category, you can view reports and edit
Report Templates.
A B
Figure 81: Report Designer Category
The Navigation Pane (Figure 81A) shows a list of all channels,

injections and report templates available in the sequence. In the
Work Area (Figure 81B), you can view and modify the report.
3.3.2.5 E lec tronic R eport C ategory

In the Electronic Report category, you can create and manage
electronic reports. This is an electronically captured snapshot of the
results.

Chromeleon 7
A B
Figure 82: Electronic Report Category
The Navigation Pane (Figure 82A) shows a list of all injections,

sheets available in the electronic report and the electronic report
itself. The Work Area (Figure 82B) shows the electronic report, or,
when no electronic report is available, the possibility to create one.
Electronic signatures can be applied in the Electronic Report
category.
3.3.2.6 S pec tral L ibrary C ategory

In the Spectral Library category, you can manage Spectral Libraries.
The Navigation Pane (Figure 83A) lists all libraries available in this
sequence. The Work Area lists the spectra in the selected library
(Figure 83B), a spectral plot showing the spectra of the selected
library entries (Figure 83C) and additional information about the
selected library entry (Figure 83D).

Chromeleon 7
A B
C D
Figure 83: Spectral Library Category
3.3.2.7 R ibbon
Via the Ribbon (Figure 84) all common functions are accessible.
B C
Figure 84: Ribbon
The content of the Ribbon changes, depending on the current

context and the selected object. This is visible with the availability of
different tabs (Figure 84A). Each Ribbon tab consists of various
groups (Figure 84B), each containing buttons to perform actions. If
more options are available, this is indicated by the dialog launcher in
the lower right corner of a group: (Figure 84C). Clicking the dialog
launcher opens a dialog with advanced options (Figure 85).

Chromeleon 7
Figure 85: Properties Dialog with Advanced Options
3.3.2.8 S tudio Menu

Some commands in the Chromeleon 7 Studio are accessible via the
Studio Menu (Figure 86).
Figure 86: Studio Menu
To access the Studio Menu, click the round button in the upper left
corner of the Studio (Figure 86A). General tasks can be executed
from here (such as Open, Save, and Print).

Chromeleon 7
Index
Administration Console 52 License Manager 52
Calibration 40, 42 Module 4, 5
Category Bars 55, 62 Monitor 8
Client 52, 54 Navigation Pane 55, 62
Cobra 24 Peak Detection 24
Component 34 Print 46, 47, 48
Component Table Wizard 34 Processing Method 14, 36, 39,
Connect 4 58
Console 3, 54 Query 59
Control 4, 5 Queue 57
Data Processing 20, 64 Report 15, 43, 46, 58, 66
Data Vault 57 Report Template 44
Data Vault Manager 53 Retention Time 38
Discovery Service 53 Ribbon 63, 68
Electronic Report 59, 66 Save 50, 51
ePanel 4, 57 Scheduler 52
eWorkflows 9, 54, 60 Sequence 9, 58
Filter Toolbar 55 Services Manager 52
Injection List 63 Smart Startup 7
Injection Types 59 SmartPeaks 31
Instrument 3, 4, 56 Spectral Library 59, 67
Instrument Configuration Start 3, 9
Manager 52 Studio 20, 54, 61
Instrument Controller Service52, Studio Menu 63, 69
53 User Manager 53
Instrument Method 12, 58, 64 View Settings 21, 59
Interactive Results 20 Work Area 55, 63

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Thermo Scientific Dionex Chromeleon

Quick Start Guide

Quick Start Guide Page i

3 Appendix: Chromeleon Overview 49

Page ii Quick Start Guide

Quick Start Guide Page iii

1.1 About this Document

Note: Indicates general information that points out specific items

Caution: Indicates areas where operations should be

1.2 Other Documentation

Quick Start Guide Page 1

2.1 Configure Instruments

2.2 Start Chromeleon

• Use the Windows Start menu:

Select Start, All Programs, Chromeleon 7, Chromeleon 7

Page 2 Quick Start Guide

2.3 Control Your Instrument

2.3.1 Connect Modules

3. On the ePanel, click Connect (Figure 1A).

Figure 1: Connect your Instrument

Quick Start Guide Page 3

Note: The ePanel sets are generated automatically, based on

To manually add ePanels to a set, follow these steps:

Figure 2: Add ePanels

Figure 3: Selecting ePanel

2.3.2 Control Modules Directly

Page 4 Quick Start Guide

Method. Sometimes (typically between sequence runs) it is

3. Use the controls (buttons, sliders, check boxes, and so forth)

4. To monitor the detector signals without starting a Sequence,

Figure 4: Control Modules via ePanel

Quick Start Guide Page 5

Note: Most common commands are available from the ePanels. If

2.3.3 Start up Instrument using Smart Startup

Note: The settings used during an Instruments Smart Startup are

To startup an Instrument using SmartStartup, follow these steps:

2. Click Smart Startup on the Instruments toolbar (Figure 5B).

a. Click using Queue Settings when the sequence to run

b. Click using Instrument Method when you want to

Page 6 Quick Start Guide

Figure 5: Start up instrument

Figure 6: Message bar

2.3.4 Monitor an Ongoing Analysis

Quick Start Guide Page 7

To monitor the ongoing analysis, follow these steps:

2. Select the ePanel for the detector in the Work Area.

3. See the chromatogram evolving on the screen.

Note: The settings of all other modules can be monitored on their

2.4 Create and Start a Sequence

Note: If no eWorkflows are available in the eWorkflows category,

To create and start a sequence via an eWorkflow, follow these steps:

2. In the Work Area, select the instrument on which you want to

3. Click Launch (Figure 7C).

Page 8 Quick Start Guide

Figure 7: Start run via eWorkflows

4. Fill in the number of samples you want to analyze and the

5. If necessary, fill in a sequence name and the sequence

The sequence is now created (Figure 8).