© 2016 Thermo Fisher Scientific Inc.
All rights reserved. 

This quick reference guide describes the Acquisition mode tasks of the Thermo TraceFinder™ 4.1 application.

Opening the

Acquisition

Mode

 To open the Acquisition mode

Click Acquisition in the navigation pane.

The navigation pane for the Acquisition mode opens. 

The task pane for the Acquisition mode tracks your actions.

TraceFinder Acquisition Quick Reference Guide

Contents

• Opening the Acquisition Mode

• Selecting a Batch

• Defining the Sample List

• Selecting and Reviewing Reports

• Submitting the Batch

• Using Quick Acquisition

• Trademarks

IMPORTANT   TraceFinder 4.1 uses the same data as TraceFinder 4.0. The application stores the method, 
project, template, and compound database data for the 4.1 release in the TraceFinderData/4.0 folder.

Acquisition mode options

Example of the task pane as you complete each task

Revision A XCALI-97821

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Selecting a

Batch

Use the Batch Selection page of the Acquisition mode to create a new batch in any of your current projects, or use a 
batch template to start a new batch. 

 To start a new batch

1. In the navigation pane, click Create a New Batch.

2. Select the Quantitation option, the Target Screening option, or the Unknown Screening option.

3. Select the batch folder where you want to create a new batch.

4. Type a unique name for the new batch in the Batch Name box.

5. Select a method from the Method Selection list.

The Method Compound Data pane displays the compounds in the method. You cannot edit the compounds list 
in the Acquisition mode.

6. To continue to the next page, click Next.

The Sample Definition page opens. See Defining the Sample List.

 To start a new batch from a template

1. In the navigation pane, click Create a New Batch.

2. Select the Quantitation option, the Target Screening option, or the Unknown Screening option.

3. In the Available Templates pane, select the template and method combination that you want to use.

The system creates a batch name with the selected template name and appends the date and time stamp. The 
application selects the default project, subproject, and method associated with this template. 

4. (Optional) Select a different batch folder where you want to create the new batch.

5. (Optional) Select a different method to use for the new batch. 

6. To continue to the next page, click Next.

The Sample Definition page opens. See Defining the Sample List.

 To select a prepared batch

1. In the navigation pane, click Submit a Prepared Batch.

The application displays all your unacquired, saved batches. The application stores all unacquired batches in the 
…\TraceFinderData\4.0\Projects\… folder.

2. Select the batch that you want to acquire.

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3. To continue to the next page, click Next.

The Finish page of the Acquisition mode opens. From the Finish page, you can save the batch, submit the batch 
for acquisition, or go back to the Sample Definition page to edit the sample list for this batch.

4. Do one of the following:

• To prepare the batch for acquisition, click Submit, .

For detailed instructions, see Submitting the Batch. 

–or–

• To edit the samples list, click Previous.

For detailed instructions about editing a samples list, see Defining the Sample List.

–or–

• To save the batch to be acquired later, click Save, .

The application saves your batch, closes the Acquisition mode, and returns you to the mode you were last 
using.

The application saves batches to the …\TraceFinderData\4.0\Projects\… folder.

 To reinject samples in a previously acquired batch

1. In the navigation pane, click Reinject Samples.

2. On the Batch page, select the batch that you want to reacquire.

The Batch page displays all previously acquired batches, both quantitative and screening.

3. To continue to the next page, click Next.

The Sample Definition page opens. See Defining the Sample List.

 To create a quantitation batch template

1. In the navigation pane, click Create or Edit a Template.

From this page, you can begin a new batch template.

2. Select the Quantitation option.

3. Click 

 and select the folder where you want to create the new batch template.

4. Type a name for the new batch template in the Template Name box.

5. Select a method from the Method Selection list.

The Method Compound Data pane displays the compounds in the method. You cannot edit the compounds list 
from the Acquisition mode.

6. To continue to the next page, click Next.

The Sample Definition page opens. See Defining the Sample List.

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 To create a target screening batch template

1. In the navigation pane, click Create or Edit a Template.

From the Template Selection page, you can begin a new batch template.

2. Select the Target Screening option.

3. Click 

 and select the folder where you want to create the new batch template.

4. Type a name for the new batch template in the Template Name box.

5. Select a method from the Method Selection list.

The Method Compound Databases pane displays the screening databases available for the selected method. 

6. Select the check box for each database that you want to use for screening.

7. To continue to the next page, click Next.

The Sample Definition page opens. See Defining the Sample List.

 To create an unknown screening batch template

1. Click Create or Edit a Template in the navigation pane.

2. Select the Unknown Screening option.

3. Click 

 and select the folder where you want to create the new batch template.

4. Type a name for the new batch template in the Template Name box.

5. Select a method from the Method Selection list.

The Method Compound Databases pane displays the unknown screening databases available for the selected 
method. 

6. Select the check box for each database that you want to use for unknown screening.

7. To continue to the next page, click Next.

The Sample Definition page of the Acquisition mode opens. See Defining the Sample List.

Note  When user security is activated, you must have Acquisition Wizard – Template Editing permission to 
create a batch template.

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Defining the

Sample List

Use the Sample Definition Page of the Acquisition mode to create a list of samples for the batch. You can add or 
insert samples to the list, import a sample list, or remove samples from the list.

As you enter sample values, you can use the Copy Down and Fill Down commands to quickly enter column values. 
For detailed instructions, refer to the “Using Copy Down and Fill Down” appendix in the TraceFinder User Guide.

After defining the list of samples, click Next.

• If you are creating a batch from scratch, creating a batch from a template, or editing a batch template, the Report 

Selection page opens. See Selecting and Reviewing Reports.

• If you are editing a previously acquired batch or a prepared batch, the Finish page opens. See Submitting the 

Batch.

 To add samples to the list

1. Select the number of sample rows to add and then click Add, .

2. For each sample, type a unique file name in the Filename column. 

3. For each sample, select a sample type from the Sample Type list. 

For a detailed description of sample types, refer to “Using the Acquisition Mode” in the TraceFinder User Guide.

4. For each Calibrator or QC sample, select a level from the Level list.

The sample levels are defined in the master method. If there are no levels to select from the Level list, ask a user 
with Supervisor or LabDirector permissions to edit the method and specify the levels. 

For detailed instructions about defining sample levels, refer to the method development chapters in the 
TraceFinder Lab Director User Guide.

5. For each sample, type a vial position in the Vial Position column. 

6. For each sample, type a volume in the Injection Volume column. 

7. (Optional) Type or edit the values for the remaining columns.

 To insert samples into the list

1. Select the sample above which you want to insert new Specimen samples.

2. Select the number of samples to insert and click Insert, .

The application inserts the Specimen samples above the selected sample.

3. For each sample, type a unique file name in the Filename column. 

4. For each sample, select a sample type from the Sample Type list. 

5. For each Calibrator or QC sample, select a level from the Level list.

Tip  To quickly add one sample row, right-click the sample list and choose Add Sample from the menu.

Available sample types

Specimen

Hydrolysis

Solvent

QC

Unextracted

Calibrator

Negative

Tip  Use the Fill Down command to make entering vial positions easier.

Note  When you use the scroll bar at the bottom of the sample list, the following columns remain fixed: 
Status, Filename, Sample Type, Groups, Qual Processing (quantitation) or Blank Subtraction (target 
screening) Level, Sample ID, and Sample Name, while the other columns scroll right and left. 

Inserted 
samples

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The sample levels are defined in the master method. If there are no levels to select from the Level list, ask a user 
with Supervisor or Lab Director permissions to edit the method and specify the levels. 

For detailed instructions about defining sample levels, refer to “Using the Method Development Mode” in the 
TraceFinder Lab Director User Guide.

6. Type a vial position in the Vial Position column for each sample. 

7. For each sample, type a volume in the Injection Volume column. 

8. (Optional) Type or edit the values for the remaining columns.

 To import samples into the list

1. Click Import, .

The Sample Import Tool dialog box opens where you can import a sample list from a CSV, an XML, or an SLD 
file.

2. Browse to and select a CSV, an XML, or an SLD file with the sample definitions that you want to import.

3. From the Imported Samples Will Be list, select either Appended to the End of the List or Inserted at the 

Selected Row.

4. Click Import.

The Sample Import Tool dialog box closes, and the application adds the specified samples to the samples list. 

When you import samples from an Xcalibur™ sequence file, the TraceFinder application makes the following 
column name and sample type substitutions.

5. For each Calibrator or QC sample, select a level from the Level list.

The sample levels are defined in the master method. If there are no levels to select from the Level list, ask a user 
with Method Development permission to edit the method and specify the levels. 

For detailed instructions about defining sample levels, refer to the method development chapters in the 
TraceFinder Lab Director User Guide.

6. For each sample, type a vial position in the Vial Position column. 

7. For each sample, type a volume in the Injection Volume column. 

8. (Optional) Enter or edit the values for the remaining columns.

9. (Optional) When using multiplexing, select a channel for each imported sample.

Imported samples default to Auto.

Tip  Use the Fill Down command to make entering vial positions easier.

Note  The .csv, .xml, or .sld data format must match the TraceFinder data format. 

Xcalibur column

TraceFinder column

Xcalibur sample type

TraceFinder sample type

Position

Vial Position

Blank

Negative

Inj Vol

Injection Volume

Std Bracket

Calibrator

Dil Factor

Conversion Factor

Tip  Use the Fill Down command to make entering vial positions easier.

Note  When you use the scroll bar at the bottom of the sample list, the following columns remain fixed: 
Status, Filename, Sample Type, Groups, Qual Processing (quantitation) or Blank Subtraction (target 
screening) Level, Sample ID, and Sample Name, while the other columns scroll right and left. 

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 To remove samples from the list

1. Select the samples you want to remove.

2. Right-click and choose Remove Selected Samples from the shortcut menu. 

 To reinject a sample from a previously acquired batch 

1. In the sample list, select the sample that you want to reinject.

2. Right-click and choose Reinject Selected Samples from the shortcut menu.

The application creates a copy of the selected sample and appends INJ001 to the file name. Additional 
reinjections of the same sample are numbered INJ002, INJ003, and so forth.

The application copies all parameter values from the original sample. A green status icon indicates previously 
acquired samples (acquired and processed), and the sample name is grayed out. A blue status icon indicates 
samples created for reinjection (not acquired).

When you submit this batch, the application acquires only the reinjection samples. 

Sample Definition Page

Tip  Use the CTRL or SHIFT keys to select multiple samples.

Table 1.  Sample Definition page parameters  (Sheet 1 of 2)

Parameter

Definition 

Previous

Returns you to the previous Acquisition page.

Next

Takes you to the next Acquisition page.

Sample Controls

Add

Adds the specified number of empty rows to the sample grid.

Insert

Inserts the specified number of empty rows above the selected row.

Import

Opens the Sample Import Tool to import samples from a CSV, an XML, or an 
SLD file. 

Multiplexing Channels 

Available only when you have activated multiplexing. Refer to “Using the 
Configuration Console” in the TraceFinder Lab Director User Guide.

All Channels

Uses all configured channels to acquire this batch.

Channel 1-n

Uses only the selected channels to acquire this batch.

Shortcut menu

Add Sample

Adds one empty row to the sample grid.

Insert Sample

Inserts one empty row to the sample grid above the selected row.

Insert Copy Sample

Copies the currently selected row and inserts a copy above the row.

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Selecting and

Reviewing

Reports

Use the Report Selection page of the Acquisition mode to specify the types of reports that you want to create. 

The Report Selection page lists all the available reports and displays the report name, report title, and the options to 
create printed, PDF, CSV, or Microsoft™ Excel™ output.

After specifying your report options, click Next to go to the Finish page and submit your batch. See Submitting the 
Batch.

The application saves the resulting output files for your reports in the following folder:

…\TraceFinderData\4.0\Projects\…\batch\Reports

 To edit a report title

Select the text in the Report Title column and edit the default text.

The default text in this column is the same as the report name. 

 To specify a report in print format or as a PDF, a CSV, or an Excel file

1. For each report that you want to create, select the check box in the Print, Create PDF, Create CSV, or Create 

Excel column.

2. To duplicate the output type for all reports, right-click the cell and choose Copy Down from the shortcut menu.

All check boxes in the column below the selected cell duplicate the selected or cleared state in the selected cell.

Reinject Selected Samples

Creates a copy of the selected samples and appends INJ001 to the end of the file 
name. Additional reinjections of the same sample are numbered INJ002, INJ003, 
and so forth.

Remove Selected Samples

Removes the selected samples from the sample grid.

Copy Down

Copies the value in the selected row to all rows below it. This command is 
available only when you have selected a value that can be copied down.

Fill Down

Enters sequential values in the column, starting with the value in the selected row 
and ending with the last row in the column. 

Modify Columns

Opens the Modify Columns dialog box to customize the column display. Refer to 
“Using the Analysis Mode” in the TraceFinder User Guide.

Enable/Disable Sample 
Weight Calculation

Displays or hides the Sample Volume, Dilution Factor, Sample Weight, 
Calculation Type, and Final Units columns.

Copy

Copies the data in the selected rows or columns to the Clipboard. Use this 
command to copy sample information to a text editor or a spreadsheet 
application. You cannot paste this data back into the Acquisition mode sample list.

Copy With Headers

Copies the data in the selected rows or columns and the associated column headers 
to the Clipboard. Use this command to copy sample information to a text editor 
or a spreadsheet application. You cannot paste this data back into the method 
development compound list.

Paste

Pastes one column of copied data from a text editor or a spreadsheet application 
into the selected column. 

Undo Last Paste

Removes the last pasted item in the sample list. 

Export to CSV File

Opens the Save As dialog box to save the batch to a CSV file.

Table 1.  Sample Definition page parameters  (Sheet 2 of 2)

Parameter

Definition 

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Report Selection Page

Submitting

the Batch

Use the Finish Page of the Acquisition mode to specify a startup method, a shutdown method, or a calibration file. 
You can save the batch to be acquired later, or you can submit the batch and acquire data, process data, or create 
reports. 

 To specify device states

In the System Status area of the Finish page, right-click the name of the device, and then choose a device state.

Parameter

Description

Report Name

The name of a report. 

Report Title 

User-editable description of the report. 

Print

Reports to be sent to the printer. 

Create PDF 

Reports to be saved as PDF files. 

Create CSV

Reports to be exported as CSV files. 

Create Excel

Reports to be exported as Excel files. 

Shortcut menu: 
Copy Down

Copies the selected or cleared state to all subsequent reports in the column. This 
action applies only to report types that make this output format available.

Note  If you are working with a batch template, the only available function is Save.

Instrument state

Turn Device On

(Default) Keeps the system in the On state when the current run finishes, so you 
can begin another run without waiting. All power and flows are maintained at 
operational levels.

Turn Device Standby

Keeps the system in the Standby state when the current run finishes, so you can 
begin another run with only a short delay between runs. 

Turn Device Off

Keeps the system in the Off state when the current run finishes. The Off state 
indicates that all power to the instrument, which the TraceFinder application can 
control, is turned off. Power to the instrument includes power to all heaters and 
most subassemblies, but in some cases not all subassemblies. 

Instrument status indicators

Green indicates that the device is turned on.

Yellow indicates that the device is in standby mode.

Red indicates a device error.

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 To specify startup or shutdown methods

1. (Optional) Select a method from the System Startup Method list on the Finish page.

The application runs this method before running the batch. No autosampler injection takes place. This feature is 
not available for all instruments.

2. (Optional) Select a method from the System Shutdown Method list.

The application runs this method after running the batch. No autosampler injection takes place. This feature is 
not available for all instruments.

 To automatically update the timed selected reaction monitoring information 

On the Finish page, select the Auto TSRM Update check box.

When you submit the batch, the application updates the TSQ™ method with mass transitions, collision energy, 
and other appropriate data for TSRM functionality.

 To specify a calibration file

1. In the Calibration area of the Finish page, select a calibration (.calx) file from the list.

2. To add calibration data from the current batch to the selected calibration file, select the Extend Calibration 

check box.

 To save a batch for later acquisition or processing

From the Finish page, click Save, .

The application saves your batch as a prepared file.

 To start an acquisition or processing

1. From the Finish page, click Submit, .

The Submit Options Dialog Box opens.

2. To acquire (or reacquire) the submitted samples, select the Acquire Data check box.

• When all submitted samples have been previously acquired, this option is (by default) not selected. 

• When there are any samples in the batch that have not been acquired, this option is (by default) selected.

3. To process the submitted samples, select the Process Data check box.

The application displays options for each type of method that the batch uses: Quantitation, Target Screening, 
Unknown Screening, or a combination of methods.

Note  You must acquire at least one batch with the current method to create a calibration (.calx) file.

Tip  You can process the data with or without performing peak detection. For example, you might want to 
turn off peak detection when reprocessing samples.

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4. For each method type, select the check box for the options that you want to use.

Peak Detect: Performs peak detection for all method types. You can process the data with or without performing 
peak detection. For example, you might want to turn off peak detection when reprocessing samples.

Quantitate: Performs quantitation for quantitation methods.

Identify: Performs identification for unknown screening methods.

Identify and Confirm: Performs both identification and confirmation for target screening methods.

With RT Alignment: Performs retention time alignment for unknown screening methods. This produces the 
heat map and group averages data in the Unknown Screening View. When you select this option, the application 
automatically selects the Peak Detect option.

5. (Optional) Select the Create Reports check box. 

6. (Optional with multiplexing activated) Select the Priority Sequence check box. 

The application acquires the priority batch on the next available channel or the assigned channel.

7. (Optional without multiplexing activated) Select the Priority Sequence check box and then select one of the 

following priority options to place the batch in the queue:

• Next Available Batch places the batch immediately after the currently acquiring batch. 

• Next Available Sample places the batch immediately after the currently acquiring sample.

8. To specify the following optional parameters, click Show Details.

a. Select the Use check box for the device that you want to use for this acquisition.

b. Select the Start Device check box to indicate the device that will initiate communication with the other 

instruments. 

This is usually the autosampler.

c. Select the Start When Ready check box, which starts all instruments together when they are all ready. 

When you clear this check box, individual instruments can start at different times and then must wait for the 
last instrument to be ready.

d. Select the system state after it acquires the last batch: On, Standby, or Off.

9. To start the selected processes, click OK.

The selected processes begin, and the application shows the real-time display at the bottom of the current 
window. You can begin another batch in the Acquisition mode while you watch the real-time display of the 
currently acquiring batch. 

Note  When you select Full Sequence Submission in the Configuration console, these options are unavailable 
because the current batch and the current sample are, in effect, the same thing. 

IMPORTANT   When your batch uses unknown screening features, after the first processing, you might see an 
error message stating that the total number of results is too large for a single batch (more than 500 000). Return 
to the Processing pages for the unknown screening features and make one or more of these parameter 
adjustments:

• Limit the RT range.
• Shorten the signal range.
• Specify a lower value for the Number of Top Matches.
• Specify a Simple Search instead of an Exhaustive Search.
• Specify Top Peaks instead of All Peaks.
• Limit the number of search types.

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Submit Options Dialog Box

Table 2.  Submit Options dialog box parameters  (Sheet 1 of 2)

Parameter

Description 

User Name

Displays the name of the current user.

Samples

Reports the batch number and number of samples.

Method Types

Lists the types of methods (quantitation, target screening, or unknown screening) used in 
the submitted batches.

Workflow Steps to Perform

Acquire Data

Submits the current batch to acquisition.

• When all submitted samples have been previously acquired, this option is (by default) 

not selected. 

• When there are any samples in the batch that have not been acquired, this option is 

(by default) selected.

Process Data

Processes the data for the current batch using any of the following options:

Peak Detect: Performs peak detection for all method types. You can process the data with 
or without performing peak detection. For example, you might want to turn off peak 
detection when reprocessing samples.

Quantitate: Performs quantitation for quantitation methods.

Identify: Performs identification for unknown screening methods.

Identify and Confirm: Performs both identification and confirmation for target screening 
methods.

With RT Alignment: Performs retention time alignment for unknown screening 
methods. This produces the heat map and group averages data in the Unknown Screening 
View. When you select this option, the application automatically selects the Peak Detect 
option.

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 To view the output files

Locate the files to view from the following directories:

• The application writes saved batches to the project folder:

…\TraceFinderData\4.0\Projects\…

• For each acquired sample, the application writes an RSX file to the batch Data folder:

…\TraceFinderData\4.0\Projects\…\Data

• The application saves method information to the batch Methods folder:

…\TraceFinderData\4.0\Projects\…\Methods

• The application writes the reports to the batch Reports folder:

…\TraceFinderData\4.0\Projects\…\batch\Reports 

Create Reports

Creates reports for the current batch.

Submit as a Priority Sequence?

Priority Sequence

With multiplexing activated, places the batch immediately after the currently acquiring 
batch. 

Without multiplexing activated, specifies one of the following priority options to place 
the batch in the queue:

Next Available Batch places the batch immediately after the currently acquiring batch. 

Next Available Sample places the batch immediately after the currently acquiring sample.

Note  When you select Full Sequence Submission in the Configuration console, these 
options are unavailable because the current batch and the current sample are, in effect, 
the same thing. 

Acquisition pane 

Device Name

Lists all configured instruments. If the instrument that you want to use is not configured, 
close the TraceFinder application, configure the instrument, and then reopen the 
application. You cannot configure an instrument while the TraceFinder application is 
running.

Use

Specifies the instruments used for this acquisition.

Start Device

Specifies the instrument that is used to initiate the communication with the other 
instruments. This is usually the autosampler.

Start When Ready

Starts the specified device when all the instruments are ready to acquire data. 

Post-run System State

Specifies the system state after it acquires the last batch: On (default), Standby, or Off.

Buttons

Hide/Show Details

Collapses or expands the acquisition details of the Submit Options dialog box.

OK

Begins the selected processes.

Cancel

Closes the Submit Options dialog box without submitting any tasks.

Table 2.  Submit Options dialog box parameters  (Sheet 2 of 2)

Parameter

Description 

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Finish Page

Using Quick

Acquisition

Use the quick acquisition feature to quickly submit samples from any mode in the application.

 To run a quick acquisition

1. Choose Tools > Quick Acquire Sample from the main menu or click the Quick Acquire Sample icon, 

.

The TraceFinder Quick Acquisition window opens.

Parameter

Description 

System Status

The System Status pane displays the following: 

• Devices used for the acquisition
• Project, subproject, and name of the batch
• Number of acquired and unacquired samples in the batch
• Number of reports to be printed and saved as PDF, CSV, or Excel files
• Local method and instrument method used for the batch
• Number of compounds in the method

System Startup Method
System Shutdown Method

The instrument methods that run before and after the batch. No autosampler 
injection takes place. These features are not available for all instruments.

Auto TSRM Update

Updates the TSQ method with mass transitions, collision energy, and other 
appropriate data for TSRM functionality.

Calibration

• Use calibration: Uses the selected calibration file to process the current data.
• Extend calibration: Adds calibration data from the current batch to the selected 

calibration file.

Previous

Returns you to the previous Acquisition page.

Save

Saves the current batch as a prepared file.

Submit

Opens the Submit Options dialog box.

Note  The Quick Acquisition feature is available only when you activate it in the Configuration console. 

15

2. To create the sequence of samples that you want to acquire, do any of the following:

• Use the Sequence buttons in the toolbar to open and save Xcalibur sequence (.sld) files.

• Use the Samples buttons in the toolbar to create a sequence of samples.

• (Optional) Use the Tools buttons in the toolbar to open a qualitative browser or the NIST library browser.

3. When you have completed your sequence of samples, click either of the Acquire buttons.

The application submits the samples for acquisition, processing, and report generation. 

Trademarks

TraceFinder and TSQ are trademarks and Xcalibur is a registered trademark of Thermo Fisher Scientific Inc. in the 
United States.

Excel and Microsoft are registered trademarks of Microsoft Corporation in the United States and other countries.

Button

Description

Replaces the current sequence with a new sequence that contains one Unknown 
sample.

Opens a saved SLD file.

Saves the current sequence as an SLD file in the C:\TraceFinderData\Sequences 
folder.

Saves the current sequence to a new file name or location.

Button

Description

Adds the specified number of new, empty samples to the end of the sample list. 

Inserts a new, empty sample or samples above the selected sample.

Removes the selected samples from the sample list. 

Button

Description

Opens the qualitative explorer that you configured as your default qualitative 
explorer in the Configuration console. 

Opens the NIST library browser. 

Button

Description

Submits only the selected samples for acquisition, processing, or report generation. 

Submits the sequence for acquisition, processing, or report generation.