Xcalibur 4.0 Data Acquisition and Processing User Guide Version A

Xcalibur 4.0 Data Acquisition and Processing User Guide Version A

3

Creating Processing Methods

To set up the workflow options for the Processing Setup window and to create processing methods to analyze your data and print reports, follow these procedures.

Contents

Opening the Processing Setup Window

Setting Up the Workflow Options for the Processing Setup Window

Setting Up the Void Time and Baseline Identification Options

Setting Up the Quantitative Processing Parameters

Setting Up the Qualitative Processing Parameters

Adding Report Templates to Processing Methods

Adding Programs or Macros to Processing Methods

When you finish setting up the parameters for a processing method in the Processing Setup window, use the Save or Save As commands to save the method. Processing methods are PMD files.

Opening the Processing Setup Window

Use the Processing Setup window to create quantitative and qualitative processing methods.

Before you create a processing method,

You can open the Processing Setup window in these ways:

• On the Roadmap view, click the Processing Setup icon, .

• From the home page, Instrument Setup, Quan Browser, or Library Browser window, choose GoTo > Processing Setup from the menu bar.

• In the sequence table of the Sequence Setup view, select a processing method in the

Processing Method column, and then choose Actions > Open File from the menu bar.

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Opening the Processing Setup Window

The window’s title bar lists the current view, page, study (if enabled), and processing method

name (

Figure 7

). The Processing Setup window has four views that you can navigate by using the View bar or the View menu. If the View bar is hidden, choose View > View Bar to display it on the left side of the window.

Figure 7.

Processing Setup window with the View bar displayed

View

Page

Method name

Calibration technique

View bar Components list

If you have not already set up the workflow options for the Processing Setup window, do so now as described in the next topic,

Setting Up the Workflow Options for the Processing Setup

Window .

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Creating Processing Methods

Setting Up the Workflow Options for the Processing Setup Window

Setting Up the Workflow Options for the Processing Setup Window

Follow these procedures to set up the workflow options for the Processing Setup window:

Setting Up the Startup Options

Dealing with Unapplied Page Parameters

Setting Up the Startup Options

You can set up the Processing Setup window to open with either the last processing method or the untitled processing method template. You can also set up the Processing Setup window to populate the chromatogram and spectrum cells with data from the raw data file that is associated with the processing method.

To set up the startup options for the Processing Setup window

1. From the Processing Setup window menu bar, choose Options > Settings.

The Settings dialog box opens ( Figure 8 ). For more information about the parameters for

this dialog box, see

Settings Dialog Box

.

Figure 8.

Settings dialog box

Thermo Scientific

2. In the Startup Mode area, select the appropriate startup option as follows:

• To load the last used processing method at startup, select the Load Last Processing

Method option.

• To start each new session with a new processing method, select the Create New

Processing Method option.

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Setting Up the Workflow Options for the Processing Setup Window

3. In the Auto-open Raw File area, select whether the chromatogram and spectrum cells are populated when you open a processing method as follows:

• To open processing methods with the chromatogram and spectrum cells populated with their associated raw data files, select the On option.

• To open processing methods with the chromatogram and spectrum cells empty, select the Off option.

4. To save the new settings and close the dialog box, click OK.

Dealing with Unapplied Page Parameters

The default setting for the Enable Warnings option is Enabled (Activated), which means that when you attempt a file operation, page or view change, or certain other actions, the

Apply

Changes? Dialog Box opens and you cannot proceed until you apply or undo the

changes ( Figure 9 ).

Figure 9.

Apply changes? dialog box

To apply the changes you made on the current page or view

In the Apply Changes dialog box, click Yes.

The data system applies changes automatically and, if appropriate, refreshes the chromatogram and spectrum views. If validation succeeds, the data system applies the modifications and proceeds with your selected action. If validation fails, the application displays an error message. If an error exists, it stops the selected action and returns you to the Processing Setup window so that you can correct or undo the changes.

To undo the changes you made on the current page or view

In the Apply Changes dialog box, click No.

The data system discards changes automatically and without prompting whenever you select a page change, file operation, or other action requiring page validation. It continues with your selected action.

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Setting Up the Void Time and Baseline Identification Options

To cancel the requested action

In the Apply Changes dialog box, click Cancel.

The data system returns you to the Processing Setup window without applying or discarding the changes. Clicking Cancel also clears the Don’t Tell Me About This Again check box if you selected it.

To turn off the Enable Warnings feature

In the Apply Changes dialog box, select the Don't Tell Me About This Again check box.

IMPORTANT Turning off the Enable Warnings feature changes the way in which the

Xcalibur data system handles unapplied parameters.

To enable the warnings feature

Choose Options > Enable Warnings.

Note If you are setting up an internal standard calibration, another dialog box appears when you click the Levels tab. This dialog box contains the following warning: This component is an ISTD and does not have any levels, so the Levels page will be empty. To turn off this warning, select the Don’t Tell Me About This Again check box.

Setting Up the Void Time and Baseline Identification Options

Use the Identification Options dialog box to specify the void time and baseline settings for the analyses to be processed with the current processing method or to change the default settings for these parameters.

The void time is the elution time of an unretained peak. The Xcalibur data system uses the void time to calculate the relative retention times of the chromatographic peaks.

To set the identification options for the current processing method

1. Choose Options > Identification from either the Quan view or the Qual view of the

Processing Setup window.

The Identification Options dialog box opens (

Figure 10 ). For parameter descriptions, see

“Identification Options Dialog Box” on page 292 .

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Setting Up the Void Time and Baseline Identification Options

Figure 10. Identification Options dialog box

2. To specify the void time, do one of the following:

• To specify an absolute void time, select the Value (min) option, and then type a value from 0.0 to 100.0 minutes in the associated box.

–or–

• To specify a relative void time that is based on the retention time of the first detected peak, select the First Peak option.

3. To adjust the Baseline parameters, do the following:

• In the Baseline and Noise Window (min) box, type a value from 0.1 to 1000.0 for the baseline and noise window.

The data system uses this window to calculate the baseline noise.

• In the Baseline Noise Tolerance (%) box, type a value from 0.0 to 100.0.

• In the Minimum Number of Scans in Baseline box, type an integer from 2 to 100.

4. To save your settings with the current processing method, click OK.

5. To save the new values as the default identification parameters, click Save As Default.

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Setting Up the Quantitative Processing Parameters

Setting Up the Quantitative Processing Parameters

Use the Quan view of the Processing Setup window to set up the quantitative processing parameters for a processing method. The Quan view contains the following pages:

Identification, Detection, Calibration, Levels, System Suitability, and Peak Purity (for PDA data only).

Before you enter the Quan view settings for the processing method, do the following:

• Specify whether the data is from a GC/MS system or an LC/MS system.

• Specify whether the processing method uses an external standard calibration or an internal standard calibration.

To open the Quan view of the Processing Setup window

From the Processing Setup window, do one of the following:

• From the menu bar, choose View > Quan.

–or–

• On the View bar, click the Quan icon, .

To set up the quantitative parameters for a processing method, follow these procedures:

Changing the Chromatography Mode

Changing the Calibration Mode

Setting Up the Quan View Identification Parameters

Setting Up the Quan View Integration and Detection Parameters

Setting Up the Calibration Parameters

Setting Up the Calibration and Quantitation Flags

Correcting for Calibration Impurities

Setting Up the Calibration and QC Levels

Setting Up the System Suitability Parameters

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Changing the Chromatography Mode

Use the Chromatography Options dialog box to specify the inlet (a liquid or gas chromatography system) used to acquire the raw data files.

To change the chromatography detection mode

1. In the Quan view of Processing Setup window, choose Options > Chromatography By.

The Chromatography Options Dialog Box opens (

Figure 11 ).

Figure 11. Chromatography Options dialog box

2. Select a detection mode as follows:

• To choose the GC detection mode, including the Spectrum detection option, select the GC option.

• To choose the LC detection mode, select the LC option.

3. To save the new setting and close the dialog box, click OK.

4. To save the detection mode as the default option for new processing methods, click Save

As Default.

Changing the Calibration Mode

Use the Calibration Options dialog box to change the calibration mode. For parameter descriptions, see

“Calibration Options Dialog Box” on page 277 .

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To change the calibration mode

1. In the Quan view of the Processing Setup window, choose Options > Calibration

Options.

The Calibration Options dialog box opens ( Figure 12 ).

Figure 12. Calibration Options dialog box

2. Select the calibration mode as follows:

• For an internal standard calibration, select the Internal Standard option.

• For an external standard calibration, select the External Standard option.

3. To save the new setting and close the dialog box, click OK.

4. To save the calibration mode as the default option for new processing methods, click Save

As Default.

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Setting Up the Quan View Identification Parameters

Use the Identification Page for Quan View

to set up the identification parameters for each analyte (component) in your sample mixture.

For parameter descriptions, see

“Identification Page for Quan View” on page 350 .

To set the identification parameters

1. From the Quan view of the Processing Setup window, click the Identification tab

( Figure 13

).

Figure 13. Identification page for Quan view

2. For each component (analyte) that you want to identify, do the following: a. In the Name box, do the following: i.

Select <New>.

ii. Type the name of the component.

Note For each component that you add to the Components list, you must select

New in the list box, and then type the name of the component.

b. From the Detector Type list, select the detector type: MS, Analog, A/D card, PDA, or UV. c.

From the Peak Detect list, select a peak detection algorithm: Genesis, ICIS, or

Avalon.

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Setting Up the Quantitative Processing Parameters d. If you selected MS as a detector type, select or type the name of a scan filter for the selected component in the Filter box.

Tip To select a scan filter from a list, you must first open an example raw data file.

To open a raw data file, choose File > Open Raw File. The Open Raw File dialog box opens. Select a raw data file and click Open.

For information about the nomenclature for scan filters, refer to the Xcalibur Qual

Browser User Guide.

e.

Select a Trace type or Trace combination in the three Trace lists as follows: i.

Select a Trace type from the first Trace list.

ii. To use a Trace type combination, select an operator (+ or ) in the second Trace list.

iii. Select the second Trace type in the third list.

f.

If needed, type the mass range or wavelength range of the selected component in the

Mass or Wavelength box.

g. Type a text comment in the Keys box. h. In the Retention Time area, type the expected retention time of the selected component in the Expected (min) box. i.

Type the allowable time deviation for the expected retention time (the window for the retention time) in the Window (sec) box.

j.

Specify whether the retention time of the selected component is to be used as a reference time for other components: i.

To use the selected component for a retention time reference, select the Use As

RT Reference check box. ii. To adjust the expected retention time of the selected component by using a retention time reference, use the Adjust Using box to select a reference.

3. To apply the settings for the selected component, click OK.

The component name appears in the Components list on the right side of the Quan view.

The Identification page remains open, and the other tabs become available.

4. To remove a component from the Components list, do the following: a. Select the component in the Components list.

b. Choose Options > Delete component name.

A dialog box appears with the following query: Confirm delete “component name”?

c.

Click OK to delete the component from the component list and close the dialog box.

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Setting Up the Quan View Integration and Detection Parameters

Use the Detection page of the Quan view to specify the integration and peak detection settings for the processing method.

The Detection page contains two areas: Peak Integration and Peak Detection. The available parameters in both the Peak Integration and Peak Detection areas depend on the peak detection algorithm selected on the Identification page of the Quan view. The three peak detection algorithms are Genesis, ICIS, and Avalon. The available Peak Detection parameters also depend on whether the data is from a GC/MS system or an LC/MS system.

These procedures show you how to set up the integration and detection parameters. Begin with the procedure for the peak detection algorithm that you selected on the Identification page of the Quan view.

Setting Up the Genesis Detection Parameters in the Quan View

Setting Up the ICIS Detection Parameters in the Quan View

Setting Up the Avalon Detection Parameters in the Quan View

Setting Up the Peak Detection Parameters for Chromatography by GC

Setting Up the Detection Data Flags in Quan View

Setting Up the Genesis Detection Parameters in the Quan View

This procedure describes how to set up the parameters for the Genesis peak detection algorithm.

When you select the Genesis peak detection algorithm for a component, the two areas on the

Detection page of the Quan view are labeled Genesis Peak Integration and Genesis Peak

Detection.

For information about the parameters for the Genesis peak detection algorithm, see

“Genesis

Detection Page for Quan View” on page 366

.

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To set up the Genesis detection parameters for a component

1. In the Quan view, click the Detection tab.

If you selected Genesis in the Peak Detect list on the Identification Page for Quan View for the component highlighted in the Components list on the right side of the window,

the Genesis Detection Page appears ( Figure 14

).

Figure 14. Genesis Detection page for Quan view

Thermo Scientific

2. Set up the integration parameters in the Genesis Peak Integration area as follows:

• To enter the smoothing level that the data system applies to the chromatogram before peak integration, type a value in the Smoothing Points box in the Genesis Peak

Integration area.

• To enter a signal-to-noise ratio threshold value, type a value in the S/N Threshold box.

The data system does not integrate peaks with a signal-to-noise ratio less than this value, but it integrates peaks with a signal-to-noise ratio greater than this value.

• To approximate the start and end points of unresolved peaks, select the Enable Valley

Detection check box and type a value for the minimum width of the peak in the

Expected Width (sec) box.

• To apply peak height and tailing factor integration criteria, select the Constrain Peak

Width check box. Then type the start integration setting in the Peak Height (%) box and the stop integration setting in the Tailing Factor box.

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3. To specify peak detection criteria, select one of the following component identification options:

• For an LC/MS system, select one of these two options:

– To choose the highest peak in the chromatogram, select the Highest Peak option.

– To choose the peak with the nearest retention time, select the Nearest RT option.

• For a GC/MS system, select one of these three options:

– To use a reference spectrum, select the Spectrum option. Then, make the appropriate entries in the spectrum and Thresholds tables.

For more information, see Setting Up the Spectrum Detection Parameters for

Chromatography by GC .

– To choose the highest peak in the chromatogram, select the Highest Peak option.

– To choose the peak with the nearest retention time, select the Nearest RT option.

When you select either the Highest Peak or Nearest RT option, the Ion Ratio

Confirmation parameters become available.

– To use ion ratio confirmation, select the Enable check box in the Ion Ratio

Confirmation area. Then, make the appropriate entries in the table.

– In the Window% area, select Relative or Absolute.

– In the Qualifier Ion Coelution area, type a value, in minutes, in the box.

For more information, see Setting Up Ion Ratio Confirmation for

Chromatography by GC .

4. To enter a signal-to-noise ratio threshold, type a value in the Minimum Peak Height

(S/N) box.

The data system ignores all chromatogram peaks that have a signal-to-noise value less than this parameter value.

5. To use the advanced detection options for the Genesis peak detection algorithm, do the following: a. Click Advanced.

The Genesis Advanced Detection Options dialog box opens. For information about

the parameters in this dialog box, see “Genesis Advanced Detection Options Dialog

Box” on page 288 .

b. Make the appropriate entries and click OK.

6. To save the settings on the Detection page, click OK.

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Setting Up the ICIS Detection Parameters in the Quan View

This procedure describes how to set up the parameters for the ICIS peak detection algorithm.

When you select the ICIS peak detection algorithm for a component, the two areas on the

Detection page of the Quan view are labeled ICIS Peak Integration and ICIS Peak Detection.

For more information about the parameters on the ICIS Detection page in the Quan view, see

“ICIS Detection Page for Quan View” on page 376 .

To set up the ICIS detection parameters for a component

1. In the Quan view, click the Detection tab.

If you selected ICIS in the Peak Detect list on the Identification page for the component highlighted in the Components list on the right side of the window, the ICIS Detection page appears (

Figure 15

).

Figure 15. ICIS Detection page for Quan view (GC mode)

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2. Set up the integration parameters in the ICIS Peak Integration area as follows:

• To set the smoothing level that the application applies to the chromatogram before peak integration, type a value in the Smoothing Points box.

• To set the baseline window parameter, type a value in the Baseline Window box.

• To set the area noise factor, type a value in the Area Noise Factor box.

• To set the peak noise factor, type a value in the Peak Noise Factor box.

• To apply peak height and tailing factor integration criteria, select the Constrain Peak

Width check box.

– To enter the start integration threshold, type a value in the Peak Height (%) box.

– To enter the stop integration criterion, type a value in the Tailing Factor box.

3. To specify peak detection criteria, select one of the following component identification options:

• For an LC/MS system, select one of these two options:

– To choose the highest peak in the chromatogram, select the Highest Peak option.

– To choose the peak with the nearest retention time, select the Nearest RT option.

• For a GC/MS system, select one of these three options:

– To use a reference spectrum, select the Spectrum option. Then, make the appropriate entries in the spectrum and Thresholds tables.

For more information, see Setting Up the Spectrum Detection Parameters for

Chromatography by GC .

– To choose the highest peak in the chromatogram, select the Highest Peak option.

– To choose the peak with the nearest retention time, select the Nearest RT option.

When you select either the Highest Peak or Nearest RT option, the Ion Ratio

Confirmation parameters become available.

– To use ion ratio confirmation, select the Enable check box in the Ion Ratio

Confirmation area. Then, make the appropriate entries in the table.

– In the Window% area, select Relative or Absolute.

– In the Qualifier Ion Coelution area, type a value, in minutes, in the box.

For more information, see Setting Up Ion Ratio Confirmation for

Chromatography by GC .

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4. To enter a signal-to-noise ratio threshold, type a value in the Minimum Peak Height

(S/N) box.

The data system ignores all chromatogram peaks that have a signal-to-noise value less than this parameter value.

5. To modify the advanced detection options for the ICIS peak detection algorithm, do the following: a. Click Advanced.

The ICIS Advanced Detection Options dialog box opens. For information about the

parameters in this dialog box, see “ICIS Advanced Parameters Dialog Box” on page 290 .

b. Make the appropriate entries and click OK to save the new settings and close the dialog box.

6. To save the settings on the Detection page, click OK.

Setting Up the Avalon Detection Parameters in the Quan View

This procedure describes how to set up the parameters for the Avalon peak detection algorithm on the Detection page of the Processing Setup – Quan view.

When you select the Avalon peak detection algorithm for a component, the two areas on the

Detection page of the Quan view are labeled Avalon Peak Integration and Avalon Peak

Detection.

For more information about the parameters on the Avalon Detection page, see

“Avalon

Detection Page for Quan View” on page 358

.

To set up the Avalon detection parameters for a component

1. In the Quan view, click the Detection tab.

The Avalon Detection page for Quan View appears (

Figure 16

).

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Figure 16. Avalon Detection page

2. To enter the smoothing level that the application applies to the chromatogram before peak integration, type a value in the Smoothing Points box in the Avalon Peak Integration area.

3. To edit the events table, do the following: a. Click Advanced.

The Avalon Event List dialog box opens (

Figure 17 ).

Figure 17. Avalon Event List dialog box

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Setting Up the Quantitative Processing Parameters b. To edit the Event list, highlight the row you that want to change, one row at a time, and enter the revised settings in the boxes. Click Change.

c.

To save the new settings and close the dialog box, click Exit.

4. To specify peak detection criteria, select one of the following component identification options:

• For an LC/MS system, select one of these two options:

– To choose the highest peak in the chromatogram, select the Highest Peak option.

– To choose the peak with the nearest retention time, select the Nearest RT option.

• For a GC/MS system, select one of these three options:

– To use a reference spectrum, select the Spectrum option. Then, make the appropriate entries in the spectrum and Thresholds tables.

For more information, see Setting Up the Spectrum Detection Parameters for

Chromatography by GC .

– To choose the highest peak in the chromatogram, select the Highest Peak option.

– To choose the peak with the nearest retention time, select the Nearest RT option.

When you select either the Highest Peak or Nearest RT option, the Ion Ratio

Confirmation parameters become available.

– To use ion ratio confirmation, select the Enable check box in the Ion Ratio

Confirmation area. Then, make the appropriate entries in the table.

– In the Window% area, select Relative or Absolute.

– In the Qualifier Ion Coelution area, type a value, in minutes, in the box.

For more information, see Setting Up Ion Ratio Confirmation for

Chromatography by GC .

5. To save the settings on the Detection page, click OK.

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Setting Up the Peak Detection Parameters for Chromatography by GC

For GC/MS data, the Xcalibur data system provides two confirmation techniques for peak detection: spectrum and ion ratio confirmation.

These procedures describe how to set the parameters for the confirmation techniques:

Setting Up the Spectrum Options for Chromatography by GC

Setting Up the Spectrum Detection Parameters for Chromatography by GC

Setting Up Ion Ratio Confirmation for Chromatography by GC

Setting Up the Spectrum Options for Chromatography by GC

For a GC/MS system, you can set up a low-intensity cutoff for the spectral data.

To change the low intensity cutoff threshold for spectrum detection

1. If you have not already done so, set up the processing method for data produced by a

GC/MS system as follows: a. Choose Options > Chromatography By.

The Calibration Options Dialog Box opens (see

Figure 11 on page 24 ).

b. Select the GC option.

c.

Click OK to accept the new setting and close the dialog box.

2. In the Quan view, click the Detection tab.

3. In the Peak Detection area, select the Spectrum option.

4. From the menu bar, choose Options > Spectrum.

The Spectrum Options Dialog Box

opens (

Figure 18

).

Figure 18. Spectrum Options dialog box

5. To enter a spectrum detection threshold, type a value in the Low Intensity Cutoff (%) box.

6. To save the new setting and close the dialog box, click OK.

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Setting Up the Spectrum Detection Parameters for Chromatography by GC

For GC/MS data, follow these procedures to set up the spectrum detection parameters for a component on the Detection page of the Quan view in the Processing Setup window.

To select the spectrum detection options for a component

1. If you have not already set up the data system to process the data from a GC/MS system, do the following: a. In the Quan view of the Processing Setup window, choose Options >

Chromatography By.

The Chromatography Options dialog box opens (see Figure 11 on page 24 ).

b. Select the GC option.

c.

Click OK to accept the new setting and close the dialog box.

2. In the Quan view, click the Detection tab (

Figure 14 on page 29

).

3. To display the spectrum options in the Peak Detection area, select the Spectrum option.

4. Enter the mass-to-charge [m/z] and intensity data for up to 50 spectrum peaks in the spectrum peak identification table (

Figure 19 ).

• To manually enter the peak data, see

To enter data manually in the spectrum table

.

• To interactively enter the peak data, see To enter data in the spectrum table by using an open raw data file .

Figure 19. Spectrum peak identification table

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To enter data manually in the spectrum table

1. For all the ions in the reference spectrum (up to a maximum of 50), do the following:

• Select an m/z table cell and type the value for an ion characteristic of the component.

• Select the Intensity (%) table cell and type a value for the relative intensity of the ion.

2. To edit the table, do the following:

• To insert a row, click the row number above the position. Right-click and choose

Insert Row from the shortcut menu.

• To delete a row, click the row number of the row to delete. Right-click and choose

Delete Rows from the shortcut menu, or press DELETE.

• To delete a range of rows, drag the cursor from the first to the final row in the selected range. Then right-click and choose Delete Rows.

To enter data in the spectrum table by using an open raw data file

1. Set the low-intensity cutoff as described in

Setting Up the Spectrum Options for

Chromatography by GC .

2. Pin the spectrum cell.

3. Click the appropriate component peak in the chromatogram cell.

The data system displays the spectrum from the selected time point in the spectrum cell and copies the m/z and intensity values of the ions in the mass spectrum to the peak identification table. It discards any ions with intensities below the Low Intensity Cutoff

(%) parameter in the

Spectrum Options Dialog Box .

4. To set threshold values for spectrum matching in the Thresholds area.

• In the Forward box, type an integer from 0 to 1000.

• In the Reverse box, type a value from 0 to 1000.

• In the Match box, type a value from 0 to 100.

For more information about the settings for these parameters, see “Detection Page for

Quan View” on page 358

.

5. To save the settings, click OK.

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Setting Up Ion Ratio Confirmation for Chromatography by GC

This procedure for setting up the ion ratio confirmation parameters applies only to GC/MS data.

To set up ion ratio confirmation for a component

1. In the Quan view of the Processing Setup window, click the Detection tab.

2. Select the Highest Peak option or the Nearest RT option in the Peak Detection area.

3. To turn on the ion ratio confirmation feature, select the Enable check box in the Ion

Ratio Confirmation area (

Figure 20

).

Figure 20. Ion ratio confirmation area

Thermo Scientific

4. To enter the information for up to four qualifier ions for the current component, do the following for each ion:

• Select an m/z box and type the value for an ion characteristic of the component.

• Select the Target Ratio (%) box and type a value for the target ratio.

• Select the Window (±%) box and type a value for the relative intensity of the ion.

5. To edit the table, do the following:

• To insert a row, click the row number above the position. Right-click and choose

Insert Row from the shortcut menu.

• To delete a row, click the row number of the row to delete. Right-click and choose

Delete Rows from the shortcut menu, or press DELETE.

• To delete a range of rows, drag the cursor from the first to the final row in the selected range. Then right-click and choose Delete Rows.

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6. Set the Window% mode as follows:

• To use the target ratio tolerances in the Window (±%) column as absolute percentages of the target ratio, select the Absolute option.

• To use the target ratio tolerances in the Window (±%) column as relative percentages of the target ratio, select the Relative option.

7. To set a value, in minutes, for the qualifier ion coelution window, type a value in the

Qualifier Ion Coelution box.

8. To save the settings, click OK.

Setting Up the Detection Data Flags in Quan View

Use the Data Flags dialog box to set up the data flags. You can access the Data Flags dialog box from the Quan view – Detection page. For more information about the Data Flags dialog

box, see Data Flags Dialog Box

.

To set up the data flag settings

1. In the Quan view of the Processing Setup window, click the Detection tab.

The Detection page opens (see Figure 15 on page 31

).

2. Click Flags.

The Data Flags dialog box opens (

Figure 21 ).

Figure 21. Data Flags dialog box

3. To set the threshold value for the Area Threshold flag, type a value in the Area Threshold box.

4. To set the threshold value for the Height Threshold flag, type a value in the Height

Threshold box.

5. To save the new settings and close the dialog box, click OK.

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Setting Up the Calibration Parameters

Use the Calibration page of the Quan view to set up the calibration information for a quantitative analysis.

If you selected the External Standard calibration option, the parameters for internal standards are not available. For an external standard calibration, one calibration curve is associated with each target compound.

If you selected the Internal Standard calibration option, the parameters for both the internal standards and the target components are available. The component list must include at least one internal standard. One calibration curve is associated with each target component. For an internal standard calibration, each target compound must have an associated internal standard component.

For more information about the parameters on the Calibration page, see

“Calibration Page for

Quan View” on page 385

.

To define the calibration curve parameters and the internal standard component for target components and the amount for internal standard components

1. In the Quan view of the Processing Setup window, click the Calibration tab.

The Calibration page opens ( Figure 22 ).

Figure 22. Calibration page

Thermo Scientific

2. Depending on the calibration technique, do one of the following:

• For an internal standard calibration, go to step 3 .

• For an external standard calibration, go to

step 4

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3. For an internal standard calibration, do the following: a. For each internal standard component, do the following: i.

Select the component in the Component list on the right side of the Processing

Setup window. ii. In the Component Type area, select the ISTD option.

iii. In the ISTD area, type the amount for the selected internal standard in the

Amount box.

Note For an internal standard calibration, you must assign the ISTD type to at least one component before you can assign the Target Compound type to other components. b. For each target compound, do the following: i.

Select the component in the Component list.

ii. Select the Target Compound option.

iii. In the ISTD list, select the internal standard component that you added to the target compound standard.

iv. To correct for isotope contributions, click Isotope%.

The Correction for Isotope Contribution dialog box opens. See

Correcting for

Calibration Impurities for information about entering values into this box.

v.

Make the appropriate entries.

vi. Click OK to accept the entries and close the dialog box.

vii. Go to step 5

.

4. For an external standard calibration, do the following: a. Select the component in the Components list.

b. Select the Target Compound option.

5. For both calibration techniques, do the following for each target compound: a. Select the component in the Components list.

b. In the Calibration Curve list, select the curve type:

• Linear • Average response factor (RF)

• Quadratic • Point-to-point

• Linear log-log

• Quadratic log-log

• Cubic spline

• Locally weighted c.

For the Linear and Quadratic curve types, select an option in the Weighting area.

If you select any of the other curve types, the Weighting area is not available.

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For more information about the curve types and the weighting options, see

“Calibration Page for Quan View” on page 385

.

d. For the Linear, Quadratic, Point-to-Point, or Cubic Spline curve types, in the Origin area select how the data system treats the origin in the calibration curve calculation as follows:

• Select the Ignore option to exclude the origin from the calibration curve calculation.

• Select the Force option to require that the calibration curve pass through the origin.

• Select the Include option to include the origin as one data point.

e.

To select the units to be displayed on graphs and reports, type the appropriate units in the Units box.

f.

In the Response area, define the basis for the quantitation:

• To quantify on the basis of the integrated area of component peaks, select the

Area option.

• To quantify on the basis of the calculated height of component peaks, select the

Height option.

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Setting Up the Calibration and Quantitation Flags

Use the Calibration and Quantitation Flags dialog box to set up calibration and quantitation flags for the processing method. You can access this dialog box from the Calibration page of the Quan view.

For more information about the Calibration and Quantitation Flags dialog box, see

“Calibration and Quantitation Flags Dialog Box” on page 276 .

To set up calibration and quantitation flags

1. From the Quan view of the Processing Setup window, click the Calibration tab.

The Calibration page opens ( Figure 23 ).

Figure 23. Calibration page for the Quan view of the Processing Setup window

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2. Click Flags.

The Calibration and Quantitation Flags dialog box opens ( Figure 24 ).

Figure 24. Calibration and Quantitation Flags dialog box

Thermo Scientific

3. In the Calibration Flag area, type a value from 0.000 to 1.000 in the R-squared box to specify the calibration flag threshold.

4. In the Quantitation Flags area, do the following:

• To adjust the detection limit flag threshold value, type a value in the Detection Limit box.

• To adjust the linearity limit flag threshold value, type a value in the Linearity Limit box.

• To adjust the quantitation limit flag threshold value, type a value in the Quantitation

Limit box.

• To adjust the carry-over limit flag threshold value, type a value in the Carry Over

Limit box.

5. To save the new settings and close the dialog box, click OK.

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Correcting for Calibration Impurities

Use the Correction for Isotope Contribution dialog box to correct for an impurity in the internal standard reagent that elutes at the same time as the target compound reagent [TM], or to correct for an impurity in the target compound reagent TM [impurity] that elutes at the same time as the internal standard reagent [ISTD], or to correct for impurities in both reagents.

To correct for calibration impurities

1. From the Quan view of the Processing Setup window, click the Calibration tab.

The Calibration Page opens (see

Figure 23 on page 44 ).

2. Click Isotope%.

The Correction for Isotope Contribution dialog box opens (

Figure 25

).

Figure 25. Correction for Isotope Contribution dialog box

3. Make the following entries:

• If you have an impurity in your internal standard that elutes at the same time as the target compound, type the ISTD [impurity] / ISTD [pure] percentage (ratio × 100%) in the Contribution of ISTD to Target Compound (%) box.

To determine this ratio experimentally, analyze the ISTD reagent using the method for quantitation of the target compound. Use the respective peak areas or heights to determine the ratio of impurity [peak at retention time of TM] to pure compound

[peak at retention time of ISTD]: ISTD [impurity] / ISTD [pure].

• If you have an impurity in your target molecule reagent that elutes at the same time as the ISTD molecule, type the TM [impurity] / TM [pure] percentage (ratio × 100%) in the Contribution of Target Compound to ISTD (%) box.

To determine this ratio experimentally, analyze the TM reagent using the method for quantitation of the target compound. Use the respective peak areas or heights to determine the ratio of impurity [peak at the retention time of ISTD] to pure compound [peak at retention time of TM]: TM [impurity] / TM [pure].

Using the data you provide in this step, the data system corrects for the ISTD

[impurity] or TM [impurity] and reports the corrected amounts of ISTD and TM.

4. To save the new settings and close the dialog box, click OK.

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Setting Up the Calibration and QC Levels

Use the Levels page of the Processing Setup – Quan view to set up the levels for the calibration standards and QC samples in the processing method.

You can set up the level information for the calibration standards in two ways: by manual entry on the Levels page or semi-automatically by using the Standard Dilutions dialog box.

You can only set up the level information for the QC samples manually.

To set up the levels for the calibration standards and QC samples, follow these topics:

Setting Up the Levels for the Calibration and QC Standards

Using the Standard Dilutions Dialog Box to Set Up the Calibration Levels

Setting Up the Levels for the Calibration and QC Standards

You can set up the calibration standard levels in the processing method either manually or by using the Standard Dilutions dialog box. You can only enter the QC levels manually.

For more information about the Levels page, see

“Levels Page for Quan View” on page 390 .

To set up the calibration and QC levels for the target components

1. From the Quan view of the Processing Setup window, click the Levels tab.

The Levels page opens ( Figure 26 ).

Figure 26. Levels page for Quan view

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2. To select a component, click a target component in the Components list on the right side of the Processing Setup window.

The Levels page is not available for ISTD components.

3. To set up the calibration levels for all the target components, do one of the following:

• Use the

Standard Dilution Dialog Box

(see Using the Standard Dilutions Dialog Box to Set Up the Calibration Levels ).

–or–

• Select a target component, and then type the settings for the selected component in the Calibration Levels table:

– To enter the calibration levels for a component, type alphanumeric text to identify the levels in the Cal Level boxes.

– To enter the amount of the target component for each level, type numeric values in the Amount boxes.

Note Enter the amount of the internal standard spiked into each sample and each calibration standard in the Internal Standard area on the Calibration page. Every sample and standard must have the same spiked amount of the internal standard associated with the target component.

4. For each target component, enter information about the quality control samples in the

QC Levels table:

• To enter the quality control levels, type alphanumeric text to identify the levels in the

QC Level boxes.

• To enter the amount of the target component added at each level, type numeric values in the Amount boxes.

• To enter the acceptable difference (as a percentage) between the known amount and the calculated amount for each QC level, type numeric values in the (%)Test boxes.

5. To save your settings, click OK.

Using the Standard Dilutions Dialog Box to Set Up the Calibration Levels

To simplify data entry, use the Standard Dilution dialog box to enter the calibration standard and QC levels in the processing method.

For more information about the Standard Dilution dialog box, see “Standard Dilution Dialog

Box” on page 299 .

To enter the calibration levels for the target components

1. From the Quan view of the Processing Setup window, click the Levels tab.

The Levels page opens.

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2. Choose Options > Standard Dilution from the menu bar.

The Standard Dilution dialog box opens (

Figure 27 ).

Figure 27. Standard Dilution dialog box

Thermo Scientific

3. For each target component, type the undiluted amount in the Amount box in the Base

Amounts table. Then, press ENTER.

4. For each calibration level, enter the dilution information in the Dilution Factors table:

• Type alphanumeric text for the calibration level in the Cal Level column.

• Type the dilution factor (from 0.00000001 to 1) for the calibration level in the

Dilution column.

5. To save the new settings and close the dialog box, click OK.

The data system uses the settings to calculate the calibration level amounts for all the target components defined in the processing method.

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Setting Up the System Suitability Parameters

Use the System Suitability page of the Processing Setup – Quan view to set up the system suitability parameters for your chromatographic analysis.

For more information about the system suitability parameters, see “System Suitability Page for

Quan View” on page 392

.

To set up the system suitability parameters

1. From the Quan view of the Processing Setup window, click the System Suitability tab.

The System Suitability page opens (

Figure 28

).

Figure 28. System Suitability page of the Processing Setup window – Quan view

2. To perform resolution testing, select the Enable check box in the Resolution Parameters area, and type a threshold for peak resolution in the Resolution Threshold (%) box.

3. To perform symmetry testing, select the Enable check box in the Symmetry Parameters area. Type a peak height for symmetry testing in the Peak Height (%) box, and type a threshold for symmetry testing in the Symmetry Threshold (%) box.

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4. To carry out classification tests, select the Enable check box in the Peak Classification

Parameters area. Then set the following parameters: a. To adjust Xcalibur peak width testing thresholds, type parameters in the Detect Peak

Width area.

• To enter a peak height for the test, type a value in the Peak Height box.

• To enter a minimum peak width threshold, type a value in the Min Peak Width

(sec) box.

• To enter a maximum peak width threshold, type a value in the Max Peak Width

(sec) box.

b. To adjust the Xcalibur peak tailing test, type parameters in the Detect Tailing area.

• To enter a peak height for the test, type a value in the Peak Height (%) box.

• To enter a threshold limit for peak tailing, type a value in the Failure Threshold box.

c.

To adjust the Xcalibur column overload test, type parameters in the Detect Column

Overload area.

• To enter a peak height for the test, type a value in the Peak Height (%) box.

• To enter a threshold limit for peak tailing, type a value in the Failure Threshold box.

d. To adjust the Xcalibur baseline clipping test, type parameters in the Detect Baseline

Clipping area and the Detect Minimum Signal-to-Noise Ratio area.

• To define the test window, type a value in the Number of Peak Widths for Noise

Detection box.

• To define the signal-to-noise threshold, type a value in the Signal-to-Noise Ratio box.

5. To save your settings, click OK.

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Setting Up the Qualitative Processing Parameters

The Qual view of the Processing Setup window has five pages: Identification, Spectrum

Enhancement, Library Search Options, Library Search Constraints, and Peak Purity (for PDA data only). This topic describes the Identification and Spectrum Enhancement pages. See

Creating and Searching Libraries with Library Browser Refer to the Creating and Searching

Libraries User Guide for information about using libraries to search for spectra.

To open the Qual view of the Processing Setup window

From the Processing Setup window, do one of the following:

• On the View bar, click the Qual icon, .

–or–

• From the menu bar, choose View > Qual.

To set up the qualitative parameters for a processing method, follow these procedures:

Setting Up the Qual View Identification Parameters

Setting Up the Qual View Spectrum Enhancement Parameters

Refer to Creating and Searching Libraries with Library Browser the Creating and Searching

Libraries User Guide for information about using libraries to search for spectra.

Setting Up the Qual View Identification Parameters

Use the Identification page of the Processing Setup – Qual view to specify the type of chromatogram that the processing method uses during qualitative processing. You can also adjust peak detection and identification criteria.

The data system displays the version of this page (ICIS, Genesis, or Avalon) that corresponds to your current default peak detection algorithm: ICIS, Genesis, or Avalon.

For parameter descriptions, see these topics:

Avalon Identification Page for Qual View

ICIS Identification Page for Qual View

Genesis Identification Page for Qual View

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To set up the Qual view identification parameters

1. From the Qual view of the Processing Setup window, click the Identification tab.

The Identification page for the Qual view opens (

Figure 29

).

Figure 29. Identification page for the Qual view

Thermo Scientific

2. To open a raw data file, do the following: a. Choose File > Open Raw File.

The Open Raw File dialog box opens.

b. Select a raw data file to analyze.

c.

Click Open.

3. In the Detector area, do the following: a. Select a detector from the Type list.

Valid detector types are MS, Analog, A/D Card, PDA, or UV.

b. If you select a non-MS detector type, type the time difference, in minutes, between

MS and non-MS detection in the Delay box to synchronize the data with the MS detector.

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In the Peak Detect list, select the peak detection algorithm that you want the data system to use to identify and integrate peaks.

The selections are ICIS, Genesis, and Avalon.

Note Select the appropriate peak detection algorithm on the basis of these criteria:

• The Genesis peak detection algorithm supports backward compatibility with

Xcalibur 1.0 studies.

• The ICIS peak detection algorithm is designed for MS data and has superior peak detection efficiency at low MS signal levels.

• The Avalon peak detection algorithm is designed for UV data. Avalon also supports negative peaks.

4. Select a Trace type or Trace combination in the three Trace lists:

• Select a Trace type from the first Trace list box.

• To use a Trace type combination, select an operator (+ or ) in the second Trace list box, and then select the second Trace type in the third list box.

5. To select or enter a scan filter for an MS trace type, type or select the name of the filter to be used for the selected component in the Filter box.

6. To enter the mass range (or wavelength range for non-MS detectors) for the chromatogram, type the mass or mass ranges or wavelength or wavelength ranges in the

Mass or Wavelength boxes.

7. To specify a retention time window of the chromatogram for qualitative processing, do one of the following:

• Type the time range in the Range box (for example, 0.30–1.55).

–or–

• Using a representative raw data file, interactively select the retention time window in the chromatogram cell as follows: i.

If you have not already done so, open a representative raw data file. ii. Pin the spectrum cell.

iii. In the chromatogram cell, drag the cursor horizontally across the peak in the chromatogram cell.

The data system updates the Range (min) box with a time span centered on the apex of the dragged peak.

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8. Select from among these peak integration options: Genesis, ICIS, Avalon.

Table 3 describes the peak integration options.

Table 3. Peak integration options (Sheet 1 of 2)

Peak detect

Genesis

Peak integration options

• In the Smoothing Points box, type the number for the amount of smoothing that the data system applies before integration.

The value must be an odd integer from 3 (minimum smoothing) to 15 (maximum smoothing).

• In the S/N Threshold box, type the signal-to-noise threshold value.

• Select or clear the Enable Valley Detection check box and, if selected, enter the value in seconds in the Expected Width box.

• To constrain the peak width, select the Constrain Peak

Width check box and type a value in the Tailing Factor box.

• To change the advanced detection parameters if required, click Advanced.

ICIS

The Genesis Advanced Chromatogram Options dialog box opens. For information about the parameters in this dialog

box, see “Genesis Advanced Chromatogram Options Dialog

Box” on page 282

• In the Smoothing Points box, type the number of points used for a moving average.

• In the Baseline Window box, type the number of scans to scan for a local minima.

• In the Area Noise Factor box, type the noise level multiplier used to determine the peak edge after the location of a possible peak.

• In the Peak Noise Factor box, type the noise level multiplier used to determine the potential peak signal threshold.

• To change the advanced detection parameters, click

Advanced.

The ICIS Advanced Parameters dialog box opens. For information about the parameters in this dialog box, see

“ICIS Advanced Parameters Dialog Box” on page 290 .

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Table 3. Peak integration options (Sheet 2 of 2)

Peak detect

Avalon

Peak integration options

• In the Smoothing Points box, type the number for the amount of smoothing that the data system applies before integration.

The valid values are odd integers from 3 (minimum smoothing) to 15 (maximum smoothing).

• To display initial peak detection settings in the Avalon Peak

Integration area, click Auto Calc Initial Events.

• To edit the peak detection settings in the Event list, do the following: a. Click Advanced.

The Avalon Event List dialog box opens. For information

about this dialog box, see “Avalon Event List Dialog Box” on page 273 .

b. Make changes to the Event list and click Change to apply them automatically to the chromatogram plot and to the

Event list on the Identification page. c.

After editing the peak detection settings, click Exit to close the dialog box.

9. To reduce the number of chromatogram peaks submitted for further processing, select from the options under Limit Peaks: a. In the Select Top Peaks area, select the Enable check box.

• To restrict processing to the most significant peaks on the basis of the peak areas, select the By Area option.

• To restrict processing to the most significant peaks on the basis of the peak heights, select the By Height option.

• Type the maximum number of peaks to be processed in the Num to Select box. b. In the Rel Peak Height Threshold area, select the Enable check box and enter the peak height threshold in the Percent of Highest Peak box.

10. To save your settings, click OK.

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Setting Up the Qual View Spectrum Enhancement Parameters

Use the Spectrum Enhancement page of the Processing Setup – Qual View to select an option for enhancing spectra.

To set up the spectrum enhancement parameters, follow the appropriate procedure:

Using the Combine Option for Spectrum Enhancement

Using the Refine Option for Spectrum Enhancement

Using the Threshold Option for Spectrum Enhancement

Using the Combine Option for Spectrum Enhancement

For information about the parameters in the Combine area on the Spectrum Enhancement page of the Processing Setup – Qual view, see

“Spectrum Enhancement Page for Qual View” on page 329

.

To use the Combine option for spectrum enhancement

1. From the Qual view of the Processing Setup window, click the Spectrum Enhancement tab.

The Spectrum Enhancement page opens.

Figure 30 shows the parameters for the

Combine option.

Figure 30. Spectrum Enhancement page of the Qual view with the Combine option selected

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2. To display the Spectrum Enhancement options, select the Enable check box.

3. To average multiple scans, select the Combine option.

4. To define the Peak Top Region, type the number of scans you want to average across the apex of the peak in the Width (points) box. Examine the chromatogram peak and estimate the number of good scans across the peak apex.

5. In the Background Subtraction Left Region area, define the baseline region used for background analysis before a peak as follows: a. In the Region Width (points) box, type the number of scans to average in the analysis of the background spectrum.

b. In the Region End area, select one of the two starting options to define the end time of the Left region as follows:

• Select the Peak Start option to use the detected peak start time.

• Select the Points Before Peak Top option to specify the Left region end point as a specific number of scans before the peak top. Then, type the number of scans in the Points Before Peak Top box.

6. In the Background Subtraction Right Region area, define the baseline region used for background analysis after a peak as follows: a. In the Region Width (points) box, type the number of scans to average in the analysis of the background spectrum.

b. In the Region Start area, select one of the two ending options to define the end time of the Right region:

• Select the Peak End option to use the detected peak end time.

• Select the Points After Peak Top option to specify the Right region end point as a specific number of scans after the peak top. Then, type the number of scans in the associated Points After Peak Top box.

7. To save your settings, click OK.

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Using the Refine Option for Spectrum Enhancement

For information about the parameters in the Refine area on the Spectrum Enhancement page

of the Processing Setup – Qual view, see “Spectrum Enhancement Page for Qual View” on page 329 .

To set up the Refine option parameters

1. From the Qual view of the Processing Setup window, click the Spectrum Enhancement tab.

The Spectrum Enhancement Page opens.

Figure 31 shows the parameters for the Refine

option.

Figure 31. Spectrum Enhancement page of the Qual view

Thermo Scientific

2. To make the spectrum enhancement options available, select the Enable check box in the

Enhancement Options area.

3. To select the refine enhancement method, select the Refine option.

4. To enter a time range for Refine, type a window size in the Window Size (sec) box. Set this parameter to the expected peak width.

5. To enter a noise threshold, type a limit for low-intensity ions in the Noise Threshold box.

Start with a value of zero, increasing the setting until the procedure eliminates spurious masses generated by background noise.

6. To save your settings, click OK.

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Using the Threshold Option for Spectrum Enhancement

For information about the parameters in the Refine area on the Spectrum Enhancement page of the Qual view, see

“Spectrum Enhancement Page for Qual View” on page 329

.

To set up the threshold option parameters for spectrum enhancement

1. From the Qual view of the Processing Setup window, click the Spectrum Enhancement tab.

The Spectrum Enhancement page opens.

2. To view spectrum enhancement options, select the Enable check box in the

Enhancement Options area.

3. Select the Threshold option.

4. To enter an intensity threshold, type a value as a percentage of the most intense ion in the

Cutoff Threshold (%) box.

5. To save your settings, click OK.

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Adding Report Templates to Processing Methods

Use the Reports view of the Processing Setup window to add template sample and summary reports to the processing method.

The following folder contains the report templates that are provided with the Xcalibur data system:

drive:\Xcalibur\Templates folder

Use one or more of the sample templates to report the results for individual data files. Use one or more of the summary templates to report the results from multiple data files, such as the calibration results or a sequence summary.

For more information about the report templates provided with the Xcalibur data system, refer to the Sample XReport Templates appendix in the XReport User Guides.

Follow these procedures to specify the appropriate reports for the processing method:

Setting Up the Report Parameters

Selecting a Sample Report Template

Selecting a Summary Report Template

Setting Up the Report Parameters

For information about the parameters on the Reports view in the Processing Setup window, see

Reports View .

To set up the report parameters

1. From the Processing Setup window, doing one of the following:

• On the View bar, click the Reports icon, .

–or–

• On the menu bar, choose View > Reports.

The Reports View opens (

Figure 32

).

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Figure 32. Reports view of the Processing Setup window

2. To add a report to either the Sample or Summary Report tables, double-click the first available cell in the Report Template Name column.

A browse dialog box opens.

3. Browse to the required template for a sample or summary report.

4. To select a sample or summary report, do the following: a. Click a cell in the Enable column.

A check box appears.

b. Select or clear the check box as required.

c.

Click outside the cell.

If the report is enabled, the application displays Yes in the cell. If the report is unavailable, the cell is blank.

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5. To change the Sample Report options for different sample types, do the following: a. Click the appropriate cell under Std, QC, Unk, or Other.

A check box appears.

b. Select or clear the check box as required. Then, click outside the cell.

If the report is enabled for the Std, QC, or Other sample type, the application displays Yes in the cell. If the report is unavailable, the cell is blank.

6. To change the export options for a sample or summary report, do the following: a. Click the appropriate cell in the Save As column. b. Select from the available export formats: None, Text, Doc, HTML, or PDF. Then, click outside the cell.

The cell displays the selected export format.

7. To insert a row in the Sample or Summary Report tables, double-click the row number where you want to insert a row. Right-click any cell in the row and choose Insert Row from the shortcut menu.

8. To delete a row in the Sample or Summary Report tables:

• Double-click the row or rows you want to delete.

• To delete a range of cells, drag across from the first to the last row in the range.

Right-click any cell in the row and choose Delete Rows from the shortcut menu.

9. To save the new settings and close the dialog box, click OK.

To save the report list as the default option for new processing methods click Save As

Default.

Selecting a Sample Report Template

Use the Reports view to select a sample report to display the results for individual sample runs.

For more information about the Reports view, see “Reports View” on page 402 .

To select a sample report template for the processing method

1. To open the Reports view, do one of the following:

• Click the Reports icon,

–or–

, on the View bar.

• Choose View > Reports from the menu bar.

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2. In the Sample Reports area, double-click in the Report Template Name column.

The Browse for Sample Report Template dialog box opens (

Figure 33

).

Figure 33. Browse for Sample Report Template dialog box

3. To select the required sample report template, click the template name. If it is not displayed, browse to the correct folder and select a template.

The template name appears in the File Name box.

4. To close the dialog box and open the template, click Open.

Selecting a Summary Report Template

Use the Reports view to select a summary report to display the results of multiple data files, such as the calibration results or a sequence summary.

For more information about the Reports view, see “Reports View” on page 402 .

To select a summary report template

1. To open the Reports view, do one of the following:

• Click the Reports icon,

–or–

, on the View bar.

• Choose View > Reports from the menu bar.

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Creating Processing Methods

Adding Report Templates to Processing Methods

2. In the Summary Reports area, double-click in the Report Template Name column.

The Browse for Summary Report Template dialog box opens.

3. To select the required summary report template, click the template name. If it is not displayed, browse to the correct folder.

The template name appears in the File Name box.

4. To close the dialog box and open a template, click Open.

Printing a Processing Method Report

Follow this procedure to print a report of the processing method settings.

To print a report for the current processing method

1. In the Processing Setup window, choose File > Print from the menu bar or click in the toolbar.

The Print Dialog Box

opens (

Figure 34

).

Figure 34. Print dialog box

Thermo Scientific

2. To specify a template for the processing method report, do one of the following:

• Type a file name and directory location in the Report Template box.

–or–

• Click the Browse icon, , and select a report template. If you have not created a template by using the Xreport program, browse to the following template:

drive:\Xcalibur\templates\ProcessingMethod.xrt.

3. To save the new settings and close the dialog box, click OK.

The hourglass cursor indicates that the processing method is being printed.

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Creating Processing Methods

Adding Programs or Macros to Processing Methods

Adding Programs or Macros to Processing Methods

Use the Programs view of the Processing Setup window to add programs and macros to processing methods.

The Xcalibur data system includes these predefined programs: Xconverter.exe,

FileConverter.exe, and Excelexp.exe.

For information about Xconverter and Excelexp.exe, refer to the Xcalibur Getting Started

Guide.

To add programs and macros to processing methods, see these topics:

Selecting a Program or Macro

Enabling and Setting Up a Program or Macro

Selecting a Program or Macro

Use the Programs view of the Processing Setup window to add programs and macros to a processing method. For information about the parameters in the Programs view, see

Programs

View .

To select a program or macro

1. To open the

Programs View

from the Processing Setup window, do one of the following:

• Click the Programs icon,

–or–

• Choose View > Programs.

, in the View bar.

2. To select a program or macro for the current table row, do the following: a. Double-click in the Program or Macro Name column.

The Browse for Program dialog box opens.

b. Browse to the macro or program that you want to add.

The program or macro name appears in the File Name box. c.

Click Open to select the program and to close the dialog box.

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3

Creating Processing Methods

Adding Programs or Macros to Processing Methods

Enabling and Setting Up a Program or Macro

You can add a program or macro to a stored processing method or a new processing method.

For more information, see “Programs View” on page 398

.

To enable a program or macro and to specify its processing parameters

1. If the Processing Setup window is not open, open it as follows from the home page window:

• Click the Processing Setup icon,

–or–

, on the Roadmap view.

• Choose GoTo > Processing Setup from the menu bar.

2. If the processing method that you want to modify is not open, open it as follows: a. Choose File > Open.

b. Browse to your processing method and select it.

c.

Click Open.

3. Do one of the following:

• Click the Programs icon,

–or–

, in the View bar.

• Choose View > Programs from the menu bar.

The Programs View opens (

Figure 35 ).

Figure 35. Programs table

Thermo Scientific

4. To select a program or macro for the current table row, do the following: a. Double-click in the Program or Macro Name column.

The Browse for Program dialog box opens.

b. Browse to the macro or program that you want to add.

The program or macro name appears in the File Name box. c.

Click Open to select the program and to close the dialog box.

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Creating Processing Methods

Adding Programs or Macros to Processing Methods

5. To enable a program or macro, do the following: a. Click the Enable column.

A check box appears. b. Select the check box to enable the program or macro. Then, click outside the cell.

If the program is enabled, the application displays Yes in the box. If the program is unavailable, the cell is blank.

6. To select the sample types affected by the program or macro, select the check boxes in the appropriate Sample Type columns.

By default, all of the sample types are selected and the table cell displays Yes. If you clear the check box for a sample type and then click outside the table cell, the cell becomes blank.

7. To select the action for a program, in the Action column, select Run Program for a program or Run Excel Macro for a macro. Then, click outside the cell.

The action for the program appears in the cell.

8. To change the Sync setting for a program, do the following: a. Click the Sync column.

A check box appears.

b. Select or clear the check box as required. Then, click outside the cell.

If synchronous program operation is available, the application displays Yes in the box.

For asynchronous operation, the cell is blank.

9. To add command parameters for a program, select the corresponding cell in the

Parameters column. Then, type the required commands.

10. To insert a row in the Programs table, double-click the row number where you want to insert the row, and then right-click any cell in the row and choose Insert Row from the shortcut menu.

11. To delete a row or rows in the Programs table, select the row or rows that you want to delete, and then choose Delete Rows from the shortcut menu.

12. To save the new settings, click OK.

13. To save the Programs table as the default table for new processing methods, click Save As

Default.

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Xcalibur Data Acquisition and Processing User Guide Thermo Scientific

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