Chromeleon 7.

2 Workshop

Chromeleon 7.2 Workshop

Setting up an Analysis

Training Course Manual

Version 05

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Table of Contents

Table of Contents .................................................................................................................................. 2

Introduction ........................................................................................................................................... 3

Introduction .......................................................................................................................................... 3

Preparing the Folder Structure ............................................................................................................ 3

Exercise 1 ............................................................................................................................................ 3

Setting up the Sequence ...................................................................................................................... 4

Exercise 2 – Creating a Sequence using the Wizard .......................................................................... 4

Exercise 3 – Creating an Instrument Method ...................................................................................... 9

Exercise 3a – Instrument Method for an Ion Chromatography Instrument (ICS 2100) ..................... 10

Exercise 3b – Instrument Method for an UltiMate 3000 RS UHPLC ................................................. 18

Exercise 3c – Instrument Method for a Trace 1300 GC .................................................................... 26

Exercise 4 – Creating an Empty Processing Method ........................................................................ 33

Exercise 5 – Finalizing the Sequence: Assigning the Methods to the Injections .............................. 34

Exercise 6 – Starting a Sequence from the Queue ........................................................................... 35

Exercise 6 – Stopping a Queue ......................................................................................................... 37

Exercise 7 – Using a Sequence Template to create a new Sequence ............................................. 38

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Introduction

Introduction

This workshop shows the workflow of creating all the files required to start measuring samples in
Chromeleon, when eWorkflows are not used. This workflow consists of:
 Setting up a Sequence using the Sequence Wizard
 Setting up Instrument Methods
 Setting up Processing Methods
 Updating the Sequence
 Starting the analysis by adding the Sequence to the Queue

The modifications to Processing Methods and Report Templates, as well as generating eWorkflows,
are topics of separate workshops.

For this workshop import the following instrument configuration:

08-03-E-DAT-Instr-Config-4Sys--CM72L1Gen--20180128.cmic

Preparing the Folder Structure

Exercise 1
1. Open the Chromeleon Console by double clicking the Chromeleon 7 icon on the computer

desktop and switch to the category Data

2. Select the Data Vault ChromeleonLocal, open the context menu with a right mouse click, and
click New Folder. Enter the name of the new folder as “Training_<YYYY-MM-DD>”. Replace
<YYYY-MM-DD> with today’s date e.g. 2017-12-31 (Figure 1).

Figure 1: Console – Data category – Folder structure created

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This folder will be your personal training folder and contain all the exercises and results of this
training.
3. Create a folder Sequences in your personal training folder.

Setting up the Sequence

We are simulating a clean system which has not yet any objects that would be
required for setting up a sequence and running it. During this part of the exercise we
will setup a sequence just containing injections. During additional exercises, we will
generate Instrument Method and Processing inside this new sequence. This keeps
everything together and emphasises the Sequence as the parent object for all
samples and injections and associated items like the Instrument Method and the
Processing Method.

Exercise 2 – Creating a Sequence using the Wizard

1. In the Console’s menu bar click Create .

A dropdown list appears allowing you to create various objects (Figure 2).

Figure 2: Starting the New Sequence Wizard from the Console’s Create menu

2. Click Sequence.
The New Sequence Wizard opens.
3. On the Instrument page (Figure 3) select the instrument for which you will create the
Instrument Method in Exercise 3 (ICS-2100, UltiMate3000_RS or TRACE 1300). The
following figures show the steps needed to create a Sequence for the UltiMate3000_RS. For
the ICS-2000 and the Trace 1300 similar dialogs will appear.
Click Next.

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Figure 3: Sequence Wizard – Instrument selection

4. In the Unknown Injections page (Figure 4), enter the following parameters:
Number of Vials: 10 for UltiMate_3000_RS and ICS-2100; 8 for Trace 1300
Injections per Vial: 1
Start Position: RA1 for UltiMate_3000_RS and ICS-2100; 1 for Trace 1300
Injection Volume: 20 µL for UltiMate_3000_RS; 5 µL for ICS-2100 and Trace.
The pattern for the Injection Name is Sample #n.

Note: The allows additional options, e.g. automatic numbering of the samples using a
“User Index”.
Click Next.

Figure 4: Sequence Wizard – Unknown Injections

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5. In the Methods and Reporting dialog, leave the fields for Instrument Methods and Processing
Method empty (Figure 5). We will assign the methods later, once we have created them in the
next steps (Exercise 3 and Exercise 4).
6. Reports Templates are not yet created either, therefore we leave the corresponding field
empty.
7. When not present in the Sequence, Chromeleon 7 will apply pre-defined View Settings
automatically, so we can leave that field empty too. Click Next.

Figure 5: Sequence Wizard – Selection of Instrument and Processing Methods, Report Template and
View Settings

8. In the following dialog you can enter a comment to provide additional information about the
Sequence. Proceed with Next and then click Finish.

Figure 6: Comment field for the Sequence

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9. Save the sequence in the folder Sequences of your training folder. Give the sequence a name
following ISO standard date format <YYYY-MM-DD> followed by a running sequence number
suffix <_XX>. For example: 2017-12-31_01 (Figure 7).

Figure 7: Save the Sequence

10. The Sequence will be created and displayed in the Console’s Data category (Figure 8).

Figure 8: Sequence / Injection list as created by the Wizard for the UltiMate 3000

Note: The New Sequence Wizard only permits to create Unknowns. After the injections are created
the sample type can be easily changed, for example to Calibration Standard.

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11. Edit a sequence with the following settings:

Injection 1: Type: Blank Name: Equilibration
Injections 2, 3, 4, 5: Type: Calibration Standard Name: Std 1, Std 1, Std 2, Std 2
Injections 6 – 10 (8): Type: Unknown Name: Sample1 – 5 (3)

Note: You can use F9 to Fill Down for the Injections with the same information, so that it’s not
necessary to edit the lines one by one.

Figure 9: Revised Sequence / Injection list for the UltiMate 3000

12. Save the changes that were made to the Sequence.

Note: At this point no Level can be defined for the Calibration Standards. This is because there is no
Processing Method present where the Level(s) could be created.

Space for Notes

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Exercise 3 – Creating an Instrument Method

In this exercise we create an Instrument Method.

- Exercise 3a describes building an Instrument Method for an Ion Chromatography Instrument
(ICS-2100),
- Exercise 3b for an (U)HPLC Instrument (UltiMate 3000RS) and
- Exercise 3c for a Trace 1300 GC.
The trainer decides which example will be used.

1. As a starting point, select the Sequence that you created in Exercise 2; Chromeleon will then
offer this Sequence as the storage place for the Instrument Method that you will create, and
this is what we want.

2. In the Console’s menu bar click Create .

A dropdown list appears allowing you to create various objects (Figure 10).

Figure 10: Starting the Instrument Method Wizard from the Console’s Create menu

2. Select Instrument Method.

The Instrument Method wizard opens.
Create one of the following Instrument Methods, using the wizard.
If the trainer doesn’t say otherwise, create the Instrument Method for the UltiMate 3000
system, i.e. follow Exercise 3b.

Note that the values for the parameters in these exercises are just examples, not general
recommendations (e.g. for the Instrument Methods in your lab).

For instance, the value for Data Collection Rate should be selected in a manner that your
narrowest peaks should have about 20 data points. Oversampling your chromatogram does
not only increase the amount of data to be stored, it negatively affects performance, and it does NOT
make peak detection better, rather the opposite.

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Exercise 3a – Instrument Method for an Ion Chromatography Instrument (ICS 2100)

1. Select the following parameters in the Wizard:

 Instrument: 01_ICS-2100
 Runtime: 5 Minutes for the conductivity detector
 Gradient: Isocratic, flow rate of 0.55 ml/min
 Eluent Generator: Isocratic, 23 mM concentration, CR-TC on
 Sampler: Default-values, no sample preparation steps
 Detector: Data collection rate = 5 Hz, Cell temperature: 35°C
and Column Temperature: 30°C
 Suppressor: AERS, 2mm, 23mM KOH, Current 32 mA

Figure 12 to Figure 22 show all the steps of the Instrument Method wizard.

Figure 11: Instrument Method Wizard – Selection of Instrument

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Figure 12: Instrument Method Wizard – Selection of Run Time and Diagnostic Channels

Figure 13: Instrument Method Wizard – Input of Gradient Type and pump flow rate.

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Figure 14: Instrument Method Wizard – Input of conditions for the Eluent Generator and CR-TC

Figure 15: Instrument Method Wizard – Selection of Autosampler Parameters

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Figure 16: Instrument Method Wizard – Selection of Autosampler Parameters

Figure 17: Instrument Method Wizard – Definition of sample preparations steps (if required)

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Figure 18: Instrument Method Wizard – Definition of Detector settings

Figure 19: Instrument Method Wizard – Definition of the Suppressor Types

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Figure 20: Instrument Method Wizard – Definition of temperatures for column and compartment

Figure 21: Instrument Method Wizard – Input of a possible Comment and finalization of the Wizard.

2. Click Finish and save the Instrument Method inside the Sequence that you created in
Exercise 2 using the name ICS-2100_01.

3. Once you have finished the Instrument Method Wizard, you can re-visit the pages for each
module via the so-called Device Views and modify the parameters (Figure 22).

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Figure 22: Instrument Method – Device View

Alternatively, you can modify the lines of the Instrument Method in the Script Editor
(Figure 23). You can also add new lines and add comments to the lines.

Space for Notes

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Figure 23: Instrument Method – Script Editor View

4. Change the concentration of sodium hydroxide in the Script Editor from 30 to 0 mM

(command Pump_ECD.Suppressor_Hydroxide). What happens?

5. Change the concentration via the Device View for the Suppressor back to 30 mM. What do
you observe?

6. Perform a check for the Instrument Method and make corrections if errors occur (Warnings
have to be checked, but not necessarily to be corrected).

7. Save the Instrument Method.

Space for Notes

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Exercise 3b – Instrument Method for an UltiMate 3000 RS UHPLC

1. Select following values in the Instrument Method Wizard:

 Instrument: 04_UltiMate3000_RS
 Runtime: 1.2 Minutes
 Diagnostic Channels: Pump_Pressure
 Pump:
 Pressure Limits: 0 bar to 800 bar

2
Flow Acceleration/Deceleration: 3 ml/min
 Gradient: Binary Gradient (see Table 1)

Time (min) Flow %B Curve

(ml/min)
0 1 5 5
0.8 1 80 5
0.9 1 80 5
1.0 1 5 5
1.2 1 5 5
Table 1: Eluent gradient

 Sampler – General Settings:

 Default-values
 Inject Wash: NoWash
 Inject Mode: Normal
 “Bypass” checkbox: Don’t activate
 Use Temperature Control: Yes (Default values)

 Thermostated Column Compartment – General Settings:

 Use Temperature Control: Yes
 Temperature: 30 °C
 Equilibration Time: 0.1 min
 Ready Time Delta: 1°C
 Temperature Control of Post Column Cooler: Off
 Thermostated Column Compartment – Columns
 Active Column : No column selection

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 DAD:
 Wavelengths: See Table 2
 Peak Width at half height: 0.03 Minutes
 Use Recommended Values: On
 3-D Feld Min. Wavelength: 220 nm
 3-D Feld Max. Wavelength: 400 nm
 3-D Feld Bunchwidth: 1 nm
 Slit Width: Wide
 No timed events

Channel Wavelength Bandwidth Reference Bandwidth

(nm) (nm) Wavelength Reference Wavelength (nm)
UV_VIS_1 230 4 Off 1
UV_VIS_2 254 4 Off 1

3DField Off 1
Table 2: Definition of Detector Channels of DAD

Figure 24 to Figure 33 show all the steps of the Instrument Method Wizard.

Figure 24: Instrument Method Wizard – Selection of Instrument

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Figure 25: Instrument Method Wizard – Selection of Run Time and Diagnostic Channels

Figure 26: Instrument Method Wizard – Pressure Limits and Flow Acceleration

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Figure 27: Instrument Method Wizard – Definition of gradient (Equilibration Stage removed)

Figure 28: Instrument Method Wizard – Sampler: General Settings

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Figure 29: Instrument Method Wizard – Sampler: Inject Mode

Figure 30: Instrument Method Wizard – Sampler: Temperature Control

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Figure 31: Instrument Method Wizard – Settings of the Column Oven

Figure 32: Instrument Method Wizard – Detector Settings

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Figure 33: Instrument Method Wizard – Finalizing the Instrument Method

2. Click Finish in the wizard and save the Instrument Method inside the Sequence that you
created in Exercise 2 using the name UltiMate_3000_RS_01.

3. Once you have finished the Instrument Method Wizard, you can re-visit the pages for each
module via the so-called Device Views and modify the parameters.

4. Alternatively you can modify the lines of the Instrument Method in the Script Editor
(Figure 34). You can also add new lines and add comments to the lines.

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Figure 34: Instrument Method – Script Editor

5. Change the wavelength UV.UV_VIS_1.Wavelength from 230 nm to 220 nm.

6. Change the following gradient settings:

 Flow rate: 0.8 ml
 %B at 0.8 min: 30%

7. Check the method for the Instrument Method and make corrections if errors
occur (Warnings have to be checked, but not necessarily to be corrected).

8. Save the Instrument Method.

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Exercise 3c – Instrument Method for a Trace 1300 GC

1. Select following values in the Instrument Method Wizard:
Use as GC Oven Temperature 180°C and Detector Temperature 250°C
For all other parameters use defaults or values that seem to fit (see Figure 35 to Figure 45)

Figure 35: Instrument Method Wizard – Selection of Instrument

Figure 36: Instrument Method Wizard – Autosampler Options

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Figure 37: Instrument Method Wizard – Autosampler Wash Options

Figure 38: Instrument Method Wizard – Component Selection

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Figure 39: Instrument Method Wizard – Front Inlet

Figure 40: Instrument Method Wizard – Front Inlet Options

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Figure 41: Instrument Method Wizard – GC Oven Settings

Figure 42: Instrument Method Wizard – Column Configuration

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Figure 43: Instrument Method Wizard – Front Detector Options

Figure 44: Instrument Method Wizard – Front Detector Temperature Program

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Figure 45: Instrument Method Wizard – Comment

1. Click Finish in the wizard and save the Instrument Method inside the Sequence that you
created in Exercise 2 using the name Trace_1300_01..

2. Once you have finished the Instrument Method Wizard, you can re-visit the pages for each
module via the so-called Device Views and modify the parameters.

3. Alternatively you can modify the lines of the Instrument Method in the Script Editor
(Figure 46). You can also add new lines and add comments to the lines.

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Figure 46: Instrument Method Wizard – Script Editor

4. Change the GC Oven temperature from 180°C to 160°C

5. Check the method for the Instrument Method and make corrections if errors
occur (Warnings have to be checked, but not necessarily corrected).

6. Save the Instrument Method.

Space for Notes

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Exercise 4 – Creating an Empty Processing Method

1. As a starting point, select the Sequence that you created in Exercise 2; Chromeleon will then
offer this Sequence as the storage place for the Processing Method that you will create, and
this is what we want.

2. In the Console’s menu bar click Create .

A dropdown list appears allowing you to create various objects (Figure 47).

Figure 47: Starting the Processing Method Wizard from the Console’s Create menu

3. Select Processing Method.

The Processing Method Wizard opens.
Select the Layout 3D Quantitative (Figure 48):

Figure 48: Layout Selection for the Processing Method

Note: The 3D Quantitative template layout includes Detection, Component Table, Calibration,
Unidentified Peak Group Table, Chromatogram Subtraction, Advanced Settings, SST/IRC, UV
Spectral Library Screening and UV Settings tab pages.
Other layouts are available to show/hide tabs/columns according to various data processing needs.

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4. Save the Processing Method with the name Method1 inside the Sequence that you created in
Exercise 2

The Processing Method does not contain any processing parameter settings yet. Those will be added
and clarified in a separate workshop.

Exercise 5 – Finalizing the Sequence: Assigning the Methods to the Injections

Initially you created a Sequence with only Injections. This step assigns Instrument Method and
Processing Method to the Injections. You may need to adjust the sample positions as the instrument
might have changed.

1. Assign your Instrument Method to all Injections (Figure 49).

Figure 49: Sequence: Assigning an Instrument Method to an Injection

2. Assign your Processing Method to all Injections.

Note: Remember that you can use F9 to Fill Down for the Injections with the same information, so
that it’s not necessary to edit the lines one by one.

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Figure 50: Sequence: Instrument and Processing Method assigned to all Injections

3. Save the changes to the Sequence.

Exercise 6 – Starting a Sequence from the Queue

1. In the Sequence Control Bar, select the Instrument .

The ePanel appears. Select the Queue tab (Figure 51).

Figure 51: ePanels – Queue tab

2. If necessary, remove sequences which you don’t want to run. Select these sequences and
click the Remove button.

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3. Click Add. This opens a dialog, to add a Sequence to be run to the Queue (Figure 52).
Select the Sequence created in Exercise 4.

Figure 52: Add Sequence dialog

4. After adding the appropriate Sequence to the Queue, perform a Ready Check in
the Queue tab to check for errors and warnings.

5. Start the analysis. Check in the Console:

- how the running Injection is marked and
- how the MiniPlots are appearing

Space for Notes

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Exercise 6 – Stopping a Queue

This exercise shows how to stop the running Sequence / Queue.

1. From the Instruments category select the Instrument, then the Queue tab, – OR –
In the Data category select the running Sequence.

2. Click Stop. A window will be opened and you will be asked if you want to stop the Queue
Immediately, After current injection or After current sequence.
Choose Immediately.

(a) (b)
Figure 53: Two ways of stopping the Queue: (a) From the Queue tab (b) From the Sequence Status Bar

3. Check the Status of the Injection that was interrupted.

4. Check the Injection Audit Trail for the interrupted Injection and look for the entry
documenting what has happened.

Space for Notes

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Exercise 7 – Using a Sequence Template to create a new Sequence

This exercise demonstrates how to use a Sequence template to create a new Sequence.
1. In the Navigation Pane of the Console, select the Sequence finalized in Exercise 5.
2. In the main menu, click File, Save As (Figure 54).

Figure 54: Save as - Command

3. (In the Save dialog) create a new folder in your personal training folder called Templates.
4. (Re)name the sequence giving it a meaningful name like the type of analysis you want to
perform. Example: Aspirin in Tablets.
5. The new Sequence does not contain any raw data and the Injection Status is set to Idle.

Note: It is advisable to store empty sequence templates in a locked folder. This way the sequence
templates cannot be modified by mistake. To lock a folder right-click and select “Read-Only” from the
context menu, or tick the corresponding checkbox in the Sequence’s Properties dialog.

Note: You could also duplicate a Sequence by Copy-Paste. Discuss in the class what would be the
difference compared to Save As… in terms of the Data Audit Trail of the copy.

In most of the times Save As… would be the preferred choice.

Space for Notes

End of Workshop “Setting up an Analysis”

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