Xcalibur 4.0 Data Acquisition and Processing User Guide Version A

Xcalibur 4.0 Data Acquisition and Processing User Guide Version A

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Processing Setup Window

This topicappendix describes the Processing Setup window, the views in the Processing Setup window, and the dialog boxes that you can access from the Processing Setup window.

Use the Processing Setup window to create a processing method for automated batch analysis.

You can also modify existing methods, save method files, and restore existing method files.

In the Sequence Setup view, when you run or batch reprocess a sequence that contains a processing method, the data system uses the processing method to initiate processing for qualitative and quantitative data, to create reports, and to run additional programs or macros, such as shutdown procedures.

Contents

Processing Setup Window Features

Processing Setup Dialog Boxes

Processing Setup Views

For information about creating processing methods, see Chapter 3, “Creating Processing

Methods.”

Processing Setup Window Features

The Processing Setup window consists of a view bar, title bar, menu bar, toolbar, workspace, status bar, and access to Help. The workspace contains one of four views. You can access each view by clicking its button on the View bar or by choosing the view from the View menu (see

Figure 7 on page 18

).

The Qual and Quan views contain chromatogram and spectrum views. In addition, these three buttons appear at the bottom of the Reports and Programs views and above the spectrum and chromatogram views in the Qual and Quan Views: OK, Cancel, and Save As

Default.

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Processing Setup Window Features

For more information about the elements of the Processing Setup window, see these topics:

Processing Setup Title Bar

Processing Setup Toolbar

Processing Setup View Bar

Processing Setup Menus

Chromatogram and Spectrum Views in the Qual and Quan Views

OK, Cancel, and Save As Default Buttons

For information about the views, see Processing Setup Views .

Processing Setup Title Bar

Figure 7 on page 18 shows the Processing Setup window.

The title bar components are as follows:

• The Processing Setup – View – Page – Study: Name – Untitled

• The active view (Quan, Qual, Reports, or Programs)

• The active page (for example, Identification)

• The active study (for example, Study:Name)

Note On the Dataset List page of the Thermo Xcalibur Configuration dialog box, you can select the term to be used for datasets. The selections are Study, Job, and

Dataset. You can also include a blank name as a dataset option.

• The name of the opened method, or Untitled if a new file has not yet been saved

• The selected type of calibration, internal or external standard

Processing Setup Toolbar

The toolbar contains shortcuts for frequently used menu commands. The Processing Setup toolbar buttons vary, depending on the view currently displayed:

Qual and Quan Views Toolbar

Reports and Programs Views Toolbar

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Processing Setup Window

Processing Setup Window Features

Qual and Quan Views Toolbar

Table 52

lists the toolbar buttons that are available for the Qual and Quan views of the

Processing Setup window.

Table 52. Processing Setup – Qual and Quan views toolbar icons (Sheet 1 of 2)

Icon or

Button

Description

New

Open

Save

Sets the processing method parameters to the default values and displays Untitled for the processing method name in the title bar.

Opens the Open dialog box, where you can browse to and select an existing processing method.

Opens the Save As dialog box, where you can enter a name for the processing method and save it.

Open Raw File Opens the Open Raw File dialog box, where you can browse to and select an existing raw data (.raw) file.

Print

Opens the Print Dialog Box

, where you can browse to and select a report template for the processing method and submit the report to the default printer.

Zoom Out Y

Zoom In Y

Zooms out on the y axis by a factor of two to show more data.

For example, you can change the y-axis range from 0–25 to

0–50.

Zooms in on the y axis by a factor of two from the current baseline to show more detail. For example, you can change the

y-axis range from 0–100 to 0–50.

Auto Range Determines the minimum and maximum signal in the chromatogram and then normalizes the data over the full range of the y axis. This option is suggested for PDA and UV data.

Normalize

Zoom In X

Normalizes the intensity scale of the data display to a fixed range on the y axis. For example, from 0–25% to 0–100%.

Zooms in on the x axis by a factor of two to show more detail.

For example, you can change the x-axis range from 0–20 to

5–15.

Zoom Out X Zooms out on the x axis by a factor of two from the center to show more data, for example, you can change the x-axis range from 7–12.5 to 5–15.

Display All Data Displays the entire x-axis range or all text in a report. For example, you can change the x-axis range from 7.5–12.5 to

0–20 minutes, if the run time for the data file is 20 minutes.

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Processing Setup Window Features

Table 52. Processing Setup – Qual and Quan views toolbar icons (Sheet 2 of 2)

Icon or

Button

Description

Reset Scaling to

Full Scale

Product Help

Resets the chromatogram and spectrum scaling to the default values.

Opens the Processing Setup window Help topic.

Reports and Programs Views Toolbar

Table 53

lists the toolbar buttons that are available for the Reports and Program views of the

Processing Setup window.

Table 53. Reports and Programs views

Icon or

Button

Description

New

Open

Save

Sets the processing method parameters to the default values and displays Untitled for the processing method name in the title bar.

Opens the Open dialog box, where you can browse to and select an existing processing method.

Opens the Save As dialog box, where you can enter a name for the processing method and save it.

Open Raw

File

Print

Opens the Open Raw File dialog box, where you can browse to and select an existing raw data file (RAW).

Opens the Print Dialog Box , where you can browse to and select

a report template for the processing method and submit the report to the default printer.

Product Help Opens the Processing Setup window Help topic.

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Processing Setup Window Features

Processing Setup View Bar

From the View bar, located to the left side of the Processing Setup window, click one of the four buttons to do the following.

Opens the Quan view, where you can set up the parameters for a quantitative

analysis. For information about the Quan view, see Quan View .

Opens the Qual view, where you can set up the processing parameters for a qualitative analysis. For information about the Qual view, see

Qual View .

Opens the Reports view, where you can set up reports for the processing method. For information about the Reports view, see

Reports View

.

Opens the Programs view, where you can add programs and macros to the

processing method. For information about the Programs view, see Programs

View .

Processing Setup Menus

The menus in the Processing Setup window are as follows from left to right:

File Menu – Processing Setup

Zoom Menu – Processing Setup

(Qual and Quan views only)

GoTo Menu – Processing Setup

View Menu – Processing Setup

Options Menu – Processing Setup

Help Menu – Processing Setup

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Processing Setup Window Features

File Menu – Processing Setup

Table 54

describes the commands in the File menu of the Processing Setup window. The equivalent toolbar button appears below the command.

Table 54. Processing Setup window – File menu (Sheet 1 of 2)

Icon or

Button

Command Description

New

Open

Save

Sets the processing method parameters to the default values and displays Untitled for the processing method name in the title bar.

Opens the Open dialog box, where you can browse to and select an existing processing method.

Update audit information, name a file, and specify file storage location (disk and directory).

Save As

Open Raw File

View audit information about the active file, rename a file, and select a storage location (disk and directory).

Opens the Open Raw File dialog box, where you can open an existing raw data (.raw) file.

Summary Information Opens the File Summary Information dialog box, where you can read the summary information about the active file or edit the text in the Comment box.

Change Dataset Name Opens the Study Name Selector dialog box, where you can select a dataset from a predefined list of names or create a new Study name.

Audit Trail

Import Method

Print Setup

The text of this menu item might be different if the administrator chooses to use another name for a dataset.

For example, this menu item might be Change Job

Name.

For more information, see

Study Name Selector Dialog

Box .

Opens the Thermo Foundation Audit Viewer, where you can view all auditable events and changes made to data files in the current view.

Opens the Open Result File dialog box, where you can locate (drive and directory) and open a result file that contains the processing method of interest.

Opens the Print Setup dialog box, where you can select the following printing options: printer, form, orientation, and one- or two-sided printing.

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Processing Setup Window Features

Table 54. Processing Setup window – File menu (Sheet 2 of 2)

Icon or

Button

Command Description

Print

A list of the most recently used files

Exit

Opens the Print Dialog Box

, where you can select a report template for printing the processing method, and then submit the report to the default printer or the printer that you selected in the Print Setup dialog box.

Displays the paths and names of the four most recently used files. These are located above the Exit command.

You can select a processing method from this list.

Close the active window. If you exit before clicking OK from an active dialog box, you receive a message about saving your changes.

GoTo Menu – Processing Setup

Table 55

describes the GoTo menu of the Processing Setup window.

Table 55. Processing Setup window – Go To menu (Sheet 1 of 2)

Command

Instrument Setup

Description

Opens the Instrument Setup window, where you can create instrument methods and access the direct controls, if available, for the chromatography system and the mass spectrometer. The direct controls for the chromatography system are also available from the

Tune window for the mass spectrometer.

Quan Browser

For information about the Instrument Setup window, see

Chapter 2, “Creating Instrument Methods and Using the Direct

Controls,” and

Appendix D, “Processing Setup Window.”

Opens the Quan Browser window, where you can open, review, and rework a sequence of processed files (SLD file type), a result file (RST file type), or a Quanbrowser file (XQN file type).

Qual Browser

For information about the Quan Browser window, refer to the

Xcalibur Quan Browser User Guide.

Opens the Qual Browser window, where you can review raw data files and result data files containing spectra and chromatograms.

For information about the Qual Browser window, refer to the

Xcalibur Qual Browser User Guide.

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Processing Setup Window Features

Table 55. Processing Setup window – Go To menu (Sheet 2 of 2)

Command

Library Browser

Description

Opens the Library Browser window, where you can work with reference spectra, spectra exported from Qual Browser, or spectra appended to libraries during qualitative processing.

For information about the Library Browser window, refer to the

Xcalibur Creating and Searching Libraries User Guide.

Xcalibur Home Page Opens the home page window if it is closed or view the home page window if it is already open.

Help Menu – Processing Setup

Table 56

describes the Help menu of the Processing Setup window.

Table 56. Processing Setup window – Help menu

Command Description

Processing Setup Help Opens the Xcalibur Help topic for the Processing Setup window.

View Help Opens the Xcalibur Help topic for the current view.

Help On Current Item Opens the Xcalibur Help topic for the currently view or dialog box.

Xcalibur Help Opens the Xcalibur Help to the Welcome topic.

Glossary

How To Use Help

View the glossary.

Opens the Xcalibur Help to the Using This Help topic, which provides instructions on how to use the Contents, Index, and

Search pages of the Help.

About Processing Setup Opens the version information. Click Version to open the Version

Info dialog box and view the version information for the Xcalibur data system, the Foundation platform, and the configured instruments.

Options Menu – Processing Setup

The commands in the Options menu of the Processing Setup window vary, depending on whether the current view is Quan, Qual, or Reports and Programs.

These tables describe the Options menus:

Options menu for the Quan view

Options menu for the Qual view

Options menu for the Reports and Programs views

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Processing Setup Window Features

Table 57

describes the Options menu for the Quan view.

Table 57. Options menu for the Quan view (Sheet 1 of 2)

Command

Identification

Masses

Description

Opens the Identification Options Dialog Box

, where you set up the void time and baseline parameters for peak identification purposes.

Opens the Masses Dialog Box

, where you set up the default settings for mass tolerance and mass precision.

Standard Dilution

This is the same dialog box for the Quan Browser window and the

Quan and Qual views of the Processing Setup window.

Opens the Standard Dilution Dialog Box , where you can set up

the calibration-level information for target components.

Chromatography By

Spectrum

Calibration Options

Delete Component

Display

This command appears in the menu only if you have defined at least one target compound on the Calibration page and the Levels page is open.

Opens the Chromatography By dialog box, where you can select the appropriate chromatography mode: GC or LC.

See Default Chromatography Options Dialog Box .

Opens the

Spectrum Options Dialog Box , where you can specify a

low-intensity cutoff percentage for peak detection purposes.

This command appears in the menu only if you have selected the

GC Chromatography mode in the Chromatography By dialog box and the Spectrum option (in the Peak Detection dialog box) on the Detection page.

Opens the Calibration Options Dialog Box , where you can select

internal or external calibration for the current processing method.

Removes the selected component from the processing method.

The data system removes the component from the Components pane.

Opens the Display Options dialog box for the selected view. Use this dialog box to change the style, color, labels, axes, and normalization of the chromatogram and spectrum views.

For information about the Display Options dialog box, refer to the Help or the Xcalibur Qual Browser User Guide.

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Processing Setup Window Features

Table 57. Options menu for the Quan view (Sheet 2 of 2)

Command

Settings

Enable Warnings

Description

Opens the Settings Dialog Box . By default, the application loads

the most recently used method into the Processing Setup window at startup. You can change this option in the Settings dialog box and also configure the Xcalibur data system to display a raw data file in the chromatogram and spectrum views at startup.

Turn on the display of warnings about operations and commands to change the processing method. To turn off warnings during a number of operations, select the Don’t Tell Me About This Again check box in an information dialog box.

If this menu command is unavailable, warnings are already enabled.

Table 58

describes the Options menu for the Qual view.

Table 58. Options menu for the Qual view

Command

Identification

Masses

Description

Opens the Identification Options Dialog Box

, where you set up the void time and baseline parameters for peak identification purposes.

Opens the Masses Dialog Box

, where you set up the default settings for mass tolerance and mass precision.

Display

Settings

Enable Warnings

This is the same dialog box for the Quan Browser window and the

Quan and Qual views of the Processing Setup window.

Opens the Display Options dialog box for the selected view. Use this dialog box to change the style, color, labels, axes, and normalization of the chromatogram and spectrum views.

Opens the Settings Dialog Box . By default, the data system loads

the most recently used method into the Processing Setup window at startup. You can change this option in the Settings dialog box and also configure the Xcalibur data system to display a raw data file in the chromatogram and spectrum views at startup.

Turns on the display of warnings about operations and commands that change the processing method. To turn off warnings during a number of operations, select the Don’t Tell Me About This Again check box in an information dialog box.

If this menu command is unavailable, warnings are already enabled.

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Processing Setup Window Features

Table 59

describes the Options menu for the Reports and Programs views.

Table 59. Options menu for the Reports and Programs views

Command

Settings

Enable Warnings

Description

Opens the Settings Dialog Box . By default, the data system loads

the most recently used method into the Processing Setup window at startup. You can change this option in the Settings dialog box and also configure the data system to display a raw data file in the chromatogram and spectrum views at startup.

Turns on the display of warnings about operations and commands that change the processing method. To turn off warnings during a number of operations, select the Don’t Tell Me About This Again check box in an information dialog box.

If the menu command is unavailable, warnings are already enabled.

View Menu – Processing Setup

Table 60

describes the View menu commands.

Table 60. Processing Setup window – View menu

Command

Quan

Qual

Reports

Programs

View Bar

Component List

Description

Opens the Quan view in the Processing Setup window.

Opens the Qual view in the Processing Setup window.

Opens the Reports view in the Processing Setup window.

Opens the Programs view in the Processing Setup window.

Shows or hides the View bar.

Shows or hides the Components pane.

Toolbar

Status Bar

This command is available only in the Quan view.

Shows or hides the toolbar.

Shows or hides the Status bar.

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Zoom Menu – Processing Setup

Table 61

describes the Zoom menu commands.

Table 61. Processing Setup window – Zoom menu

Icon Command

Zoom In Y

Description

Zooms in on the y axis by a factor of two from the current baseline to show more detail. For example, you can change the y-axis range from 0–100 to 0–50.

Zoom Out Y Zooms out on the y axis by a factor of two to show more data. For example, you can change the y-axis range from 0–25 to 0–50.

Normalize

Zoom In X

Normalizes the intensity scale of the data display to a fixed range on the y axis, for example, from 0–25% to 0–100%.

Zooms in on the x axis by a factor of two to show more detail. For example, you can change the x-axis range from 0–20 to 5–15.

Zoom Out X Zooms out on the x axis by a factor of two from the center to show more data. For example, you can change the x-axis range from

7.5–12.5 to 5–15.

Display All Displays the entire x-axis range or all text in a report. For example, you can change the x-axis range from 7.5–12.5 to 0–20.

Reset Scaling Resets the scaling to the full scale display.

Chromatogram and Spectrum Views in the Qual and Quan Views

The chromatogram and spectrum views display the chromatogram and spectrum from the currently opened raw data file. Initially, the data system displays the spectrum corresponding to the apex scan of the first detected peak. If no peak has been detected in the chromatogram view, the spectrum for the first scan in the raw data file appears.

When you change a parameter such as the Detector Type, Filter, and Trace in the Qual and

Quan views, click OK to change the chromatogram displayed in the chromatogram view.

These views are available on the following pages:

• Identification, Detection, and Peak Purity pages for the Quan View

• Identification, Spectrum Enhancement, and Peak Purity pages for the Qual View

You can use the chromatogram and spectrum views to assess the effects of the processing method settings and to automate data entry for some of the processing method parameters.

For example, you can use the chromatogram view to set the expected retention time and retention time window on the Identification page of the Qual or Quan views. You can use the spectrum view in the Qual view to set Mass Ranges on the Identification page and the parameters in the Combine area on the Spectrum Enhancement page.

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Processing Setup Window Features

To rescale the chromatogram displayed in the chromatogram view, use the following:

• Toolbar buttons

• Zoom menu commands

• The cursor

Note The cursor action is always applied to the pinned cell. Within an active cell, cursor actions rescale the chromatogram shown in the view.

OK, Cancel, and Save As Default Buttons

The Processing Setup window has OK, Cancel, and Save As Default buttons that are located above the chromatogram and spectrum views in the Qual and Quan views and at the bottom of the view in the Reports and Programs views.

These buttons are enabled only if you change one or more parameters on the page; otherwise, they are unavailable.

When you change or edit a parameter, do one of the following:

• To apply the changes to the current processing method, click OK.

The data system reports any validation errors.

Tip When you change a parameter such as the Detector type, Filter, and Trace in the

Qual and Quan views, click OK to change the chromatogram displayed in the chromatogram view.

• To undo all changes made to the page and revert to the previously applied values, click

Cancel.

• To validate and save the settings on the current page as default settings, click Save As

Default.

The data system uses these settings for all new processing methods. The data system writes over the previous default values and cannot recover them.

These actions do not affect the saved version of the processing method. You can only modify the saved version by choosing File > Save.

The data system displays the Apply Changes? Dialog Box if you attempt to change pages,

views, or programs without applying or discarding changes. Use this dialog box to apply or discard the changes before continuing with your intended action.

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Processing Setup Dialog Boxes

Processing Setup Dialog Boxes

You can open the following dialog boxes from the Processing Setup window. These dialog boxes are listed in alphabetical order.

Apply Changes? Dialog Box

Avalon Event List Dialog Box

Calibration and Quantitation Flags Dialog Box

Calibration Options Dialog Box

Chromatography Options Dialog Box

Correction for Isotope Contribution Dialog Box

Data Flags Dialog Box

Default Chromatography Options Dialog Box

Display Options Dialog Box

Genesis Advanced Detection Options Dialog Box

Genesis Advanced Chromatogram Options Dialog Box

ICIS Advanced Parameters Dialog Box

Identification Options Dialog Box

Masses Dialog Box

Print Dialog Box

Search List Dialog Box

Settings Dialog Box

Spectrum Options Dialog Box

Standard Dilution Dialog Box

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Processing Setup Dialog Boxes

Apply Changes? Dialog Box

The Apply Changes? dialog box opens in the Processing Setup window when you make changes to the current page and attempt one of the following actions without first clicking

OK or Cancel:

• Switch to another page

• Switch to another component in the Quan view

• Switch to another view, using either the buttons in the View bar or the options on the

View menu

• Change chromatography type (Options > Chromatography By)

• Change calibration type (Options > Calibration By)

• Click Close on the title bar

• Choose one of the following menu items:

File > Open

File > most recently used file list

File > Save

File > Save As

File > Exit

File > Import Method

File > New

Options > Standard Dilution

Before proceeding with any of these actions, you must apply or undo the page modifications.

Table 62

describes the parameters in the Apply Changes? dialog box.

Table 62. Apply Changes? dialog box parameters (Sheet 1 of 2)

Parameter

Don't Tell Me

About This Again

Description

Selecting this check box suppresses the display of the Apply Changes? dialog box.

In the future when the data system displays this dialog box, it will treat changes according to your final selection in the dialog box:

• If you click Yes, the data system applies changes, if the validation is successful, and continues with your selected action. If the validation fails, the data system stops your intended action and returns you to Processing Setup to correct or discard changes made to the page.

• If you click No, the data system discards all changes and continues with your selected action.

To restore the dialog box, choose Options > Enable Warnings.

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Table 62. Apply Changes? dialog box parameters (Sheet 2 of 2)

Parameter

Buttons

Yes

Description

Applies changes to a Processing Setup page before proceeding with your selected action.

When you click Yes, the data system applies the changes and reports any errors. If an error occurs, the data system stops your intended action and returns you to Processing Setup so that you can correct or discard the changes.

No

If you also select the Don’t Tell Me About This Again check box, the data system does the following in the future:

• Does not display the Apply Changes? dialog box.

• Applies changes automatically.

• If a validation error occurs, the data system stops your intended action and returns you to the Processing Setup window. If the validation is successful, the data system applies the changes and proceeds with your selected action.

Discards unapplied changes to a Processing Setup page before proceeding with your selected action.

The data system discards all changes, as though you pressed Cancel on the page. Then it continues with your selected action.

If you also select the Don’t Tell Me About This Again check box, the data system does the following in the future:

• Does not display the Apply Changes? dialog box.

• Always discards unapplied changes automatically and without prompting.

• Proceeds with your intended action.

You must click OK to apply changes made on a page; otherwise, the data system discards them.

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Processing Setup Dialog Boxes

Avalon Event List Dialog Box

Use the Avalon Event List dialog box to specify advanced component detection criteria in the

Quan or Qual views of the Processing Setup window.

Tip On the Detection page of the Quan view or the Identification page of the Qual view, automatically calculate values for the Initial Value events before you modify the timed

events in the Avalon Event List dialog box. See Avalon Identification Page for Qual View

or

Avalon Detection Page for Quan View

.

To change an existing event in the event list

1. Select the row that you want to change.

The time, integration event, and value for the selected event appear in the Time (Min),

Event, and Value boxes below the table.

2. In the Time (Min) box, type a time for the event to begin. If you type a new time for an initial value event, a new event appears in the list.

There are seven initial entry integration events, identified by the Initial Value setting in the Time column. These are the default integration events that the Avalon integration algorithm requires. You can change the value of an initial entry integration event, but you cannot delete it or change its time value.

3. In the Value box, type a new value for the event.

The valid range is specific to each event.

4. Click Change to automatically update the Event list, both here and on the Detection page of the Quan view or the Identification page of the Qual view, and automatically update the chromatogram display.

To add an event to the event list

1. Type a time in the Time (Min) box.

2. Select an event from the list.

3. Type a value in the Value box.

The valid range is specific to each event.

4. Click Add.

To delete an event from the event list

1. Select the row you want to delete.

The time, integration event, and value for the selected event appear in the boxes below the table.

2. Click Delete.

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Table 63

describes the parameters in the Avalon Event List dialog box.

Table 63. Avalon Event List dialog box parameters (Sheet 1 of 3)

Parameter

Integration Events

Description

Initial value events: Start/End Threshold, Bunch Factor, Area Threshold, P-P Resolution,

Negative Peaks, Tension, and Tangent Skim. The Threshold and Bunch Factor parameters are the most important ones in controlling peak detection.

Start/End Threshold This integration event is directly related to the root-mean-square

(RMS) noise in the chromatogram. It specifies the start and end thresholds, the fundamental control used for peak detection.

Bunch Factor Specifies the number of points grouped together during peak detection. It controls the bunching of chromatographic points during integration and does not affect the final area calculation of the peak.

Area Threshold

P-P Resolution

Range: 1.000–999.000; however, for best results, use an integer between 1 and 6. A bunch factor larger than 6 groups peaks into clusters.

Controls the area cutoff. The data system does not detect any peaks with a final area less than the area threshold. This control is in units of area for the data.

The peak-to-peak resolution threshold controls how much peak overlap must be present before two or more adjacent peaks create a peak cluster. Peak clusters have a baseline drop instead of valley-to-valley baselines. This baseline drop is specified as a percent of peak height overlap.

Negative Peaks

Tension

Range: 0.010–99.990

Controls the integration of negative chromatographic peaks.

Selecting On turns this integration event on at the specified time.

Selecting Off turns this integration event off at the specified time.

Controls how closely the baseline should follow the overall shape of the chromatogram. A lower tension traces the baseline to follow changes in the chromatogram more closely. A high baseline tension follows the baseline less closely, over longer time intervals.

Range: 0.000–999.990

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Table 63. Avalon Event List dialog box parameters (Sheet 2 of 3)

Parameter

Tangent Skim

Description

For fused peaks that are significantly different in size, the tangent skim method provides a method of allocating area to the various peaks. By default, the data system chooses the tallest peak in a cluster as the parent. You can also identify which peak in the cluster is the parent. The data system detects tangent skim peaks on either side (or both sides) of the parent peak. Tangent skim automatically resets at the end of the peak cluster.

Range: 0.000–1.000

Additional timed events

Shoulders On Turns on the detection of shoulders.

Shoulders Off

Force Cluster On

Force Cluster Off

Disable Cluster On

Turns off the detection of shoulders.

Turns on the grouping of peaks into a single peak.

Turns off the grouping of peaks into a single peak.

Turns on the grouping effect in the specified time range.

Turns off the grouping effect in the specified time range.

Disable Cluster Off

Event List Entry

Time The time entry for events that are listed as Initial Value cannot be changed.

Event

Use this box to enter a time value for an event.

Contains a list of integration events. Select an integration event from this list.

Use this box to enter a value for an event.

Value

Buttons

Add

Delete

Adds a timed event to the Event list. When you click Add, the data system automatically changes the peak detection results with the added specification in the currently selected chromatogram.

Removes a highlighted event from the Event list. You cannot delete initial values.

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Processing Setup Dialog Boxes

Table 63. Avalon Event List dialog box parameters (Sheet 3 of 3)

Parameter

Change

Exit

Description

Updates a highlighted timed event in the Event list. When you click Change, the data system automatically changes the peak detection results with the added specification in the currently selected chromatogram. For initial events, you can change only the values, not the events.

Closes the active window. If you exit before clicking OK from an active dialog box, the data system prompts you to save your changes.

Calibration and Quantitation Flags Dialog Box

Use the Calibration and Quantitation Flags dialog box to set the threshold values for calibration and quantitation flags. The Xcalibur data system reports these flags in result files, in printed reports, and in Quan Browser.

For information about setting up the flags in the processing method, see “Setting Up the

Calibration and Quantitation Flags” on page 44 .

Table 64

describes the parameters in the Calibration and Quantitation Flags dialog box.

Table 64. Calibration and Quantitation Flags dialog box parameters (Sheet 1 of 2)

Parameter

Calibration Flag

R-Squared

Description

Specifies a flag threshold for the goodness of fit of the calibration curve. The data system calculates a coefficient of determination

(R-squared) whenever it computes a calibration curve. If the value is less than the R-squared threshold, the data system sets the

R-squared flag in the result file to True; otherwise, it is set to False.

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Table 64. Calibration and Quantitation Flags dialog box parameters (Sheet 2 of 2)

Parameter

Quantitation Flags

Detection Limit

Description

Linearity Limit

Quantitation Limit

Carry Over Limit

Specifies a flag threshold for the limit of detection. If the quantified component concentration is less than the Detection

Limit threshold, the data system sets the Detection Limit flag in the result file to True; otherwise, it is set to False.

Specifies a flag threshold for the linearity limit. If the quantified component concentration is less than the Linearity Limit threshold, the data system sets the Linearity Limit flag in the result file to True; otherwise, it is set to False.

Specifies a flag threshold for the limit of quantitation. If the quantified component concentration is less than the Quantitation

Limit threshold, the data system sets the Quantitation Limit flag in the result file to True; otherwise, it is set to False.

Specifies a flag threshold for the carry over limit. If the quantified component concentration is less than the Carry Over Limit threshold, the data system sets the Carry Over Limit flag in the result file to True; otherwise, it is set to False.

Calibration Options Dialog Box

Use the Calibration Options dialog box to choose the calibration mode and method of calculating relative standard deviations. Your choice of calibration mode affects the options available on the Processing Setup – Quan View – Calibration page. The default calibration mode is Internal Standard.

For information about using the Calibration Options dialog box, see “Changing the

Calibration Mode” on page 24 .

Table 65

describes the parameters in the Calibration Options dialog box.

Table 65. Calibration Options dialog box parameters (Sheet 1 of 2)

Parameter

Calibration By

Internal Standard

Description

External Standard

When you select this option, the data system uses the internal standard calibration technique and displays the ISTD options on

the Calibration Page for Quan View

.

When you select this option, the data system uses the external standard calibration technique and hides the ISTD options on the

Calibration Page for Quan View .

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Table 65. Calibration Options dialog box parameters (Sheet 2 of 2)

Parameter

%RSD Calculation Method

Description

Use Calculated

Amounts

When you select this option, the data system computes the standard deviation on the basis of the calculated amounts for each standard. This is the behavior of previous Xcalibur versions.

Use Response Values When you select this option, the data system uses the response value (area or height) for each sample when computing the standard deviation. When using response values in analyses, a change in the calibration curve has no effect on the standard deviation or the %RSD values, since the response is not affected.

Chromatography Options Dialog Box

Use the Chromatography Options dialog box to choose the chromatography detection mode for the processing method.

You can access this dialog box from the Processing Setup window by choosing Options >

Chromatography from the menu bar.

For information about using the Chromatography Options dialog box, see

“Changing the

Chromatography Mode” on page 24 .

Your choice affects the options available on the Detection page of the Quan view in the

Processing Setup window. The data system attempts to detect the type of instrument connected when you run the instrument for the first time and makes this the default type. If

the data system fails to determine the type of instrument, the system displays the Default

Chromatography Options Dialog Box .

Table 66

describes the parameters in the Chromatography Options dialog box.

Table 66. Chromatography Options dialog box parameters

Parameter

Chromatography By

GC

Description

LC

Specifies the gas chromatography mode. Select the GC (gas chromatography) option to make the Spectrum Option available on the Detection page in Quan view.

Specifies the liquid chromatography mode. Select the LC option for liquid chromatography peak detection.

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Correction for Isotope Contribution Dialog Box

Use the Correction for Isotope Contribution dialog box to correct for an impurity in the internal standard compound that elutes at the same time as the target compound or to correct for an impurity in the target compound that elutes at the same time as the internal standard.

You can access this dialog box from the Calibration page of the Quan view in the Processing

Setup window by clicking Isotope%. For information about using the Correction for Isotope

Contribution dialog box, see “Correcting for Calibration Impurities” on page 46 .

Table 67

describes the parameters in the Correction for Isotope Contribution dialog box.

Table 67. Correction for Isotope Contribution dialog box parameters (Sheet 1 of 2)

Parameter

Contribution of ISTD to Target Compound

(%)

Description

Specifies the following ratio:

ISTD [impurity]/ISTD [pure] where:

ISTD [impurity] is an impurity compound in the internal standard reagent that elutes at the same time as the target compound.

ISTD [pure] is the pure internal standard compound.

To determine this ratio experimentally, analyze the ISTD reagent using the same method used for quantitation of the target compound. Use the respective peak areas or heights to determine the ratio of impurity to pure compound.

The valid range is 0.00 to 100.00 percent (ratio × 100%). To change the impurity ratio, type a new value in the Contribution of ISTD to Target Compound box.

The data system uses this ratio as the x value in the following impurity correction expressions:

ISTD [corr] = [ISTD [obs] – y TM [obs]]/[1 – yx]

TM [corr] = [TM [obs] – x ISTD [obs]]/[1 – yx] where:

ISTD [corr] is the corrected amount of internal standard.

ISTD [obs] is the apparent amount of ISTD, as measured by the data system at the retention time for ISTD. This peak consists of ISTD [corr] + TM [impurity].

TM [corr] is the corrected amount of the target molecule.

TM [obs] is the apparent amount of TM, as measured by the data system at the retention time for TM. This amount consists of TM [corr] + ISTD [impurity].

See the next parameter, Contribution of Target Compound to Internal Standard box, for a complete description of the y variable.

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Table 67. Correction for Isotope Contribution dialog box parameters (Sheet 2 of 2)

Parameter Description

Contribution of Target

Compound to ISTD

(%)

Specifies the following ratio:

TM [impurity]/TM [pure] where:

TM [impurity] is an impurity compound in the target molecule reagent that elutes at the same time as the internal standard.

TM [pure] is the pure target compound.

To determine this ratio experimentally, analyze the TM reagent using the method to be used for its quantitation. Use the respective peak areas or heights to determine the ratio of impurity to pure compound.

The valid range is 0.00 to 100.00 percent (ratio × 100%). To change the impurity ratio, type a new value in the Contribution of Target Compound to Internal Standard box.

The Xcalibur data system uses this ratio as the y value in the following impurity correction expressions:

ISTD [corr] = [ISTD [obs] – y TM [obs]]/[1 – yx]

TM [corr] = [TM [obs] – x ISTD [obs]]/[1 – yx] where:

ISTD [corr] is the corrected amount of internal standard.

ISTD [obs] is the apparent amount of ISTD, as measured by the data system at the retention time for ISTD [pure]. This peak consists of ISTD [corr] + TM [impurity].

TM [corr] is the corrected amount of the target molecule.

TM [obs] is the apparent amount of TM, as measured by the data system at the retention time for TM [pure]. This amount consists of TM [corr] + ISTD [impurity].

See the previous row, Contribution of Internal Standard to Target Compound box, for a complete description of the x variable.

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Data Flags Dialog Box

Use the Data Flags dialog box to set flags for peak area and height thresholds. Flags are reported as True or False in the result file. If you set a value to 0.0, the flag is always reported as False.

You can access this dialog box from the Detection page of the Processing Setup – Quan view by clicking Flags. For information about using the Data Flags dialog box, see

“Setting Up the

Detection Data Flags in Quan View” on page 40

.

Table 68

describes the parameters in the Data Flags dialog box.

Table 68. Data Flags dialog box parameters

Parameter

Area Threshold

Height Threshold

Description

Specifies a value for the Area Threshold Data Flag. This value is an absolute value of peak area (in counts × seconds). If a quantified peak has an area less than the threshold value, the Area Threshold flag is set to True.

Specifies a value for the Height Threshold Data Flag. This value is an absolute value of peak height (in counts). If a quantified peak has a height less than the threshold value, the Height Threshold flag is set to True.

Default Chromatography Options Dialog Box

The first time that you run Processing Setup, the data system attempts to determine whether it is connected to an LC or GC instrument. If the data system fails to detect the type of instrument, the Default Chromatography Options dialog box opens where you can set the default chromatography detection mode. Your choice affects the parameters available on the

Detection page of the Quan view:

• Select the GC option if you want GC detection modes in Quan view.

• Select the LC option if you want LC detection modes in Quan view.

You can change the chromatography type at any time by using the

Chromatography Options

Dialog Box

.

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Table 69

describes the parameters in the Default Chromatography Options dialog box.

Table 69. Default Chromatography Options dialog box parameters

Parameter

Chromatography By

GC

Description

LC

Select this option to configure the Quan view for GC chromatography peak detection. Selecting the GC option turns on the Spectrum Option on the Detection page in Quan view.

Select this option to configure the Quan view for LC chromatography peak detection.

Display Options Dialog Box

In the Qual and Quan views of the Processing Setup window, use the pages of the Display

Options dialog box to select Style, Color, Labels, Axis, Band Width, Normalization, and

Composition settings. The available parameters on these pages depend on whether the view in the active cell is a chromatogram or spectrum.

For information about the Display Options dialog box, refer to the Help or the Xcalibur Qual

Browser User Guide.

Genesis Advanced Chromatogram Options Dialog Box

Use the Genesis Advanced Chromatogram Options dialog box to specify advanced criteria to detect your chromatographic peak. You can use these additional criteria if the standard detection criteria do not provide the desired results.

To open the Genesis Advanced Chromatogram Options dialog box

On the Processing Setup – Qual view – Identification page, select Genesis in the Peak

Detect list. Then, click Advanced.

The Genesis Advanced Chromatogram Options dialog box opens ( Figure 90 ).

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Figure 90. Genesis Advanced Chromatogram Options dialog box

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Table 70

describes the parameters in the Genesis Advanced Chromatogram Options dialog box.

Table 70. Genesis Advanced Chromatogram Options dialog box parameters (Sheet 1 of 4)

Parameter

Peak Identification

Spectrum

Description

Select this option to identify peaks using the maximizing masses technique. This technique is based on the assumption that each spectrum across a peak in a mass chromatogram contains one or more masses, m/z values, that are representative of the compound producing the peak. Assuming that there is no mass distortion across the apex of a peak, all masses rise, maximize, and fall in a consistent pattern. Noise by contrast is random: while noise at one

m/z value might increase, it is unlikely to occur consistently over multiple m/z values. You can then use this process to detect peaks in the presence of noise contamination.

Highest Peak

Minimum Masses

Required

The Spectrum Option is only available when the selected Detector

Type on the Qual Identification page is either MS or PDA. Also, if you have selected Spectrum detection and subsequently change the Detector Type to something other than MS or PDA, the data system automatically changes the detection mode to Highest Peak.

When you select this option, the Minimum Masses Required and the Minimum Percent of Masses Found parameters become available. The data system keeps the setting only if the minimum number of masses is set to greater than one, or the minimum percentage of masses found is greater than zero.

Select this option to identify the highest peaks within the retention time window that are above the minimum peak height.

This option uses the Minimum Peak Height (S/N) parameter.

Specifies the minimum number of masses that are simultaneously reaching a maximum intensity as a criterion for peak detection.

The valid range is 1 to 999.

This parameter becomes available when you select the Spectrum option.

To change the minimum number, type the new number in the

Minimum Mass Required box.

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Table 70. Genesis Advanced Chromatogram Options dialog box parameters (Sheet 2 of 4)

Parameter

Minimum Percent of

Masses Found

Description

Specifies the minimum percent of masses that are simultaneously reaching a maximum intensity as a criterion for peak detection.

For example, if you set this value at 25% and only 10% of the mass spectral peaks being monitored reach a maximum intensity during the elution of a chromatographic peak, the data system rejects the peak. The valid range is 0 to 100%.

This parameter becomes available when you select the Spectrum option.

Minimum Peak Height

(S/N)

To change the minimum percent of masses found, type the new percentage value in the Minimum Percent of Masses Found box.

Specifies the minimum peak height (signal-to-noise) for peak detection. The data system ignores all chromatogram peaks that have signal-to-noise values that are less than the Minimum Peak

Height (S/N) value.

To enter a minimum peak height, type the value in the Minimum

Peak Height (S/N) box. The valid range is 1.0 to 999.0.

Peak Edge Detection

Set a chromatogram peak detection criterion that uses the peak signal-to-noise cutoff value to assist in peak edge detection. This test assumes an edge of a peak is found when the baseline-adjusted height of the edge is less than the ratio of the baseline-adjusted apex height and the peak signal-to-noise cutoff ratio.

Peak S/N Cutoff Specifies the signal-to-noise ratio below which the data system defines the peak edge. For example, if the signal-to-noise ratio at the apex is 500 and the Peak S/N Cutoff value is 200, the data system defines the right and left edges of the peak when the signal-to-noise ratio reaches a value less than 200. The valid range is 50.0 to 10000.0.

To change the cutoff value, type the new value in the Peak S/N

Cutoff box. When you click OK, the data system applies the new peak detection parameter.

Report Noise As

RMS

Peak To Peak

Specifies that the data system calculate noise as RMS.

Specifies that the data system calculate noise as peak-to-peak.

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Table 70. Genesis Advanced Chromatogram Options dialog box parameters (Sheet 3 of 4)

Parameter

Peak Apex Detection

Description

The data system uses these parameters to detect multiple peaks. To detect multiple peaks, it slides a scan window across the chromatogram. The width of this window is specified in the number of scans in the Window Size box. When the peak identification conditions are met, the data system examines the region around this possible peak apex to determine whether the other peak identification criteria are satisfied.

The data system calculates a filter window to examine the corresponding scans for each scan window position as it slides along the mass chromatogram. Specify the width of the filter window in the Filter Width box.

Window Size

Filter Width

Specifies a time window for the Refine spectrum enhancement method. The Refine algorithm applies the window across a chromatogram peak apex and uses it to search for the peak start and peak end, and to estimate the background noise. Set this parameter to the peak width.

Specifies the number of scans included in the moving average across the peak apex detection Window Size parameter. A larger width tends to reduce the number of spurious peaks. The valid range is 1 to 3.

Valley Detection

Use a valley detection approximation method to detect unresolved peaks. This method drops a vertical line from the apex of the valley between unresolved peaks to the baseline.

The intersection of the vertical line and the baseline defines the end of the first peak and the beginning of the second peak.

Rise (%) Specifies the percentage that the peak trace can rise above the baseline after passing through a minimum (before or after the peak). If the trace exceeds this rise percentage, the data system applies valley detection peak integration criteria. This test is applied to both the left and right edge of the peak. These criteria are useful for integrating peaks with long tails. The valid range is

0.1 to 500.0.

Valley S/N

To change the rise percentage, type a new value in the Rise

Percentage box. When you click OK, the data system applies the new peak detection criteria.

Specifies the signal-to-noise criteria that the data system uses for valley detection. The valid range is 1.0 to 100.0.

To change the valley signal-to-noise criteria, type the new value in the Valley S/N box. When you click OK, the data system applies the new peak detection criteria.

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Table 70. Genesis Advanced Chromatogram Options dialog box parameters (Sheet 4 of 4)

Parameter

Background Subtraction

Description

Minimizes the contaminating effect of background on the peak identification process.

When you select background subtraction, the data system does the following:

1. Locates the lowest-intensity scan in the Baseline and Noise window, as specified in the

Identification Options dialog box.

2. Sums the specified Number of Scans in Background taken around the lowest scan.

3. Normalizes this representative background spectrum.

4. Subtracts the background spectrum from all scans in the detection window.

The data system periodically recalculates the representative background scan used for background subtraction using the Background Recomputation Interval parameter. This recalculation compensates for the possibility that the composition of the background might change over the course of a run.

Background

Recomputation

Interval (min)

To compensate for the possibility that the composition of the background might change over the course of a run, the data system periodically recalculates the representative background scan it uses for background subtraction. The Background

Recomputation Interval is the time interval (in minutes) between these recalculations.

Number of Scans in

Background

To change the interval, type the new value in the Background

Recomputation Interval box. The valid range is 0.5 to 10.0 minutes.

Specifies the number of background scans used to determine the background. The valid range is 1 to 100.

To change the number of background scans, type the new value in the Number of Scans in Background box. When you click OK, the data system applies the new baseline parameter.

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Genesis Advanced Detection Options Dialog Box

Use the Genesis Advanced Detection Options dialog box to specify advanced component detection criteria. Use these additional criteria if the standard detection criteria do not provide the desired results.

To open the Genesis Advanced Detection Options dialog box

1. On the Identification page of the Processing Setup – Quan view, select Genesis in the

Peak Detect list.

2. On the Detection page of the Processing Setup – Quan view, click Advanced.

Table 71

describes the parameters in the Genesis Advanced Detection Options dialog box.

Table 71. Genesis Advanced Detection Options dialog box parameters (Sheet 1 of 3)

Parameter

Peak Edge Detection

Description

Set a chromatogram peak edge detection criterion that uses the peak signal-to-noise cutoff value to assist in the detection of a peak edge. This test assumes an edge of a peak is found when the baseline-adjusted height of the edge is less than the ratio of the baseline-adjusted apex height and the peak signal-to-noise cutoff ratio.

Peak S/N Cutoff Specifies the signal-to-noise ratio below which the data system defines the peak edge. For example, if the signal-to-noise ratio at the apex is 500 and the Peak S/N Cutoff value is 200, the data system defines the right and left edges of the peak when the signal-to-noise ratio reaches a value less than 200. The valid range is 50.0 to 10 000.0.

To change the cutoff value, type the new value in the Peak S/N

Cutoff box. When you click OK, the data system applies the new peak detection parameter.

Report Noise As

RMS

Peak To Peak

Select this option to calculate noise as RMS.

Select this option to calculate noise as peak-to-peak.

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Table 71. Genesis Advanced Detection Options dialog box parameters (Sheet 2 of 3)

Parameter

Valley Detection

Description

Use a valley detection approximation method to detect unresolved peaks. This method drops a vertical line from the apex of the valley between unresolved peaks to the baseline.

The intersection of the vertical line and the baseline defines the end of the first peak and the beginning of the second peak.

Rise (%) Specifies the percentage that the peak trace can rise above the baseline after passing through a minimum (before or after the peak). If the trace exceeds this rise percentage, the data system applies valley detection peak integration criteria. The data system applies this test to both the left and right edge of the peak. This integration parameter is useful for integrating peaks with long tails. The valid range is 0.1 to 500.0.

Valley S/N

To change the rise percentage, type the new value in the Rise

Percentage box. When you click OK, the data system applies the new peak detection setting.

Specifies the signal-to-noise criterion that the data system uses for valley detection. The valid range is 1.0 to 100.0.

To change the valley signal-to-noise criterion, type the new value in the Valley S/N box. When you click OK, the data system applies the new peak detection setting.

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Table 71. Genesis Advanced Detection Options dialog box parameters (Sheet 3 of 3)

Parameter Description

Background Subtraction (For All Components)

Minimize the contaminating effect of background on the peak identification process by performing background subtraction. The Xcalibur data system does the following:

• Locates the lowest-intensity scan in the Baseline and Noise window (as specified in the

Identification Options dialog box).

• Sums the specified Number of Scans in Background taken around the lowest scan.

• Normalizes this representative background spectrum.

• Subtracts the background spectrum from all scans in the detection window.

The data system periodically recalculates the representative background scan used for background subtraction to compensate for the possibility that the composition of the background can change over the course of a run.

Number of Scans in

Background

Specifies the number of background scans used to determine the background. The valid range is 1 to 100.

To change the number of background scans, type the new value in the Number of Scans in Background box. When you click OK, the data system applies the new baseline parameter.

ICIS Advanced Parameters Dialog Box

Use the ICIS Advanced Parameters dialog box to specify advanced component detection criteria. Use these additional criteria if the standard detection criteria do not provide the desired results.

To open the ICIS Advanced Parameters dialog box

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

• From the

Quan View of the Processing Setup window, click the Detection tab to

display the

Detection Page for Quan View

and click Advanced.

• From the

Qual View of the Processing Setup window, click the Identification tab to

display the

Identification Page for Qual View

and click Advanced.

The ICIS Advanced Parameters dialog box opens (

Figure 91 ).

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Figure 91. ICIS Advanced Parameters dialog box

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Thermo Scientific

Table 72

describes the parameters in the ICIS Advanced Parameters dialog box.

Table 72. ICIS Advanced Parameters dialog box parameters (Sheet 1 of 2)

Parameter

Noise Method

INCOS Noise

Description

Repetitive Noise

RMS

Selecting this option specifies the use of a a single-pass algorithm to determine the noise level. The ICIS peak detection algorithm uses this value.

Selecting this option specifies the use of a multiple-pass algorithm to determine the noise level. The ICIS peak detection algorithm uses this value. In general, this algorithm is more accurate in analyzing the noise than the INCOS Noise algorithm, but it takes longer.

When this check box is selected, the data system calculates noise as

RMS. By default, the data system uses Peak-To-Peak for the noise calculation. RMS is automatically selected if you determine the noise region manually.

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Table 72. ICIS Advanced Parameters dialog box parameters (Sheet 2 of 2)

Parameter

Peak Parameters

Min Peak Width

Description

Multiple Resolution

Area Tail Extension

Area Scan Window

Type the minimum number of scans required in a peak. The valid range is 0 to 100 scans. The default value is 3 scans. The ICIS peak detection algorithm uses this value.

Type the minimum separation, in scans, between the apexes of two potential peaks. This criterion determines if two peaks are resolved. Type an integer in this box. The valid range is 1 to 500 scans. The default value is 10 scans. The ICIS peak detection algorithm uses this value.

Type the number of scans past the peak endpoint to use in averaging the intensity. The valid range is 0 to 100 scans. The default value is 5 scans. The ICIS peak detection algorithm uses this value.

Type the number of scans on each side of the peak apex to be included in the area integration. The valid range is 0 to 100 scans.

The default value of 0 scans specifies that all scans from peak start to peak end are to be included in the area integration. The ICIS peak detection algorithm uses this value.

Identification Options Dialog Box

Use the Identification Options dialog box to adjust the parameters used by the Xcalibur data system to estimate baseline noise and to correct retention time assignments for void time.

You can access this dialog box by choosing Options > Identification from the Qual or Quan view of the Processing Setup window.

For information about using this dialog box, see “Setting Up the Void Time and Baseline

Identification Options” on page 21

.

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Table 73

describes the parameters in the Identification Options dialog box.

Table 73. Identification Options dialog box parameters

Parameter

Void Time

Value

Description

First Peak

Type a value for the void time, in minutes. The data system subtracts this time from the elution time of all recorded peaks to obtain the correct relative retention times.

Select this option to set the void time to the retention time of the first detected peak. The data system processes data using the specified peak detection parameters to obtain the retention time of the first peak.

This peak is assumed to be non-retained, and its retention time is subsequently used as the void time. The data system subtracts this time from the elution time for all remaining peaks to estimate the correct relative retention time.

Baseline

Baseline and Noise

Window

Specifies the time range that the data system applies to each peak before calculating the baseline and baseline noise within it. If the window is too small, the data system cannot calculate the baseline for a peak correctly because the baseline is positioned up the sides of the peak. To ensure accurate noise calculation, the window should include the base width of the peak and an appreciable amount of baseline.

Baseline Noise

Tolerance

Minimum

Number of Scans in Baseline

Specifies a value that controls how the data system draws the baseline in the noise data. The higher the baseline noise tolerance value, the higher the baseline it draws through the noise data. The valid range is

0.0 to 100.0.

Specifies the minimum number of scans that the data system uses to calculate a baseline. A larger number includes more data in determining an averaged baseline. The valid range is 2 to 100.0.

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Masses Dialog Box

In the Quan and Qual views of the Processing Setup window and in the Quan Browser window, use this dialog box to specify tolerance and precision settings for the mass data displayed in the chromatogram, spectrum, map, and ion map plots.

Specify the default values for tolerance and precision on the Mass Options page of the

Xcalibur Configuration dialog box.

Table 74

describes the parameters in the Masses dialog box.

Table 74. Masses dialog box parameters

Parameter

Mass tolerance

Mass tolerance

Description

Units

Specifies the value for mass tolerance. Type a value in the range of

0.1 to 50 000, and select the units to apply to the value. The data system uses the tolerance value to create the mass range limit.

Specifies the units of measurement in which the data system processes your data. Select mmu (millimass units) or ppm (parts per million).

Mass precision

Decimals Specifies the number of decimal places (mass precision) that the data system uses to display mass values. You can specify from 0 to

5 decimal places. The number of decimal places applies to the mass data in a window.

Print Dialog Box

Use the Print dialog box to choose a report template for printing a processing method. Select

a report template in the Report template box ( Figure 92

).

You can access this dialog box by choosing File > Print from the Processing Setup window menu bar.

Figure 92. Processing Setup Print dialog box

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Note The data system prints a processing method using the name of the person who is currently logged in and requesting the print job, not the name of the person who developed the method. Similarly, the date and time on the printed report is the time of the print job, not the time that the method was created.

Table 75

describes the parameters in the Print dialog box.

Table 75. Print dialog box parameter

Parameter

Report Template

Description

This box displays the path name of the default processing method report template, for example: c:\xcalibur\templates\default processing method report.doc.

You can specify a new template, either by typing directly in the box or by browsing using the Browse button.

If you select a new template and then click OK on the Print dialog box, the template becomes the new default processing method report template.

Search List Dialog Box

Use the Search List dialog box to specify the names and search order of libraries used by the processing method.

To open the Search List dialog box

From the Processing Setup – Qual view – Library Search Options page, click Search List.

The Search List dialog box opens ( Figure 93 ).

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Figure 93. Search List dialog box

Table 76

describes the parameters in the Search List dialog box.

Table 76. Search List dialog box parameters (Sheet 1 of 2)

Parameter

Available Libraries

Selected Libraries

Description

Displays the libraries that are currently excluded from searching during processing. The data system regenerates this list when you open the dialog box.

Displays the libraries that are currently included in searches during processing. The order of the libraries defines the order in which they are searched by the data system.

The data system generates the Available Libraries list dynamically so this box always lists the libraries stored on your system. The

Selected Libraries list is contained in the processing method and might contain libraries that are not present on your system. When you click OK, the data system checks the Selected Libraries list and displays a warning dialog box if any of these are not available on your system.

Buttons

Add

Remove

Top

Up

Moves a library from the Available Libraries list box to the

Selected Libraries list box.

Moves a library from the Selected Libraries list box to the

Available Libraries list box.

Moves a library in the Selected Libraries list box to the top of the list (first in the search order).

Moves a library in the Selected Libraries list box up one position

(earlier in the search order).

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Processing Setup Dialog Boxes

Table 76. Search List dialog box parameters (Sheet 2 of 2)

Parameter

Down

Bottom

Description

Moves a library in the Selected Libraries list box down one position (later in the search order).

Moves a library in the Selected Libraries list box to the final position (last in the search order).

Settings Dialog Box

Use the Settings dialog box to customize the Processing Setup window. By default, the

Xcalibur data system loads the most recently used method into Processing Setup at startup.

You can change this option and also configure the data system to open a raw data file in the

Chromatogram and Spectrum views when you open a processing method.

You can access this dialog box by choosing Options > Settings from the menu bar of the

Processing Setup window.

For information about using the Settings dialog box, see

Setting Up the Startup Options .

Table 77

describes the parameters in the Settings dialog box.

Table 77. Settings dialog box parameters (Sheet 1 of 2)

Parameter

Startup Mode

Description

Specifies whether the Processing Setup window opens with a new method or with the most recently used method.

Load Last Processing

Method

Selecting this option specifies that the data system loads the most recently used method when you start a Processing Setup session.

Create New Processing

Method

Selecting this option specifies that the data system starts a new method when you begin a Processing Setup session.

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Processing Setup Dialog Boxes

Table 77. Settings dialog box parameters (Sheet 2 of 2)

Parameter

Auto-Open Raw File

Description

Specifies whether Processing Setup opens a raw data file in the chromatogram and spectrum cells when you open a method. For this feature to operate, a raw data file must be associated with the method. This association occurs when the method is saved—if a raw data file is present, it is saved with the method.

On

Off

When you select this option, the data system automatically opens the raw data file associated with the processing method. The data system populates the chromatogram and spectrum cells with the raw data file associated with the processing method when it was last saved.

When you select this option, no raw data file opens when you open a processing method. To open a raw data file, you must use the Open Raw File command.

Spectrum Options Dialog Box

Use the Spectrum Options dialog box to set a low-intensity cutoff (%) value for use in

Spectrum detection mode.

For information about using the Spectrum Options dialog box, see

“Setting Up the Spectrum

Options for Chromatography by GC” on page 36

.

Table 78

describes the parameters in the Spectrum Options dialog box.

Table 78. Spectrum Options dialog box parameter

Parameter

Low Intensity Cutoff

(%)

Description

Specifies the intensity cutoff value used by the Spectrum detection method. If you use a spectrum from a raw data file to generate the

Spectrum m/z – intensity (%) grid, the data system discards any ions in the selected range that have an intensity below the cutoff value.

The data system only activates the Spectrum menu option and

Spectrum Options dialog box when you select the Spectrum option on the Detection page in GC chromatography mode.

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Processing Setup Dialog Boxes

Standard Dilution Dialog Box

Use the Standard Dilution dialog box to enter calibration level information for all target components.

When you are working on the Levels page of the Processing Setup – Quan view, you can access this dialog box by choosing Options > Standard Dilutions from the menu bar.

For information about using the Standard Dilution dialog box, see

“Using the Standard

Dilutions Dialog Box to Set Up the Calibration Levels” on page 48

.

Table 79

describes the parameters in the Standard Dilution dialog box.

Table 79. Standard Dilution dialog box parameters (Sheet 1 of 2)

Parameter

Target Compound

Components

(read-only)

Selected Components

(read-only)

Base Amounts

Component

(read-only)

Amount

Description

This parameter displays the total number of target compound components defined in the processing method, including ISTD and non-ISTD component types.

This parameter displays the selected number of non-ISTD components for standard dilution.

This column displays the names of the target components listed in the Components pane of the Processing Setup – Quan view.

Specifies the base amount (for example, the stock concentration) for each target compound.

To enter a base amount, type the value in the Amount box. You must provide a value for each listed Component for the data system to be able to calculate the amounts for each calibration level.

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Table 79. Standard Dilution dialog box parameters (Sheet 2 of 2)

Parameter

Dilution Factors

Cal Level

Description

Specifies the names of the calibration levels. The data system can accommodate up to 50 calibration levels.

Dilution

To enter a calibration level, type the new name in the appropriate

Cal Level box (32 characters maximum). To delete a Cal Level row, click the numbered tile to the left of the row. The data system highlights the row. Press DELETE.

The data system transfers these Cal Level values to the Cal Level column of the Calibration Levels table on the Levels page for each component.

Specifies the stock dilution factor for each calibration level. To enter a dilution factor, type the value in the appropriate Dilution box. The value must be greater than 0.00000001 and less than or equal to 1.

In calculating the calibration level amount for each component, the data system multiplies the dilution factor with the base amount value. The result is transferred to the corresponding

Amount box in the calibration levels table on the Levels page for the component. The data system repeats this procedure for all calibration levels and all components.

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Processing Setup Views

Processing Setup Views

These topics describe the Processing Setup views.

Qual View

Identification Page for Qual View

Spectrum Enhancement Page for Qual View

Library Search Options Page for Qual View

Library Search Constraints Page for Qual View

Peak Purity Page for Qual View

Quan View

Identification Page for Quan View

Detection Page for Quan View

Calibration Page for Quan View

Levels Page for Quan View

System Suitability Page for Quan View

Peak Purity Page for Quan View

Programs View

Reports View

Qual View

Use the Qual view of the Processing Setup window to set up a method for qualitative processing. For processing qualitative data, the Xcalibur data system identifies peaks and can submit a representative mass spectrum of each chromatogram peak to the Library Browser

(NIST MS Search) for matching against reference spectra. You can choose various spectrum enhancement and library search options.

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Processing Setup Views

These topics describe the Qual view pages:

Identification Page for Qual View

Avalon Identification Page for Qual View

ICIS Identification Page for Qual View

Genesis Identification Page for Qual View

Spectrum Enhancement Page for Qual View

Library Search Options Page for Qual View

Library Search Constraints Page for Qual View

Peak Purity Page for Qual View

For information about the OK, Cancel and Save as Default buttons, see

OK, Cancel, and

Save As Default Buttons . For information about the chromatogram and spectrum views, see

Chromatogram and Spectrum Views in the Qual and Quan Views

.

Identification Page for Qual View

Use the Identification page of the 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 information about using this page, see “Setting Up the Qual View Identification

Parameters” on page 52

.

For parameter descriptions, see these topics:

Avalon Identification Page for Qual View

ICIS Identification Page for Qual View

Genesis Identification Page for Qual View

For information about the valid trace combinations, see these topics:

Valid MS Trace Combinations

Valid Analog Trace Combinations

Valid A/D Card Trace Combinations

Valid PDA Trace Combinations

Valid UV Trace Combinations

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Processing Setup Views

Valid MS Trace Combinations

Table 80

shows the valid trace combinations available on the Trace lists. Your choice of combination affects other controls on the page as described in the Resulting Controls column.

Table 80. Valid MS trace combinations parameters

Trace 1

Mass Range

Mass Range

Mass Range

Operator

[blank]

+

Trace 2

[unavailable]

Mass Range

Mass Range

Resulting controls

Mass (m/z) box

Mass1 (m/z) box 2 text box

Mass1 (m/z) box 2 text box

TIC

TIC

Base Peak

Base Peak

Base Peak

Neutral Fragment

(MS/MS data only)

[blank]

+

[unavailable]

Mass Range

Base Peak

[unavailable]

Mass Range

Mass Range

[unavailable]

Mass (m/z) box

Mass (m/z) box

Mass (m/z) box

BP box MR text box

BP box MR text box

Mass

Valid Analog Trace Combinations

Table 81

shows the valid trace combinations available in the Trace lists. The Mass

Range/Wavelength Range control is unavailable.

Table 81. Valid Analog trace combinations parameters

Trace 1

Analog n

(1

n

4)

Analog n

(1

n

4)

Analog n

(1

n

4)

Operator

[blank]

Trace 2 Resulting controls

[unavailable] None

(1

(1

m

4, m /= n)

m

4, m /= n)

None

None

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Valid A/D Card Trace Combinations

Table 82

shows the valid trace combinations available in the Trace lists when you have selected an A/D Card detector type. The Mass Range/Wavelength Range control is unavailable.

Table 82. Valid A/D Card trace combinations parameters

Trace 1

A/D Card Channel n

(1

n

4)

A/D Card Channel n

(1

n

4)

A/D Card Channel n

(1

n

4)

Operator

[blank]

+

Trace 2 Resulting controls

[unavailable] None

A/D Card Channel m

(1

m

4, m /= n)

A/D Card Channel m

(1

m

4, m /= n)

None

None

Valid PDA Trace Combinations

Table 83

shows the valid trace combinations available in the Trace lists when you have selected a PDA detector type in the Type list box on the Identification page of Qual or Quan views.

Your choice of combination affects other controls on the page as described in the Resulting

Controls column.

Table 83. Valid PDA trace combinations parameters

Trace 1

Wavelength Range

Wavelength Range

Wavelength Range

Total Scan

Total Scan

Total Scan

[blank]

Spectrum Maximum [blank]

Spectrum Maximum +

Spectrum Maximum

Operator

[blank]

+

Trace 2

[unavailable]

Wavelength Range

Resulting controls

Wavelength (nm) box

Wavelength1 (nm) box

2 text box

Wavelength Range Wavelength1 (nm) box

2 text box

None [unavailable]

Wavelength Range Wavelength (nm) box

Spectrum Maximum Wavelength (nm) box

[unavailable]

Wavelength Range

Wavelength Range

Wavelength (nm) box

Wavelength1 (nm) box

2 text box

Wavelength1 (nm) box

2 text box

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Valid UV Trace Combinations

Table 84

lists the valid trace combinations available in the Trace lists for UV detectors. The

Mass Range/Wavelength Range control is unavailable.

Table 84. Valid UV trace combinations parameters

Trace 1

Channel n

(A

n

D)

Channel n

(A

n

D)

Channel n

(A

n

D)

Operator

[blank]

Trace 2 Resulting controls

[unavailable] None

(A

(A

m

D, m /= n)

m

D, m /= n)

None

None

Avalon Identification Page for Qual View

Use the Avalon Identification page for the Qual view of the Processing Setup window to specify the type of chromatogram to be used by the processing method during qualitative processing. You can also adjust peak detection and identification criteria for the Avalon peak detection algorithm.

Note Use the Avalon integration algorithm for chromatograms acquired with a PDA or

UV detector.

For more information, see “Setting Up the Qual View Identification Parameters” on page 52

.

Table 85

describes the parameters on the Qual view – Avalon Identification page.

Table 85. Avalon Identification page for Qual view parameters (Sheet 1 of 8)

Parameter

Detector

Type

Description

Specifies the type of detector used to acquire the data:

• MS (mass spectrometer)

Peak Detect

• Analog (analog detector)

• A/D Card (analog-to-digital converter)

• PDA (photodiode array detector)

• UV (UV or UV-Vis detector)

Specifies the peak detection algorithm for the Qual view: Genesis,

ICIS, or Avalon.

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Table 85. Avalon Identification page for Qual view parameters (Sheet 2 of 8)

Parameter

Delay

Filter

Description

Specifies the delay time, in minutes, required to synchronize analog or digital data with MS scans. The Delay value compensates for any difference (negative or positive) in the sample arrival time at the UV and MS detectors. The valid range is –5.0 to +5.0 minutes.

Specifies the scan filter to be applied. Use a scan filter to specify that processing is to be applied to a subset of the scans in a raw data file.

The Filter list contains the scan filters for the current raw data file.

To apply a different scan filter, select a new filter from the scan filter list (most common method), select a new filter from the list and edit the scan filter, or type a new scan filter command string in the box using the scan filter format.

This scan filter example: c full ms [26.8–251] finds all scans in a raw data file that have the following properties:

Centroid data

Scan Mode: Full

Scan Power: MS

Product Ion Mass Range: m/z 26.81 to 251.00

For more information, refer to the Xcalibur Qual Browser User

Guide for information about scan formats.

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Table 85. Avalon Identification page for Qual view parameters (Sheet 3 of 8)

Parameter

Trace

Description

From the three Trace lists, specify the type of chromatogram that you want to use for data processing as follows:

1. From the first list, select a basic chromatogram type, for example, TIC.

2. From the second list, select a logical operator: + or –.

Your selection of an operator makes the third list available.

3. In the third list, select a second chromatogram type to add to, or subtract from, the first type, for example, Mass Range. The list includes the valid remaining trace types.

You can use trace combinations to subtract from a chromatogram the contributions from a solvent or noise. Combinations are limited to traces of the same type.

MS detector

Analog detector

A/D card

PDA detector

UV detector

The valid trace types depend on the detector type.

For MS scans, valid trace types are TIC, Mass Range, and Base

Peak. For more information, see

Valid MS Trace Combinations.

For Analog data, the data system supports up to four channels

(labeled Analog 1–4). For more information, see

Valid Analog

Trace Combinations.

For data from an A/D Card, the data system supports four channels (labeled A/D Card Ch 1–4). For more information, see

Valid A/D Card Trace Combinations

.

For PDA data, valid trace types are Wavelength Range, Total Scan, or Spectrum Maximum. For more information, see

Valid PDA

Trace Combinations .

For UV detector data, the data system supports four channels

(labeled Channel A–D). For more information, see

Valid UV

Trace Combinations .

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Table 85. Avalon Identification page for Qual view parameters (Sheet 4 of 8)

Parameter

Mass

Description

Specifies the mass range for the Mass Range trace type. The data system displays this box when you select a Mass Range trace type or a TIC ± Mass Range trace combination for an MS detector type.

Mass 1

To change the range or to add a new range, type the range in the box. The valid range depends on the configured detector. The format is LowMass–HighMass. For example, for the range of m/z values from 123 through 456, type 123–456.

You can sum up to 50 mass ranges by entering mass ranges or single mass values separated by your computer list separator

character. To view or set the list separator character, see “Changing the List Separator Character” on page 123 .

Specifies the mass range for the first trace type. The data system displays this box when you select a Mass Range ± Mass Range trace combination for an MS detector type.

To change the range or to add a new range, type the range in the box. The valid range depends on the configured detector. The format is LowMass–HighMass. For example, for the range of m/z values from 123 through 456, type 123–456.

[Mass] 2

BP

You can sum up to 50 mass ranges by entering mass ranges or single mass values separated by your computer list separator

character. To view or set the list separator character, see “Changing the List Separator Character” on page 123 .

Specifies the mass range for the second trace type. The data system displays this box when you select a Mass Range ± Mass Range trace combination for an MS detector type.

To change the range or to add a new range, type the range in the box. The format is LowMass–HighMass. For example, for the range of m/z values from 123 through 456, type 123–456.

You can sum up to 50 mass ranges by entering mass ranges or single mass values separated by your computer list separator

character. To view or set the list separator character, see “Changing the List Separator Character” on page 123 .

Specifies the mass value for the base peak. The data system displays this box when you select a Base Peak trace for an MS detector type.

To change the base peak mass, type the value in the box.

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Table 85. Avalon Identification page for Qual view parameters (Sheet 5 of 8)

Parameter

MR

Description

Specifies the mass range for the second Mass Range trace type.

The data system displays this box when you select a Base Peak ±

Mass Range trace combination for an MS detector type.

Wavelength

To change the range or to add a new range, type the range in the box. The format is LowMass–HighMass. For example, for the range of m/z values from 123 through 456, type 123–456.

Specifies the wavelength range for the Wavelength Range or

Spectrum Maximum trace type. Xcalibur displays this box when you select one of the following trace combinations for a PDA detector type:

• Spectrum Maximum

• Wavelength Range

• Total Scan – Wavelength Range

Wavelength 1

To change the range or to add a new range, type the range in the box. The valid range depends on the configured detector. The format is LowWavelength–HighWavelength. For example, for the range of m/z values from 123 through 456, type 123–456.

You can sum up to 50 wavelength ranges by entering ranges or single values separated by your computer list separator character.

To view or set the list separator character, see

“Changing the List

Separator Character” on page 123 .

Specifies the wavelength or wavelength range for the first trace type. The data system displays this box when you select one of the following trace combinations for a PDA detector type:

• Wavelength Range ± Wavelength Range

• Spectrum Maximum ± Wavelength Range

To change the range or to add a new range, type the range in the box. The valid range depends on the configured detector. The format is LowWavelength–HighWavelength. For example, for the range of m/z values from 123 through 456, type 123–456.

You can sum up to 50 wavelength ranges by entering ranges or single values separated by your computer list separator character.

To view or set the list separator character, see

“Changing the List

Separator Character” on page 123 .

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Table 85. Avalon Identification page for Qual view parameters (Sheet 6 of 8)

Parameter

[Wavelength] 2

Description

Specifies the wavelength or wavelength range for the second trace type. The data system displays this box when you select one of the following trace combinations for a PDA detector type:

• Wavelength Range ± Wavelength Range

• Spectrum Maximum ± Wavelength Range

To change the range or to add a new range, type the range in the box. The valid range depends on the configured detector. The format is LowWavelength–HighWavelength. For example, for the range of m/z values from 123 through 456, type 123–456.

You can sum up to 50 wavelength ranges by entering ranges or single values separated by your computer list separator character.

To view or set the list separator character, see

“Changing the List

Separator Character” on page 123 .

Selected Retention Time Window

Use the Ranges box to define the detection window for qualitative processing.

Range (min) Enter a time span to limit qualitative processing. A qualitative processing method processes a peak only if its apex retention time lies in the specified range. The valid range is 0.1 to 999.0 minutes.

To change the time window or to enter a new time window, type the number of seconds in the Range box. Type an asterisk (*) to represent the full chromatogram range of the active raw data file.

Avalon Peak Integration

Specifies peak integration criteria. These parameters are used by the Avalon peak detection algorithm. To change the settings in the Event list, click Advanced to display the Avalon

Event List dialog box.

Smoothing Points Specifies the degree of data smoothing to be performed on the active component peak before peak detection and integration. The valid range is any odd value from 1 (no smoothing) through 15

(maximum smoothing). To smooth your component peak data before integration, type a value in the Smoothing Points box. See

also the Avalon Detection Page for Quan View

.

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Table 85. Avalon Identification page for Qual view parameters (Sheet 7 of 8)

Parameter

Event List

Description

To modify the event list

Click Advanced to open the Avalon Event List dialog box.

For information about using the Avalon Event List dialog box to edit the Event list, see

Avalon Event List Dialog Box .

Event List The table contains a minimum of seven integration events that are identified by the initial value setting in the Time column. These are the default integration events required by the Avalon integration algorithm. You can change the value of an initial entry integration event, but you cannot delete it or change its Time value.

Time

Event

Value

Auto Calculate Initial

Events

To detect peaks, Avalon uses the settings for initial value events and user-defined timed events that are in the Event list.

This column contains either the term initial value or a time value, in minutes. You cannot change the time value for an initial value

This column displays the integration events.

This column displays the values associated with initial value events and timed events. The range of allowed values is specific to each event.

This button is available when a raw data file is open in the

Processing Setup window.

When you click this button, the data system automatically determines the best value for each of the seven initial value events on the basis of the data in the current raw data file and then displays these values in the Value column of the event list.

The data system does not estimate values for timed events; that is, events that have a time value in the Time column. It determines initial values for these events only: Start Threshold, End

Threshold, Area Threshold, P-P [Resolution] Threshold, Bunch

Factor, Negative Peaks, and Tension.

Limit Peaks

Select Top Peaks

Enable

Select by Area

Selecting this check box limits peak detection to a specified number that is based on either peak area or peak height.

Selecting the Select by Area option restricts detection to the most significant peaks on the basis of area rather than height.

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Table 85. Avalon Identification page for Qual view parameters (Sheet 8 of 8)

Parameter

Select by Height

Num to Select

Rel Peak Height Threshold

Selecting the Select by Height option restricts detection to the most significant peaks on the basis of height rather than area.

Specifies the maximum number of peaks to be detected. The data system selects the largest peaks on the basis of intensity (height) or area.

Enable

Description

% of Highest Peak

Selecting this check box limits the list of detected chromatogram peaks to those exceeding the specified value, entered as a percentage of the most intense peak in the chromatogram.

Specifies a percentage threshold to limit the number of peaks submitted for further processing. The data system discards any detected peaks with an intensity less than the threshold percentage of the most intense peak.

Buttons

Save As Default

Advanced

Validates and saves the settings on the current page as default settings. The Processing Setup application uses these settings for all new processing methods. The application writes over the previous default values and cannot recover them.

Opens the Avalon Event List dialog box, where you can edit the list of peak integration events.

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ICIS Identification Page for Qual View

Use the ICIS Identification page for the Qual View of the Processing Setup window to specify the type of chromatogram to be used by the processing method during qualitative processing.

You can also adjust peak detection and identification criteria for the ICIS peak detection algorithm.

For more information, see “Setting Up the Qual View Identification Parameters” on page 52

.

Table 86

describes the parameters on the Qual view – ICIS Identification page.

Table 86. ICIS Identification page for Qual view parameters (Sheet 1 of 8)

Parameter

Detector

Type

Description

Specifies the currently selected detector type:

• MS

• Analog

• A/D Card

• PDA

• UV

Peak Detect

Delay

To change the detector type, click the arrow to display the list of detector types, and then click the required detector type.

Specifies the peak detection algorithm.

Type a delay time, in minutes, to synchronize analog or digital data with MS scans. The Delay value compensates for any difference (negative or positive) in the arrival time of eluents at the

UV and MS detectors. The valid range is –5.0 to +5.0 minutes.

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Table 86. ICIS Identification page for Qual view parameters (Sheet 2 of 8)

Parameter

Filter

Description

Specifies the current scan filter for the active raw data (.raw) file.

You can use a scan filter to apply processing to a subset of the scans in a raw data file.

To apply a different scan filter, select a new filter from the scan filter list (most common method), select a new filter from the list and edit the scan filter, or type a new scan filter command string into the box using the scan filter format.

To select from the list of scan filters used to create the raw data file, click the arrow on the box to display the list. Click one of the scan filters. The data system displays the scan filter in the Filter box.

Trace

This scan filter example: c full ms [26.81–251] finds all scans in a raw data file that have the following properties:

Centroid data

Scan Mode: Full

Scan Power: MS

Product Ion Mass Range: m/z 26.81 to 251.00

Specifies the type of chromatogram you want to use for data processing. From the three Trace lists, you can select:

1. From the first list, a basic chromatogram type, for example,

TIC.

2. From the second list, a logical operator: + or –.

Your selection of an operator activates the third list.

3. In the third list, select a second chromatogram type to add to, or subtract from, the first type, for example, Mass Range. The list includes the valid remaining trace types.

MS detector

You can use trace combinations to subtract the contributions from a solvent or noise from a chromatogram. Combinations are limited to traces of the same type.

The valid trace types depend on the detector type.

For MS scans, valid trace types are TIC, Mass Range, and Base

Peak. For more information, see

Valid MS Trace Combinations.

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Table 86. ICIS Identification page for Qual view parameters (Sheet 3 of 8)

Parameter

Analog detector

A/D card

PDA detector

UV detector

Mass (m/z)

Description

For Analog data, the data system supports up to four channels

(labeled Analog 1–4). For more information, see

Valid Analog

Trace Combinations.

For data from an A/D Card, the data system supports four channels (labeled A/D Card Ch 1–4). For more information, see

Valid A/D Card Trace Combinations

.

For PDA data, valid trace types are Wavelength Range, Total Scan, or Spectrum Maximum. For more information, see

Valid PDA

Trace Combinations .

For UV detector data, the data system supports four channels

(labeled Channel A–D). For more information, see

Valid UV

Trace Combinations .

Specifies the mass range for the Mass Range trace type. The data system displays this box when you select a Mass Range trace type or a TIC ± Mass Range trace combination for an MS detector type.

Mass 1 (m/z)

To change the range or to add a new range, type the range in the box. The valid range depends on the configured detector. The format is LowMass–HighMass. For example, for the range of m/z values from 123 through 456, type 123–456.

You can sum up to 50 mass ranges by entering mass ranges or single mass values separated by your computer list separator

character. To view or set the list separator character, see “Changing the List Separator Character” on page 123 .

Specifies the mass range for the first trace type. The data system displays this box when you select a Mass Range ± Mass Range trace combination for an MS detector type.

To change the range or to add a new range, type the range in the box. The valid range depends on the configured detector. The format is LowMass–HighMass. For example, for the range of m/z values from 123 through 456, type 123–456.

You can sum up to 50 mass ranges by entering mass ranges or single mass values separated by your computer list separator

character. To view or set the list separator character, see “Changing the List Separator Character” on page 123 .

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Table 86. ICIS Identification page for Qual view parameters (Sheet 4 of 8)

Parameter

[Mass] 2 (m/z)

Description

Specifies the mass range for the second trace type. The data system displays this box when you select a Mass Range ± Mass Range trace combination for an MS detector type.

BP

To change the range or to add a new range, type the range in the box. The format is LowMass–HighMass. For example, for the range of m/z values from 123 through 456, type 123–456.

You can sum up to 50 mass ranges by entering mass ranges or single mass values separated by your computer list separator

character. To view or set the list separator character, see “Changing the List Separator Character” on page 123 .

Specifies the mass value for the base peak. The data system displays this box when you select a Base Peak trace for an MS detector type.

MR

Wavelength (nm)

To change the base peak mass, type the value in the box.

Specifies the mass range for the second trace type, Mass Range.

The data system displays this box when you select a Base Peak ±

Mass Range trace combination for an MS detector type.

To change the range or to add a new range, type the range in the box. The format is LowMass–HighMass. For example, for the range of m/z values from 123 through 456, type 123–456.

Specifies the wavelength range for the Wavelength Range or

Spectrum Maximum trace type. The data system displays this box when you select one of the following trace combinations for a

PDA detector type:

• Spectrum Maximum

• Wavelength Range

• Total Scan – Wavelength Range

To change the range or to add a new range, type the range in the box. The valid range depends on the configured detector. The format is LowWavelength–HighWavelength. For example, for the range of m/z values from 123 through 456, type 123–456.

You can sum up to 50 wavelength ranges by entering ranges or single values separated by your computer list separator character.

To view or set the list separator character, see

“Changing the List

Separator Character” on page 123 .

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Table 86. ICIS Identification page for Qual view parameters (Sheet 5 of 8)

Parameter

Wavelength 1 (nm)

Description

Specifies the wavelength or wavelength range for the first trace type. The data system displays this box when you select one of the following trace combinations for a PDA detector type:

• Wavelength Range ± Wavelength Range

• Spectrum Maximum ± Wavelength Range

To change the range or to add a new range, type the range in the box. The valid range depends on the configured detector. The format is LowWavelength–HighWavelength. For example, for the range of m/z values from 123 through 456, type 123–456.

You can sum up to 50 wavelength ranges by entering ranges or single values separated by your computer list separator character.

To view or set the list separator character, see

“Changing the List

Separator Character” on page 123 .

[Wavelength] 2 (nm) Specifies the wavelength or wavelength range for the second trace type. The data system displays this box when you select one of the following trace combinations for a PDA detector type:

• Wavelength Range ± Wavelength Range

• Spectrum Maximum ± Wavelength Range

To change the range or to add a new range, type the range in the box. The format is Low Wavelength–HighWavelength. For example, for the range of m/z values from 123 through 456, type 123–456.

You can sum up to 50 wavelength ranges by entering ranges or single values separated by your computer list separator character.

To view or set the list separator character, see

“Changing the List

Separator Character” on page 123 .

Selected Retention Time Window

Range Enter a time span to limit qualitative processing. The qualitative processing method processes a peak only if its apex retention time lies in the range. The valid range is 0.1 to 999.0 minutes. To change the time window or to enter a new time window, type the number of seconds in the Range box. Type an asterisk (*) to represent the full chromatogram range of the active raw data file.

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Table 86. ICIS Identification page for Qual view parameters (Sheet 6 of 8)

Parameter

ICIS Peak Integration

Smoothing Points

Description

Specifies the number of points in the moving average used to smooth the data.

Default: 1

Range: 1–15

Baseline Window

The ICIS peak detection algorithm uses this value.

Specifies the number of scans to review for a local minima.

Default: 40

Range: 1–500

The ICIS peak detection algorithm uses this value.

Area Noise Factor

Peak Noise Factor

Specifies the noise-level multiplier used to determine the peak edges after the data system determines the start and end points of a possible peak for the selected component. As you increase this value, the integrated peak area decreases.

Default: 5

Range: 1–500

The ICIS peak detection algorithm uses this value.

Specifies the noise-level multiplier used to determine the potential peak signal threshold.

Default: 10

Range: 1–1000

The ICIS peak detection algorithm uses this value.

Constrain Peak Width Select this check box to constrain the integrated area of a component peak by specifying a peak height threshold and a tailing factor.

When you select the Constrain Peak Width check box, the Peak

Height (%) and Tailing Factor boxes become available.

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Table 86. ICIS Identification page for Qual view parameters (Sheet 7 of 8)

Parameter

Peak Height (%)

Description

Specifies the percent of the total peak height (100%) that a signal must be above the baseline the data system turns integration on or off.

Tailing Factor

To enter a value for this parameter, select the Constrain Peak

Width check box. Then type a value in the Peak Height (%) box.

Range: 0.0–100.0.

Specifies a tailing factor that controls how the data system integrates the tail of a peak. This factor is the maximum ratio of the trailing edge to the leading edge of a constrained peak.

To enter a value for this parameter, select the Constrain Peak

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

Min

(graphical representation)

Max

(graphical representation)

Range: 0.5–9.0

Displays a representative drawing of the minimum value for the selected parameter. The location of the cursor defines the selected parameter.

For example, if you click the Smoothing Points box, the graphic shows the typical result obtained with the minimum number of smoothing points: a peak with reduced noise.

The number in the upper left corner of the graphic is a representative low value for the active parameter. It is not necessarily the minimum value for the parameter.

Displays a representative drawing of maximum value for the selected parameter. The location of the cursor defines the selected parameter.

For example, if you click the Smoothing Points box, the graphic shows the typical result obtained with a high number of smoothing points: a peak without noise.

The number in the upper left corner of the graphic is a representative high value of the active parameter. It is not necessarily the maximum value for the parameter.

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Processing Setup Views

Table 86. ICIS Identification page for Qual view parameters (Sheet 8 of 8)

Parameter

Limit Peaks

Select Top Peaks

Enable

Description

Select by Area

Select by Height

Num to Select

Selecting this check box limits peak detection to a specified number on the basis of either peak area or peak height.

Select the Area option to restrict detection to the most significant peaks on the basis of area rather than height.

Select the Height option to restrict detection to the most significant peaks on the basis of height rather than area.

Enter the maximum number of peaks to be detected. The data system selects the largest peaks on the basis of intensity (height) or area.

Rel Peak Height Threshold

Enable Selecting this check box limits the list of detected chromatogram peaks to those exceeding the specified value, entered as a percentage of the most intense peak in the chromatogram.

% of Highest Peak Enter a percentage threshold to limit the number of peaks submitted for further processing. The data system discards any detected peaks with an intensity less than the threshold percentage of the most intense peak.

Buttons

Save As Default

Advanced

Validates and saves the settings on the current page as default settings. The Processing Setup application uses these settings for all new processing methods. The application writes over the previous default values and cannot recover them.

Opens the ICIS Advanced Parameters Dialog Box . These

parameters are used by the ICIS peak detection algorithm.

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Processing Setup Views

Genesis Identification Page for Qual View

Use the Genesis Identification page of the Qual view of the Processing Setup window to specify the type of chromatogram the processing method uses during qualitative processing.

You can also adjust peak detection and identification criteria for the Genesis peak detection algorithm.

For more information, see “Setting Up the Qual View Identification Parameters” on page 52

.

Table 87

describes the parameters on the Genesis Identification page of the Qual view.

Table 87. Genesis Identification page for Qual view parameters (Sheet 1 of 8)

Parameter

Detector

Type

Description

Specifies the currently selected detector type:

• MS

• Analog

• A/D Card

• PDA

• UV

Peak Detect

Delay

To change the detector type, click the arrow to display the list of detector types, and then click the required detector type.

Specifies the peak detection algorithms.

Enter a delay time, in minutes, to synchronize analog or digital data with MS scans. The Delay value compensates for any difference (negative or positive) in the arrival time of eluents at the

UV and MS detectors.

The valid range is –5.0 to +5.0 minutes.

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Table 87. Genesis Identification page for Qual view parameters (Sheet 2 of 8)

Parameter

Filter

Description

Specifies the current scan filter for the active raw data (.raw) file.

You can use a scan filter to apply processing to a subset of the scans in a raw data file.

To apply a different scan filter, select a new filter from the scan filter list (most common method), select a new filter from the list and edit the scan filter, or type a new scan filter command string into the box using the scan filter format.

To select from the list of scan filters used to create the raw data file, click the arrow to display the list. Click one of the scan filters.

The data system displays the scan filter in the Filter box.

This scan filter example: c full ms [26.81–251]

Trace

MS detector finds all scans in a raw data file that have the following properties:

• Centroid data

• Scan Mode: Full

• Scan Power: MS

• Product Ion Mass Range: m/z 26.81 to 251.00

Specifies the type of chromatogram you want to use for data processing. From the three Trace lists, you can select:

1. From the first list, a basic chromatogram type, for example,

TIC.

2. From the second list, a logical operator: + or –.

Your selection of an operator activates the third list.

3. In the third list, a second chromatogram type to add to, or subtract from, the first type, for example, Mass Range. The list includes the valid remaining trace types.

You can use trace combinations to subtract the contributions from a solvent or noise from a chromatogram. Combinations are limited to traces of the same type.

The valid trace types depend on the detector type.

For MS scans, valid trace types are TIC, Mass Range, and Base

Peak. For more information, see

Valid MS Trace Combinations.

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Table 87. Genesis Identification page for Qual view parameters (Sheet 3 of 8)

Parameter

Analog detector

Mass

A/D card

PDA detector

UV detector

Description

For Analog data, the data system supports up to four channels

(labeled Analog 1–4). For more information, see

Valid Analog

Trace Combinations.

For data from an A/D Card, the data system supports four channels (labeled A/D Card Ch 1–4). For more information, see

Valid A/D Card Trace Combinations

.

For PDA data, valid trace types are Wavelength Range, Total Scan, or Spectrum Maximum. For more information, see

Valid PDA

Trace Combinations .

For UV detector data, the data system supports four channels

(labeled Channel A–D). For more information, see

Valid UV

Trace Combinations .

Specifies the mass range for the Mass Range trace type. The data system displays this box when you select a Mass Range trace type or a TIC ± Mass Range trace combination for an MS detector type.

Mass 1

To change the range or to add a new range, type the range in the box. The valid range depends on the configured detector. The format is LowMass–HighMass. For example, for the range m/z 123 through 456, type 123–456.

You can sum up to 50 mass ranges by entering mass ranges or single mass values separated by your computer list separator

character. To view or set the list separator character, see “Changing the List Separator Character” on page 123 .

Specifies the mass range for the first trace type. The data system displays this box when you select a Mass Range ± Mass Range trace combination for an MS detector type.

To change the range or to add a new range, type the range in the box. The valid range depends on the configured detector. The format is LowMass–HighMass. For example, for the range m/z 123 through 456, type 123–456.

You can sum up to 50 mass ranges by entering mass ranges or single mass values separated by your computer list separator

character. To view or set the list separator character, see “Changing the List Separator Character” on page 123 .

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Table 87. Genesis Identification page for Qual view parameters (Sheet 4 of 8)

Parameter

[Mass] 2

Description

Specifies the mass range for the second trace type. The data system displays this box when you select a Mass Range ± Mass Range trace combination for an MS detector type.

BP

To change the range or to add a new range, type the range in the box. The format is LowMass–HighMass. For example, for the range m/z 123 through 456, type 123–456.

You can sum up to 50 mass ranges by entering mass ranges or single mass values separated by your computer list separator

character. To view or set the list separator character, see “Changing the List Separator Character” on page 123 .

Specifies the mass value for the base peak. The data system displays this box when you select a Base Peak trace for an MS detector type.

MR

Wavelength

To change the base peak mass, type the value in the box.

Specifies the mass range for the second trace type, Mass Range.

The data system displays this box when you select a Base Peak ±

Mass Range trace combination for an MS detector type.

To change the range or to add a new range, type the range in the box. The format is LowMass–HighMass. For example, for the range of m/z values from 123 through 456, type 123–456.

Specifies the wavelength range for the Wavelength Range or

Spectrum Maximum trace type. The data system displays this box when you select one of the following trace combinations for a

PDA detector type:

• Spectrum Maximum

• Wavelength Range

• Total Scan – Wavelength Range

To change the range or to add a new range, type the range in the box.

The valid range depends on the configured detector. The format is

LowWavelength–HighWavelength. For example, for the range of

m/z values from 123 through 456, type 123 –456.

You can sum up to 50 wavelength ranges by entering ranges or single values separated by your computer list separator character.

To view or set the list separator character, see

“Changing the List

Separator Character” on page 123 .

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Table 87. Genesis Identification page for Qual view parameters (Sheet 5 of 8)

Parameter

Wavelength 1

Description

Specifies the wavelength or wavelength range for the first trace type. The data system displays this box when you select one of the following trace combinations for a PDA detector type:

• Wavelength Range ± Wavelength Range

• Spectrum Maximum ± Wavelength Range

[Wavelength] 2

To change the range or to add a new range, type the range in the box.

The valid range depends on the configured detector. The format is

LowWavelength–HighWavelength. For example, for the range of

m/z values from 123 through 456, type 123–456.

You can sum up to 50 wavelength ranges by entering ranges or single values separated by your computer list separator character.

To view or set the list separator character, see

“Changing the List

Separator Character” on page 123 .

Specifies the wavelength or wavelength range for the second trace type. The data system displays this box when you select one of the following trace combinations for a PDA detector type:

• Wavelength Range ± Wavelength Range

• Spectrum Maximum ± Wavelength Range

To change the range or to add a new range, type the range in the box. The format is LowWavelength–HighWavelength. For example, for the range of m/z values from 123 through 456, type 123–456.

You can sum up to 50 wavelength ranges by entering ranges or single values separated by your computer list separator character.

To view or set the list separator character, see

“Changing the List

Separator Character” on page 123 .

Selected Retention Time Window

Range Specifies a retention time window to limit qualitative processing.

The qualitative section of a processing method processes a peak only if its apex retention time lies in the range. The valid range is

0.1 to 999.0 minutes. To change the time window or to enter a new time window, type the number of seconds in the Range box.

Type an asterisk (*) to represent the full chromatogram range of the active raw data file.

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Processing Setup Views

Table 87. Genesis Identification page for Qual view parameters (Sheet 6 of 8)

Parameter

Genesis Peak Integration

Description

Smoothing Points Specifies the degree of data smoothing to be performed on the active chromatogram before peak detection and integration.

S/N Threshold

To change this value, type a value in the Smoothing Points box.

Default: 1

Range: Odd integers from 1 (no smoothing) through 15

(maximum smoothing)

Specifies the signal-to-noise threshold for peak integration. The data system only integrates peaks with a signal-to-noise value that is greater than this value.

To change this value, type a value in the S/N Threshold box.

Enable Valley

Detection

Default: 0.5

Range: 0.0–999.0

Selecting this check box turns on the valley detection integration algorithm and activates the Expected Width parameter. This integration algorithm drops a vertical line from the apex of the valley between unresolved peaks to the baseline. The intersection of the vertical line and the baseline defines the end of the first peak and the beginning of the second peak.

Expected Width (sec) Specifies the expected peak width, in seconds, for valley detection.

This parameter controls the minimum peak width for a peak when the valley detection algorithm is turned on. Selecting the

Enable Valley Detection check box makes this box available.

When valley detection is turned on, the data system ignores a valley (local minima) that is within the following window: peak apex ± expected width/2

When the data system finds a valley outside the expected peak width window, it terminates the peak at that point. The data system always terminates a peak when the signal reaches the baseline, independent of the value set for the expected peak width.

To enter a value for this parameter, select the Enable Valley

Detection check box. Then type a value in the Expected Width box.

Range: 0.0–999.0

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Table 87. Genesis Identification page for Qual view parameters (Sheet 7 of 8)

Parameter

Constrain Peak Width Selecting this check box turns on the constrain peak width integration algorithm and activates the Peak Height (%) and

Tailing Factor boxes.

Peak Height (%)

Description

Specifies the percent of the total peak height (100%) that determine the start and end points for the peak. To integrate the area under a peak, the data system drops a vertical line to the baseline at these points. The integrated area of a peak is constrained to the peak width between these points.

Tailing Factor

To enter a value for this parameter, select the Constrain Peak

Width check box. Then type a value in the Peak Height (%) box.

Range: 0.0–100.0

Controls how the data system integrates the tail of a peak. The tailing factor is the maximum ratio of the trailing edge to the leading edge of a constrained peak.

Min

(graphical representation)

Max

(graphical representation)

To enter a value for this parameter, select the Constrain Peak

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

Range: 0.5–9.0

Displays a representative drawing of the minimum value for the selected parameter. The location of the cursor defines the selected parameter.

For example, if you click the Smoothing Points box, the graphic shows the typical result obtained with the minimum number of smoothing points: a peak with reduced noise.

The number in the upper left corner of the graphic is a representative low value for the active parameter. It is not necessarily the minimum value for the parameter.

Displays a representative drawing of maximum value for the selected parameter. The location of the cursor defines the selected parameter.

For example, if you click the Smoothing Points box, the graphic shows the typical result obtained with a high number of smoothing points: a peak without noise.

The number in the upper left corner of the graphic is a representative high value of the active parameter. It is not necessarily the maximum value for the parameter.

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Table 87. Genesis Identification page for Qual view parameters (Sheet 8 of 8)

Parameter

Limit Peaks

Select Top Peaks

Description

Enable

Select by Area

Select by Height

Select the Area option to restrict detection to the most significant peaks on the basis of area rather than height.

Select the Height option to restrict detection to the most significant peaks on the basis of height rather than area.

Num to Select

Rel Peak Height Threshold

Type the maximum number of peaks to be detected. The data system selects the largest peaks on the basis of intensity (height) or area.

Enable

% of Highest Peak

Select this check box to activate the parameters in the Select Top

Peaks area. These parameters limit peak detection to a specified number of peaks on the basis of either peak area or peak height.

Select this check box to activate the % of Highest Peak parameter.

This parameter limits the list of detected chromatogram peaks to those exceeding the specified value, entered as a percentage of the most intense peak in the chromatogram.

Specifies a percentage threshold that limits the number of peaks submitted for further processing. The data system discards any detected peaks with an intensity less than the threshold percentage of the most intense peak.

Buttons

Save As Default

Advanced

Validates and saves the settings on the current page as default settings. The Processing Setup application uses these settings for all new processing methods. The application writes over the previous default values and cannot recover them.

Opens Genesis Advanced Chromatogram Options dialog box, where you can set advanced peak identification and detection parameters. The Genesis peak detection algorithm uses these parameters.

For more information, see Genesis Advanced Chromatogram

Options Dialog Box .

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Spectrum Enhancement Page for Qual View

Use the Spectrum Enhancement page for the Qual view of the Processing Setup window to select the algorithm to be used to remove the background noise from the spectrum of interest.

When you select the Enable check box, these three options become available:

Refine Option in the Spectrum Enhancement Page for Qual View

Combine Option in the Spectrum Enhancement Page for Qual View

Threshold Option in the Spectrum Enhancement Page for Qual View

Refine Option in the Spectrum Enhancement Page for Qual View

Select the Refine option to remove the contribution of background ions from the spectrum of interest. The Refine algorithm determines which ions in the selected spectrum are part of the background noise and removes them to produce a “refined” spectrum.

For more information, see “Using the Refine Option for Spectrum Enhancement” on page 59 .

Refine requires two parameters that you can set and test interactively: Window Size (sec) and

Noise Threshold. Using these settings, the Refine algorithm does the following:

1. Discards masses without a peak maximum within ±1 scan of the defined chromatogram peak apex.

2. Searches for a minimum intensity in the user-specified window on either side of the peak apex. These points define the peak start and peak end.

3. Measures the background noise level in the mass chromatogram using scans at and beyond the peak start and peak end, and then estimates the contribution of noise to the peak apex scan through extrapolation.

4. Adjusts the mass intensity of the apex scan by subtracting the estimated noise contribution.

5. Uses the user-specified noise threshold to determine whether the adjusted intensity is significant in comparison to the background noise. If the ion meets the following condition, the data system discards the m/z value for the ion from the final spectrum.

Adjusted Intensity < Noise Threshold × Background Noise

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Table 88

describes the parameters for the Refine option on the Spectrum Enhancement page of the Processing Setup – Qual view.

Table 88. Refine option parameters

Parameter

Enhancement Options

Refine

Window Size

Description

Noise Threshold

Specifies a time window for the Refine option. The Refine algorithm applies the window across a chromatogram peak apex and uses it to search for the peak start and peak end and to estimate the background noise. Set this parameter to the peak width.

Specifies a value for the Noise Threshold parameter. The Refine algorithm uses the Noise Threshold parameter to determine whether adjusted ion intensities are significant in comparison to the background noise. The parameter is actually a factor rather than a threshold. For example, with a Noise Threshold value of 2, the data system discards ions from the enhanced spectrum unless their intensities are twice the measured background noise.

Button

Save As Default Validates and saves the settings on the current page as default settings. The Processing Setup application uses these settings for all new processing methods. The application writes over the previous default values and cannot recover them.

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Combine Option in the Spectrum Enhancement Page for Qual View

Combine option

Select the Combine option to use the Combine algorithm to remove the background noise

from the spectra or spectrum of interest. For more information, see “Using the Combine

Option for Spectrum Enhancement” on page 57

.

The Combine algorithm produces a single enhanced spectrum for each detected peak as follows:

• Averages all the scans across each peak top region

• Subtracts the background contribution (averaged from a number of scans and scaled appropriately) determined from the baseline regions on either side of each peak.

The Combine algorithm requires six parameters that you can set and test interactively. The data system applies the algorithm to all detected chromatogram peaks in the time range that is specified in the Selected Retention Time Window area on the Qual view – Identification page. You might need to examine the peaks in a reference chromatogram carefully to make sure the Combine settings are appropriate for all the peaks of interest.

In setting up the Combine parameters, you might find it helpful to display scan numbers in the chromatogram cell.

To display the scan number label in the chromatogram view

1. Open a raw data file of interest by choosing File > Open Raw File from the menu bar.

2. Pin the chromatogram view.

3. Right-click the chromatogram view and choose Display Options from the shortcut menu.

The Display Options dialog box opens.

4. Click the Labels tab to display the Labels page.

5. In the Label With area, select the Scan Number check box.

Table 89

describes the parameters for the Combine option on the Spectrum Enhancement page of the Processing Setup – Qual view.

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Table 89. Combine option parameters

Parameter Description

Background Subtraction Left Region

Region Width (points) Specifies the number of scans to average in the analysis of the background spectrum in the Left region. The Combine algorithm uses this, together with a similar region from the right of each peak, for background analysis.

Region End

Peak Start

Points Before Peak Top Select this option to define the left region start point as a specific number of scans before the peak top. Use the associated box to enter the number of scans.

Peak Top Region

Select this option to use the peak start time to define the end time of the left background subtraction region.

Peak Top Region

Width (points)

Determine the number of scans used by the Combine algorithm.

Enter the number of scans to average across the apex of the peak.

Examine the chromatogram peak and estimate the number of good scans across the peak apex.

Chromatogram Peak diagram

Chromatogram Peak diagram

View a schematic diagram that illustrates the three regions of a chromatogram peak used by the Combine spectrum enhancement method: Peak Top, Left, and Right.

Background Subtraction Right Region

Region Width (points) Enter the number of scans to average in the analysis of the background spectrum in the Left region. The Combine algorithm uses this, together with a similar region from the left of each peak, for background analysis.

Region Start

Peak End

Points After Peak Top Select this option to define the right region end point as a specific number of scans after the peak top. Use the associated box to enter the number of scans.

Button

Activate this option to use the peak end time. This is the default option.

Save As Default Validate and save the settings on the current page as default settings. The Processing Setup application uses these settings for all new processing methods. The application writes over the previous default values and cannot recover them.

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Processing Setup Views

Threshold Option in the Spectrum Enhancement Page for Qual View

Threshold option

Select the Threshold option to use the Threshold algorithm to remove the background noise from the spectrum of interest.

For more information, see “Using the Threshold Option for Spectrum Enhancement” on page 60 .

The Threshold algorithm limits the number of ions in the final spectrum before library searching by applying an intensity threshold. If the intensity of an ion is below the specified threshold, the ion is discarded from the spectrum.

Table 90

describes the parameters for the Threshold option on the Spectrum Enhancement page of the Processing Setup – Qual view.

Table 90. Threshold option on the Spectrum Enhancement page for Qual view parameters

Parameter

Enhancement Options

Threshold

Description

Cutoff Threshold (%) Enter a limiting intensity value as a percentage of the most intense mass. The data system produces an enhanced spectrum by discarding any ions with an intensity below the specified threshold.

Button

Save As Default Validate and save the settings on the current page as default settings. The Processing Setup application uses these settings for all new processing methods. The application writes over the previous default values and cannot recover them.

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Library Search Options Page for Qual View

The Library Search Options page in the Processing Setup – Qual view consists of the parameters to define a comparison search of your compound to published compound data or a defined user library. It consists of three main areas: Search Type, Options, and Append to

User Library.

Use the Library Search Options page to set up the library search criteria for the processing method.

For more information about running an automated library search, refer to the Xcalibur

Creating and Searching Libraries User Guide.

Figure 94 shows the Library Search Options page.

Figure 94. Library Search Options page

Table 91

describes the parameters on the Library Search Options page.

Table 91. Library Search Options page for Qual view parameters (Sheet 1 of 5)

Parameter

Search Type

Identity

Description

Selecting this option makes the Normal, Quick, and Penalize Rare

Compounds options available.

Normal

Select this option to apply an identity search algorithm for library matching of spectra.

Select this option to apply a normal identity search algorithm for library matching of spectra. This is the default option. A normal identity search is suited to low-quality or unusual spectra. The search algorithm uses a standard pre-screen search filter.

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Table 91. Library Search Options page for Qual view parameters (Sheet 2 of 5)

Parameter

Quick

Penalize Rare

Compounds

Description

Select this option to apply a quick identity search algorithm for library matching of spectra. Use this option when you are sure the spectrum or compound exists in the library. The search algorithm uses a fast pre-screen search filter.

Select this option to reduce the match factor of rare compounds.

This option is effective only when you have selected one or more of the NIST databases (such as MAINLIB). It has no effect on spectra in user libraries or other commercial libraries.

Similarity

Simple

Hybrid

Each reference spectrum in a NIST library contains a record of other commercial databases containing information about the compound. A compound is considered rare if it is found in a limited number of these databases. When you select the Penalize

Rare Compounds option, matching compounds (hits) that are found in few databases or only in NIST libraries have their match factors reduced (the maximum penalty is 50 out of 1000). This limitation, in effect, leads to a relative increase in the match factors of common compounds, placing them higher on the library search result list (search result list) than exotic isomers with near identical spectra.

Selecting this option makes the Simple, Hybrid, and Neutral Loss options available.

Select this option to apply a Similarity search algorithm for library matching of spectra.

Selecting this option applies a simple similarity search algorithm for library matching of spectra. This option finds a large set of spectra to compare with the submitted spectrum and is generally slower than an identity search.

Use a simple similarity search in either of these cases:

• You know that the unknown spectrum is not in the library.

• The spectrum is of poor quality so that a reliable match is unlikely.

Selecting this option applies a hybrid similarity search algorithm for library matching of spectra. This option uses a combination of the simple and neutral loss search strategies. The neutral loss search requires an estimate of the unknown’s molecular weight. If the unknown compound contains chemical structures that generate both characteristic ions and neutral loss patterns, the search result list from this search can identify these structures.

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Table 91. Library Search Options page for Qual view parameters (Sheet 3 of 5)

Parameter

Neutral Loss

Description

Selecting this option applies a neutral loss similarity search algorithm for library matching of spectra. The neutral losses in a spectrum are the mass differences between the molecular ion and other major ions in the spectrum. For certain classes of compound, neutral losses can be very characteristic spectral features.

In a neutral loss search, the data system examines the submitted spectrum and identifies the molecular ion. The data system submits the mass value of the molecular ion to the search along with the spectrum. The search algorithm calculates the significant neutral losses and compares them with library data. Search results are returned according to matches of the molecular ion and its neutral losses.

Options

Maximum Number of

Hits

Reverse Search

Search with MW =

Specifies the maximum number of search results to be returned by a library search and reported in the result file. The data system selects the search results with the highest matching factors. The default limit is 5.

Select this check box if you want search results—matching library spectra—to be sorted by the Reverse Search Match Factor. By default, the data system sorts search results by the Forward Match

Factor.

Select this check box to restrict the search to library entries with a particular molecular weight. Use the associated box to enter the molecular weight.

Append to User Library

Enable Select this check box to add processed spectra to a specified user library.

Spectra are added to the specified user library in these situations:

• The library search produces no search results.

• The top search result fails to exceed one or more of the match factors.

With the match factors you can select new or unusual spectra and avoid duplicate entries.

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Table 91. Library Search Options page for Qual view parameters (Sheet 4 of 5)

Parameter

User Library

Description

Specifies the name of the user library to be used to store spectra.

To select a user library, click the arrow to display the list of

Xcalibur user libraries. Select a user library in the list.

Thresholds

Match Factor Specifies a forward match factor threshold for spectra subject to the Append to User Library option. The data system submits the spectrum from each identified peak to a library search as determined by the other parameters on the Library Search

Options page. If the top search result (hit) from a library search exceeds the Match Factor threshold or any of the other threshold values, the data system records the search result list in the result file and the spectrum is not appended to the specified library.

If the top search result fails to match any of the threshold values, the data system discards the search result list and appends the spectrum to the specified library.

The match is scored on a scale of 0 to 999.

Reverse Match Factor Specifies a Reverse Match Factor threshold for spectra subject to the Append to User Library option. The data system submits the spectrum from each identified peak to a library search as determined by the other parameters on the Library Search

Options page. If the top search result from a library search exceeds the Reverse Match Factor threshold or any of the other threshold values, the data system records the search result list in the result file, and the spectrum is not appended to the specified library.

If the top search result fails to match any of the threshold values, the data system discards the search result list and appends the spectrum to the specified library.

The match is scored on a scale of 0 to 999.

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Table 91. Library Search Options page for Qual view parameters (Sheet 5 of 5)

Parameter

Probability

Description

Specifies a Probability threshold for spectra subject to the Append to User Library option. The data system submits the spectrum from each identified peak to a library search as determined by the other parameters on the Library Search Options page. If the top search result from a library search exceeds the Probability threshold or any of the other threshold values, the data system records the search result list in the result file, and the spectrum is not appended to the specified library.

If the top search result fails to match any of the threshold values, the data system discards the search result list and appends the spectrum to the specified library.

The limits of probability are 0 to 100.

Mass Defect

Enable

Defect

At Mass

Selecting this check box makes the mass defect boxes available.

Select this check box to include mass defect values for library searches in a processing method.

Specifies values (in millimass units) for mass defect to correct for the differences between the actual masses and the nominal integer masses of the atoms in a molecule. Assign a larger value (in millimass units) for mass defect to larger molecules because, in general, they are composed of more atoms than smaller molecules; larger molecules need a larger correction factor to approximate the linear function that the Xcalibur data system uses to calculate masses.

Specify a smaller value for lower mass ranges in the first box and a larger value for higher mass ranges in the second box.

Specifies the masses at which the data system applies specified mass defect values to calculations of mass. Specify a smaller mass value in the first box, and specify a larger mass value in the second box.

Buttons

Save As Default

Search List

Validates and saves the settings on the current page as default settings. The Processing Setup application uses these settings for all new processing methods. The application writes over the previous default values and cannot recover them.

Opens the Search List Dialog Box .

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Library Search Constraints Page for Qual View

Use the Library Search Constraints page for Qual View to limit a library search to increase processing efficiency. For example, you might want to exclude certain high-intensity ions that appear in many compounds or that are present in the spectrum background. You can target a search to a particular range of molecular weights or to compounds containing certain elements.

For more information about running an automated library search, refer to the Xcalibur

Creating and Searching Libraries User Guide.

Figure 95 shows the Library Search Constraints page.

Figure 95. Library Search Constraints page

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Table 92

describes the parameters on the Library Search Constraints page.

Table 92. Library Search Constraints page for Qual view parameters (Sheet 1 of 7)

Parameter

Molecular Weight

Enable

Description

Range

Selecting this check box limits the library search to compounds with a specific molecular weight or molecular weight range.

Type a molecular weight or molecular weight range in the box (for example, 200–250). During a search, the data system only compares processed spectra with reference data derived from compounds with a molecular weight inside the specified range.

Other Databases

Enable Selecting this check box limits the library search to entries in the

NIST library that are also featured in other databases. Each entry in the NIST library contains a list of other commercial databases containing information about the compound.

Fine

TSCA

RTECS

EPA

USP

HODOC

NIH

The data system reports search results featured in one or more of the selected databases. (A search result does not have to be found in all the selected databases.)

Select this check box to report search results from reference compounds or spectra also found in the commercially available

Fine Chemical Index.

Select this check box to report search results from reference compounds or spectra also found in the Toxic Substances Control

Act Inventory (TSCA).

Select this check box to report search results from reference compounds or spectra also to be found in the Registry of Toxic

Effects of Chemical Substances (RTECS).

Select this check box to report search results from reference compounds or spectra also found in the Environmental Protection

Agency (EPA) Environmental Monitoring Methods Index.

Select this check box to report search results from reference compounds or spectra also found in the US Pharmacopoeia

(USP)/U.S.A.N.

Select this check box to report search results from reference compounds or spectra also found in the CRC Handbook of Data of Organic Compounds (HODOC).

Select this check box to report search results from reference compounds or spectra also to be found in the NIH-NCI

Inventory File.

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Table 92. Library Search Constraints page for Qual view parameters (Sheet 2 of 7)

Parameter

EINECS

IR

Description

Select this check box to report search results from reference compounds or spectra also found in the European Index of

Commercial Chemical Substances (EINECS).

Select this check box to report search results from reference compounds or spectra also found in the NIST/EPA Gas Phase IR

Database.

Clear all the check boxes in the Other Databases area. Clear All

Name Fragment

Enable

Name

Selecting this check box limits the library search results to compounds with a specific name or name fragment.

Enter a text string of up to 39 characters to represent a fragment of a compound name, for example, “cyclo.” During the library search, the data system filters search results and only returns those containing the specified text in their names. The entry is case insensitive: “CYCLO” returns compounds containing the fragments “cyclo,” “Cyclo,” and “CYCLO.”

Element Constraints

Enable Selecting this check box limits the library search to compounds containing specific elements using the Individual Element and/or

Elements in Compound methods.

You can use the two types of elemental limits together, but you must make sure there are no contradictions. For example, you might put “C=0” in the Individual Element group and then list

“C” in the Elements in Compound box. When a contradiction occurs, the data system displays a warning dialog box.

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Table 92. Library Search Constraints page for Qual view parameters (Sheet 3 of 7)

Parameter

Individual Element

Individual Element table

Description

Use this table to set up the criteria for the elements required in a library search result. Each row in the table represents an element limit. There are three parts to each limit:

• Element, a IUPAC approved abbreviation for an element, for example “Cl” for chlorine.

• Condition, a mathematical operator, < (less than), > (greater than) or = (equals).

• Value, a numerical value representing the number of atoms of the specified element required to satisfy the limit.

[Row Number]

Element

In the example shown here, the data system would only return search results for compounds that contain

• More than five fluorine atoms, and

• Exactly three chlorine atoms

You do not need to provide a complete elemental profile. The library search returns compounds if they satisfy all the specified criteria regardless of any other elements present.

Each numbered row represents an item in the table. The asterisk symbol indicates the last unused row in the table. Use this row to enter a new item.

Enter the IUPAC-approved abbreviation for the element that you want to use an element limit. It is used in conjunction with the

Condition list and Value box in the same row of the Individual

Element table.

To enter an element limit, type the required abbreviation. For example, to apply carbon as an element limit, type C. The data system adds a new row to the table for further entries.

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Table 92. Library Search Constraints page for Qual view parameters (Sheet 4 of 7)

Parameter

Condition

Description

Enter a condition for an element limit. The data system uses this value together with the Condition list and Value box in the same row of the Individual Element table. Valid conditions are as follows:

• < (less than)

• > (greater than)

• = (equals)

Value

To enter an element limit condition, double-click the box to open the list. Then select the required condition.

Enter a numerical value for an element limit. This value is used in conjunction with the Condition list and Value box in the same row of the Individual Element table. The value represents the number of atoms of the specified element required for library compounds to satisfy the limit.

To enter an element limit value, type the required number. The valid range is 0 to 99.

Elements in Compound

Elements

All

Some

Clear

Specifies the elements that must be present in returned search results. To enter an element list, type the IUPAC-approved abbreviation for each element. Separate each element in the list (of up to 30 characters) by a comma.

Selecting this option specifies that the data system return search results containing all, and only, the listed elements. For example

“C, H, O” would return HCHO but not CO2, CH4, or

CH2Cl2. Compare with the Some option.

Selecting this option specifies that the data system return search results that contain at least one of the specified elements and no elements that are unlisted. For example, “C, H, O” would return

CO2, CH4, and HCHO but not CH2Cl2. Compare with the All option.

Deletes the text in the Elements box.

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Table 92. Library Search Constraints page for Qual view parameters (Sheet 5 of 7)

Parameter Description

Mass Spectral Peak Constraints

Enable Selecting this check box makes the mass spectral peak constraints table available. Use this table to build a profile of ions and ion abundances to be matched against library entries during the search. The search algorithm only returns search results matching the specified limits.

Mass Spectral Peak Constraints table

Set specific criteria about the mass spectral peaks required in a library search result. Each row in the table represents an individual mass spectral peak limit. There are four components to each limit represented by the table columns: Type, m/z, From, and To.

Type

Normal

Specifies the type of ion. The available selections are as follows:

Normal, Loss, Rank, or Maxmass.

This limit applies to a specific ion represented by its m/z value.

The From and To values represent the abundance of the ion.

Loss This limit describes a neutral loss from a molecular ion. In this case, the m/z value (limited to 64) represents the mass of the lost neutral group, for example, for methyl m/z = 15. For this limit to be matched, a library spectrum must contain the following:

Rank

• A fragment ion at an m/z value 15 less than the molecular ion

• An abundance in the range specified in the From and To columns

This limit tests the order of an ion in the spectrum in terms of relative abundance. Ions are ranked from the largest (the base peak) to the 16th largest. A compound matches a Rank limit if its library spectrum contains a mass spectral peak that meets these conditions:

• At the specified m/z value

• Ranked between the range specified in the From and To columns

If you specify the same number in both fields, the designated ion must have that rank in the retrieved spectrum.

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Table 92. Library Search Constraints page for Qual view parameters (Sheet 6 of 7)

Parameter

Maxmass

Description

Maxmass sets a limit on the m/z value of the most significant high-mass ion. Library search results must feature the following:

• An ion at the specified m/z value

• No significantly larger masses at higher m/z values m/z

• An abundance in the range specified in the From and To columns

Enter the m/z value of the mass spectral peak to be constrained in a Normal, Rank, or Maxmass type limit. The data system discards a library search result if it does not contain a mass spectral peak at the specified m/z value.

From

For a Loss type limit, use this column to enter the value of a neutral loss. The data system discards a library search result if it does not feature a fragment ion at an m/z value appropriate to the specified neutral loss (in relation to the molecular ion).

For a Normal, Loss, or Maxmass type limit, use this column to enter the minimum abundance of the constrained mass spectral peak. In a Rank type limit, use this box to enter the lowest position of the ion in an intensity ordered list of spectral peaks.

To

[Row Number]

You can specify the same number in both From and To boxes. In this case, the data system discards a library search result unless the designated mass spectral peak is present in exactly the specified abundance or rank in the retrieved spectrum.

For a Normal, Loss, or Maxmass type limit, use this box to enter the maximum abundance of the constrained mass spectral peak. In a Rank type limit, use this box to enter the highest position of the ion in an intensity ordered list of spectral peaks.

You can specify the same number in both From and To boxes. In this case, the data system discards a library search result unless the designated mass spectral peak is present in exactly the specified abundance or rank in the retrieved spectrum.

Each numbered row represents an item in the table. The asterisk

(*) indicates the last unused row in the table. Use this row to enter a new item.

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Table 92. Library Search Constraints page for Qual view parameters (Sheet 7 of 7)

Parameter

Absolute

Description

Specifies how the data system applies the From and To parameters in the Mass Spectral Peak Constraints table.

Relative

Select the Absolute option if you want the data system to evaluate all table entries as a percentage of the base (largest) ion in the spectrum. Values must be between 0 and 100%. For example, if you enter 10 and 50 in the From and To fields of a Normal type limit, the data system discards any search results in which the specified mass spectral peak is not present at an abundance of between 10 and 50%.

For Normal and Loss type limits, the abundance values can also be relative.

Specifies how the data system applies the From and To parameters in the Mass Spectral Peak Constraints table.

Select the Relative option if you want the data system to treat the first entry as an absolute Normal or Loss type. It then considers subsequent entries in the table relative to the first. In this example, library search results must contain the following:

• An ion at m/z 125 with an abundance between 10 and 50% of the base ion

• An ion at m/z 250 with an intensity between 50 and 999% of the observed intensity of the first ion in the list

Relative mode is not available for Rank or Maxmass types.

Button

Save As Default Validates and saves the settings on the current page as default settings. The Processing Setup application uses these settings for all new processing methods. The application writes over the previous default values and cannot recover them.

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Peak Purity Page for Qual View

Use the Peak Purity page of the Qual view to specify the values of the peak purity parameters to be included in a qualitative processing method for the PDA detector type only. After you specify the processing method in a sequence, you can apply the parameters to your qualitative

PDA analysis as you acquire data. Use a raw data file of PDA data in Qual Browser to determine which peak purity parameter values you want to use in the processing method.

For PDA data, the data system can calculate the spectral purity of your chromatographic peaks by comparing the similarity of the spectra across the peak to a spectrum from the peak apex. The calculation is affected by the integration of the scan chromatogram and by the scan threshold, peak coverage, and scan wavelengths that you set on the Peak Purity page.

Figure 96 shows the Peak Purity page for the Qual view.

Figure 96. Peak Purity page in the Qual view

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Table 93

describes the parameters on the Peak Purity page.

Table 93. Peak Purity page for Qual view parameters

Parameter

Purity Parameters

Description

Enable Selecting this check box activates the peak purity parameters.

Scan Threshold (mAU) Specifies a minimum value of intensity for wavelength scans in milliabsorbance units (mAU). A peak purity calculation starts with the scan at the apex of the peak and then collects wavelength data from scans on both sides of the apex until the specified Scan

Threshold (mAU) value is reached.

Peak Coverage (%)

Default: 3 mAU

Range: 0 to 1000 mAU (or 1 AU)

In a sample with high background or noise, start with a value of

40 mAU for the scan threshold.

Specifies a maximum percent value for the width of the integrated peak. A peak purity calculation starts with the scan at the apex of the peak and then collects wavelength data from scans on both sides of the apex until the specified Peak Coverage (%) value is reached. Use peak coverage for symmetrical peaks.

Limit Scan Wavelength Select this check box to limit the scan wavelength range for a peak purity calculation. Selecting this check box activates the Range

(nm) box.

[Wavelength] Range

Default: 95% of the integrated peak

Range: 0–100

Specifies a range of UV-Vis scans (in nanometers). A peak purity calculation starts with the scan at the apex of a peak and then collects wavelength data from scans on both sides of the apex until all the wavelengths in the range are included.

Select the Limit Scan Wavelength check box to activate this box.

The default wavelength range is the full width of the scan.

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Quan View

Use the Quan view of the Processing Setup window to set up a quantitative processing method. For processing quantitative data, you can identify multiple target compounds and give each its own calibration with unique amounts and curve fitting. Xcalibur quantitative processing supports multiple internal standards with individual amount corrections if required.

Note Use the New Sequence Template dialog box of the Sequence Setup view to generate a sequence semi-automatically, on the basis of a processing method. When you use the

New Sequence Template dialog box to set up a sequence, you can also set up the None,

Overlapped, and Non-Overlapped bracket types.

The Quan view consists of a menu bar, a toolbar, and five or six pages. The first five pages are available for all detector types. The Peak Purity page is available for the PDA (photo diode array) detector type only. The chromatogram and spectrum views appear at the bottom of the

Identification, Detection, and Peak Purity pages. The following buttons, which are part of the

Processing Setup window, appear in every Quan view page: OK, Cancel, and Save As Default.

For information about the OK, Cancel, and Save As Default buttons, see

OK, Cancel, and

Save As Default Buttons . For information about the chromatogram and spectrum views, see

Chromatogram and Spectrum Views in the Qual and Quan Views

.

These topics describe the Quan view pages:

Identification Page for Quan View

Detection Page for Quan View

Avalon Detection Page for Quan View

Genesis Detection Page for Quan View

ICIS Detection Page for Quan View

Levels Page for Quan View

System Suitability Page for Quan View

Peak Purity Page for Quan View

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Identification Page for Quan View

Use the Identification page to name components and specify retention time, detector type, and peak identification, detection, and integration criteria for each named component.

To set up the parameters on the Identification page, follow these procedures.

To add analytes (components) to the components list in the Components pane

1. For each component that you want to add to the components list, select the <New> entry in the Name list, and then type the name of the new component.

2. Press ENTER or click OK to add the new component.

The new component appears in the Components pane.

To delete a component in the components list

1. In the list in the Components pane, select the name of the component that you want to delete.

2. From the menu bar, choose Options > Delete component name.

A confirmation message appears.

3. Click OK to complete the deletion and close the message box. Or, click Cancel to close the message box without deleting the selected component.

To select the detector type

In the Detector Type list, select the detector type used to acquire the trace.

To select a peak detection algorithm

1. Select the component of interest in the Components pane.

2. In the Peak Detect list, select an algorithm.

3. Click OK.

The default parameters for the selected peak detection algorithm appear on the

Identification and Detection pages.

To select a scan filter in the Filter list

In the Filter list, select a scan filter from the list of filters used to acquired the mass spectral data.

The selected scan filter appears in the Filter box.

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To apply a scan filter that is not listed in the Filter list

Do one of the following:

• Select a new filter from the list and edit the scan filter.

–or –

• Type a new scan filter into the box using the appropriate scan filter format (see Scan

Filter Format ).(refer to the Xcalibur Qual Browser User Guide.)

To specify the trace (chromatogram) to be processed

1. In the first list, select a basic chromatogram type, for example, TIC.

2. In the second list, select a logical operator: + or .

The third list becomes available.

3. In the third list, select a second chromatogram type to add to, or subtract from, the first type, for example, Mass Range.

The list includes the valid remaining trace types.

Table 94

describes the parameters on the Quan view – Identification page. For information

about using the Quan view – Identification page, see “Setting Up the Quan View

Identification Parameters” on page 26 .

Table 94. Identification page for Quan view parameters (Sheet 1 of 7)

Parameter

Name

Description

Displays a list of component names for the active processing method. For a new processing method, this list displays only

<New>. Use this list to add new components to the processing method. See

“To add analytes (components) to the components list in the Components pane” on page 350

.

Detector Type

To display the identification settings for a component in the list, click the name of the component in the Components pane on the right side of the page.

Specifies the detector type:

• MS (mass spectrometer)

• Analog

• A/D Card (analog-to-digital converter)

• PDA (photodiode array detector)

• UV (ultraviolet or ultraviolet-visible detector)

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Table 94. Identification page for Quan view parameters (Sheet 2 of 7)

Parameter

Peak Detect

Description

Specifies the peak detection algorithm for the component selected in the Components pane:

• Genesis—for Xcalibur 1.0 data files

• ICIS—for mass spectrum traces

• Avalon—for UV-Vis and analog traces

Filter

The default parameters for the selected peak detection algorithm appear on the Identification and Detection pages.

Lists the scan filters for the current raw data file (RAW). You can use a scan filter to specify that processing is to be applied to a subset of the scans in a raw data file.

Trace

MS detector

Analog detector

A/D card

To select a scan filter from the list of filters used to acquire the raw data file, select one of the scan filters in the Filter list. The selected scan filter appears in the Filter box.

You can also apply a scan filter that is not listed in Filter box by typing a new scan filter in the Filter box. The scan filter must follow the format described in Scan Filter Format the Xcalibur

Qual Browser User Guide.

From the three Trace lists, specify the type of chromatogram that

you want to use for data processing. See “To select a scan filter in the Filter list” on page 350 and

“To apply a scan filter that is not listed in the Filter list” on page 351

.

You can use trace combinations to subtract from a chromatogram the contributions from a solvent or noise. Combinations are limited to traces of the same type.

The valid trace types depend on the detector type.

For MS scans, valid trace types are TIC, Mass Range, and Base

Peak. For more information, see

Valid MS Trace Combinations.

For Analog data, the data system supports up to four channels

(labeled Analog 1–4). For more information, see

Valid Analog

Trace Combinations.

For data from an A/D Card, the data system supports four channels (labeled A/D Card Ch 1–4). For more information, see

Valid A/D Card Trace Combinations

.

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Table 94. Identification page for Quan view parameters (Sheet 3 of 7)

Parameter

PDA detector

UV detector

Description

For PDA data, valid trace types are Wavelength Range, Total Scan, or Spectrum Maximum. For more information, see

Valid PDA

Trace Combinations .

For UV detector data, the data system supports four channels

(labeled Channel A–D). For more information, see

Valid UV

Trace Combinations .

For MS detector type:

Mass (m/z) Specifies the mass range for the Mass Range trace type. This box becomes available when you select a Mass Range trace type or a

TIC ± Mass Range trace combination for an MS detector type.

Mass1

To change the range or to add a new range, type the range in the box. The valid range depends on the configured detector. The format is LowMass–HighMass. For example, for the range m/z 123 through 456, type 123–456.

You can sum up to 50 mass ranges by entering mass ranges or single mass values separated by your computer list separator

character (see “Changing the List Separator Character” on page 123 ).

Specifies the mass range for the first trace type. This box becomes available when you select a Mass Range ± Mass Range trace combination for an MS detector type.

To change the range or to add a new range, type the range in the box. The valid range depends on the configured detector. The format is LowMass–HighMass. For example, for the range m/z 123 through 456, type 123–456.

You can sum up to 50 mass ranges by entering mass ranges or single mass values separated by your computer list separator

character. To view or set the list separator character, see “Printing a

Vial or Sequence List” on page 95 .

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Table 94. Identification page for Quan view parameters (Sheet 4 of 7)

Parameter

[Mass] 2

Description

Specifies the mass range for the second trace type. This box becomes available when you select a Mass Range ± Mass Range trace combination for an MS detector type.

BP

To change the range or to add a new range, type the range in the box. The format is LowMass–HighMass. For example, for the range m/z 123 through 456, type 123456.

You can sum up to 50 mass ranges by entering mass ranges or single mass values separated by your computer list separator

character (see “Changing the List Separator Character” on page 123 ).

Specifies the range in which to search for the highest peak. This box appears when you select a Base Peak trace for an MS detector type.

MR

If you enter a single m/z value in this box, that m/z value defines the base peak.

To change the base peak mass range, type the value in the box. A mass range from m/z A to m/z B is entered in the format A–B.

Specifies the mass range for the second Mass Range trace type.

This box appears when you select a Base Peak ± Mass Range trace combination for an MS detector type.

To change the range or to add a new range, type the range in the box. The format is Low Mass–HighMass. For example, for the range m/z 123 through 456, type 123–456.

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Table 94. Identification page for Quan view parameters (Sheet 5 of 7)

Parameter

For PDA detector type:

Wavelength

Description

Specifies the wavelength range for the Wavelength Range or

Spectrum Maximum trace type. This box appears when you select one of the following trace combinations for a PDA detector type:

• Spectrum Maximum

• Wavelength Range

• Total Scan – Wavelength Range

Wavelength 1

To change the range or to add a new range, type the range in the box. The valid range depends on the configured detector. The format is LowWavelength–HighWavelength. For example, for the range m/z 123 through 456, type 123–456.

You can sum up to 50 wavelength ranges by entering ranges or single values separated by your computer list separator character

(see

“Changing the List Separator Character” on page 123

).

Specifies the wavelength or wavelength range for the first trace type. This box appears when you select one of the following trace combinations for a PDA detector type:

• Wavelength Range ± Wavelength Range

• Spectrum Maximum ± Wavelength Range

To change the range or to add a new range, type the range in the box. The valid range depends on the configured detector. The format is LowWavelength–HighWavelength. For example, for the range m/z 123 through 456, type 123–456.

You can sum up to 50 wavelength ranges by entering ranges or single values separated by your computer list separator character

(see

“Changing the List Separator Character” on page 123

).

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Table 94. Identification page for Quan view parameters (Sheet 6 of 7)

Parameter

[Wavelength] 2

Description

Specifies the wavelength or wavelength range for the second trace type. This box appears when you select one of the following trace combinations for a PDA detector type:

• Wavelength Range ± Wavelength Range

• Spectrum Maximum ± Wavelength Range

To change the range or to add a new range, type the range in the box. The format is LowWavelength–HighWavelength. For example, for the range m/z 123 through 456, type 123–456.

Keys

You can sum up to 50 wavelength ranges by entering ranges or single values separated by your computer list separator character

(see

“Changing the List Separator Character” on page 123

).

Specifies user comments about the analysis. The box holds up to

50 characters and is case-sensitive for alphabetic characters (for example, “abc” is recognized as being different from “Abc”).

Retention Time

Expected (min)

Window (sec)

Specifies the expected retention time for the selected component.

The valid range depends on the configured hardware. For GC/MS and LC/MS systems, the valid range is 0 to 999 minutes. To change the time or to enter a new time, type the number of minutes in the Expected (retention time) box.

Specifies the retention time window for the selected component.

The valid range is 1.0 to 999.0 seconds.

Use as RT Reference Select whether to use the actual retention time (RT) of the selected component to adjust the expected retention time of another component. To use the selected component as an RT Reference

(retention time reference), select this check box. If you do not want to use this component as an RT reference, clear this check box. All components that you select as RT Reference components appear in the Adjust Using list.

View Width

To change the time window or to enter a new time window, type the number of seconds in the (retention time) Window box.

Specifies the current view width, in minutes. The valid range depends on the configured hardware. To change the view width, enter the desired time in the View Width box.

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Table 94. Identification page for Quan view parameters (Sheet 7 of 7)

Parameter

Adjust Using check box Select whether to adjust the expected retention time (RT) of the selected component (selected in the Components pane and displayed in the Name box) using the actual retention time of a

RT Reference component, such as an internal standard. The

Adjust Using list to the right of this check box contains a list of components that you have set up as RT Reference components.

There must be at least one RT Reference component in the processing method for this check box to be available.

Adjust Using list

Description

Specifies the RT Reference component that the data system uses to adjust the expected retention time of the selected component.

This list is only active if you select the Adjust Using check box to the left of this list. To change the RT Reference component, select a component in the Adjust Using list. The data system uses the actual retention time of the RT Reference component to correct the retention time of the selected component. It provides the following correction to the expected retention time:

Adjusted RT Component Expected =

[RT Component Expected] – [RT Reference Actual] / [RT

Reference Expected].

Components

List of components in the Components pane

Lists all of the component names that are defined for the active processing method. This list is located in the Components pane on the right side of the window.

Buttons

Save as Default Validates and saves the settings on the current page as default settings. The Processing Setup application uses these settings for all new processing methods. This option guarantees that the settings for the component are consistent and valid. The

Processing Setup application uses these default settings for all new components. The application writes over the previous default values and cannot recover them.

Those settings that you are likely to change, such as Name,

Expected Retention Time, Trace Type, and so on, are not stored as default settings.

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Detection Page for Quan View

Use the Detection page of the Processing Setup – Quan view to specify peak integration and detection criteria.

On the basis of your selected default peak detection algorithm or your selection in the Peak

Detect list on the Identification page for the selected component, the data system displays the corresponding version of this page:

Avalon Detection Page for Quan View

Genesis Detection Page for Quan View

ICIS Detection Page for Quan View

For information about using the Quan view – Detection page, see

“Setting Up the Quan

View Integration and Detection Parameters” on page 28 .

Avalon Detection Page for Quan View

Use the Avalon Detection page of the Quan view to view or specify the peak detection and integration criteria for the Avalon peak detection algorithm.

After selecting Avalon as the peak detection algorithm on the Identification page of the Quan view, this page appears when you open the Detection page of the Quan view.

Note Click Advanced to open the Avalon Event List dialog box where you can change parameters in the Event list.

These topics describe the parameters on the Avalon Detection page for the Processing Setup –

Quan view:

Quan View – Avalon Detection Page Buttons

Avalon Peak Integration Parameters

Avalon Peak Detection Parameters – LC Mode

Avalon Peak Detection Parameters – GC Mode

For information about changing the chromatography mode, see

Chromatography Options

Dialog Box

.

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Quan View – Avalon Detection Page Buttons

Table 95

describes the buttons at the bottom of the Quan view – Detection page.

Table 95. Buttons at the bottom of the Quan view – Detection page for the Avalon algorithm

Parameter

Save As Default

Advanced

Description

Validates and saves the settings on the current page as default settings. The Processing Setup application uses these settings for all new processing methods and all new components. This option guarantees that the settings for the components are consistent and valid. The application writes over the previous default values and cannot recover them.

For the Avalon peak detection algorithm, this button opens the

Avalon Event List dialog box, where you can modify the integration events list that is displayed on the Detection page.

Flags

For information about the Avalon Event List dialog box, see

Avalon Event List Dialog Box .

Opens the Data Flags dialog box, where you can set peak area and peak height threshold values. The data system reports these data flags in result files, printed reports, and Quan Browser.

For information about the Data Flags dialog box, see

Data Flags

Dialog Box

.

Avalon Peak Integration Parameters

Table 96

describes the parameters in the Avalon Peak Integration area of the Quan view –

Detection page.

Table 96. Avalon peak Integration parameters (Sheet 1 of 2)

Parameter

Avalon Peak Integration

Description

Specifies the peak integration settings. Use the Auto Calculate Initial Events feature to determine optimal values for the seven initial value (time = 0.0) integration events that are required by the Avalon integration algorithm. You can change the value of an initial value

(time = 0.0) integration event, but you cannot delete it.

Smoothing Points Specifies the degree of data smoothing to be performed on the active component peak before peak detection and integration. The valid range is any odd integer from 1 (no smoothing) through 15

(maximum smoothing). To smooth your component peak data before integration, enter a value in the Smoothing Points box.

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Table 96. Avalon peak Integration parameters (Sheet 2 of 2)

Parameter

Event List

Description

The event list consists of three columns: Time, Event, and Value.

To change the settings in the Event list

Click Advanced to open the Avalon Event List dialog box.

For information about the available integration events or adding, changing, or deleting the

events from the event list, see Avalon Event List Dialog Box .

Time Displays the time of a timed event. This column contains either the term initial value or a time value.

Event Displays initial value (time = 0) and timed integration events.

Value

Auto Calculate Initial

Events

Displays the value for a integration event.

This button is available when a raw data file is open in the

Processing Setup window.

When you click this button, the data system automatically determines the best value for each of the seven initial value events on the basis of the data in the current raw data file and then displays these values in the Value column of the event list.

The data system does not estimate values for timed events; that is, events that have a time value in the Time column. It determines initial values for these events only: Start Threshold, End

Threshold, Area Threshold, P-P [Resolution] Threshold, Bunch

Factor, Negative Peaks, and Tension.

To automatically calculate values for initial events

1. Open a raw data file and make the chromatogram view active.

2. Click Auto Calculate Initial Events to update the Event list.

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Avalon Peak Detection Parameters – LC Mode

Table 97

describes the parameters in the Avalon Peak Detection area for the liquid chromatography (LC) mode.

Table 97. Avalon Peak Detection parameters for the liquid chromatography (LC) mode

Parameter

Avalon Peak Detection

Highest Peak

Description

Nearest RT

When you select this option, the data system uses the highest peak in the chromatogram within the specified retention time window for component identification.

When you select this option, the data system uses the peak with the nearest retention time in the chromatogram to the expected retention time for component identification.

Avalon Peak Detection Parameters – GC Mode

Table 98

describes the parameters in the Avalon Peak Detection area for the gas chromatography (GC) mode.

Table 98. Avalon Peak Detection parameters for the gas chromatography (GC) mode (Sheet 1 of 6)

Parameter Description

Avalon Peak Detection (GC mode)

Spectrum This option is only available in the GC chromatography mode for the data acquired with an MS detector.

Highest Peak

When you select this option, the data system uses the user-defined reference spectrum for component identification. The data system attempts to match the reference spectrum with a series of unknown spectra and calculates a score value for each comparison.

When you select the Spectrum option, a mass-intensity list and

the Thresholds area appear (see Additional parameters for the

Spectrum option (Avalon)

).

When you select this option, the data system uses the highest peak in the chromatogram within the specified retention time window for component identification, and the Ion Ratio Confirmation window appears.

You can use the parameters in the Ion Ratio Confirmation area to confirm the identify of the chromatographic peak on the basis of spectral information (see

Ion Ratio Confirmation (Avalon)

).

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Table 98. Avalon Peak Detection parameters for the gas chromatography (GC) mode (Sheet 2 of 6)

Parameter

Nearest RT

Description

When you select this option, the data system uses the peak with the nearest retention time in the chromatogram to the expected retention time for component identification, and the Ion Ratio

Confirmation window appears.

You can use the parameters in the Ion Ratio Confirmation area to confirm the identify of the chromatographic peak on the basis of spectral information (see

Ion Ratio Confirmation (Avalon)

).

Additional parameters for the Spectrum option (Avalon)

Mass intensity list for the Spectrum option

Enter mass-to-charge [m/z] and intensity percentages for up to 50 spectrum peaks. The data system uses this data to identify the component. For information about interactively using

the spectrum in a representative raw data file to enter the spectral data in the list, see “To enter data in the spectrum table by using an open raw data file” on page 38 .

m/z

Each m/z value in this column specifies the mass-to-charge [m/z] value for one spectral peak in the reference spectrum. The adjacent Intensity (%) box specifies the intensity percentage for this m/z value.

Intensity

Range: 0.5–999 999

Each intensity percentage in this column specifies the relative intensity for one spectral peak in the reference spectrum. The adjacent m/z box specifies the m/z value for the spectral peak.

Range: 0–100

Thresholds (Spectrum option)

The Thresholds area appears when you select the Spectrum option in the GC mode.

Forward Specifies a threshold value for forward comparisons between the reference spectrum and candidates in the chromatogram. A forward search is a direct matching algorithm comparing unknowns against the reference spectrum in the peak identification table. The match is scored on a scale of 0 to 999. A perfect match results in a score of 999. As a general guide, 900 or greater is an excellent match; 800 to 900, a good match; 700 to

800, a fair match. Less than 600 is a poor match. Unknown spectra with many peaks tend to score lower than similar spectra with fewer peaks.

Range: 0–1000

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Table 98. Avalon Peak Detection parameters for the gas chromatography (GC) mode (Sheet 3 of 6)

Parameter

Reverse

Description

Specifies a threshold value for reverse comparisons between the reference spectrum and candidates in the chromatogram. A reverse search ignores any peaks in the unknown that are not in the reference spectrum in the peak identification table. The match is scored on a scale of 0 to 999. A perfect match results in a score of

999. As a general guide, 900 or greater is an excellent match; 800 to 900, a good match; 700 to 800, a fair match. Less than 600 is a poor match. A spectrum with many peaks tends to score more highly in a reverse match than in a forward match.

Match

Range: 0–1000

Specifies a threshold value for match comparisons between the reference spectrum and candidates in the chromatogram. The match threshold is scored on a scale of 0 to 999. The match algorithm is a complex probability factor that is based on the differences between the forward factors of all the candidates. If one candidate has a forward matching factor of 900 and the next best is only 300, the probability of the component being correctly identified is high and so the match factor is scored highly for the first candidate. If the forward factors for all the candidates are similar, whether high or low, the match factor is low.

Range: 0–1000

Ion Ratio Confirmation (Avalon)

This area appears when you select the Highest Peak or Nearest RT option in the GC mode for data from an MS detector.

Use the parameters in this area to specify up to five qualifier ions to confirm the detection of a target analyte. You can also set the coelution window and select a method for calculating the target ion ratio window and tolerance.

Enable Selecting this check box activates the parameters in the Ion Ratio

Confirmation area.

Ion Ratio Using: Area or Height

(read-only)

This read-only parameter shows the currently selected peak quantitation method: area or height. The data system uses the same method to calculate the qualifier ion peak response and then the target ratio. You can change this parameter by selecting the

Area or Height options in the Response area on the Calibration page.

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Table 98. Avalon Peak Detection parameters for the gas chromatography (GC) mode (Sheet 4 of 6)

Parameter

Qualifier ion table

Description

Use this table to enter mass-to-charge [m/z] and target ratio tolerances [Window (±%)] data for up to five qualifier ions.

m/z

Target Ratio (%)

Window (±%)

If you select Area response, the data system integrates each qualifier ion peak and calculates a ratio using the integrated qualifier ion peak and the quantitation peak area. It then compares this ratio with your specified target ratio. If the calculated ratio is outside of the target ratio by more than your specified tolerance [Window (±%)], it rejects the quantitation peak.

If you select Height response, the data system calculates a ratio using the qualifier ion peak height with the height of the quantitation peak. It then compares this ratio with your specified target ratio. If the calculated ratio is outside of the target ratio by more than your specified tolerance [Window(±%)], it rejects the quantitation peak.

The value in this column specifies the mass-to-charge [m/z] value for a qualifier ion.

Range: 0.5–999 999

The value in this column specifies the Target Ratio (%) value for a qualifier ion.

Range for a manual target ratio for the qualifier ion:

0.00–1 000 000

The value in this column specifies the Target Ratio tolerance for a qualifier ion.

Range: 0.00–100.00

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Table 98. Avalon Peak Detection parameters for the gas chromatography (GC) mode (Sheet 5 of 6)

Parameter

Window%

Relative

Description

Selecting this option specifies that the target ratio tolerance values in the Window (±%) column of the qualifier ion table are relative values.

For example, if you set the target ratio to 50% and the Window

(±%) parameter to 20%, the expected target ion ratio range is 40 to 60%. (With the Absolute option this range would be 30 to

70%.) If the ion ratio is outside this range, the ion ratio confirmation test fails, and the data system sets the IRC Flag to

False. If the qualifier ion peak-to-quantitation peak ratio is within range, the ion ratio confirmation test passes, and the data system sets the IRC Flag to True. The response of all specified qualifier ions must be inside the respective ratio ranges for IRC to succeed.

Absolute

In assessing a target ion ratio range, the data system truncates the range at 0% to avoid negative values.

Selecting this option specifies that the target ratio tolerance values in the Window (±%) column of the qualifier ion table are absolute values.

For example, if you set the target ratio to 50% and the Window

(±%) parameter to 20%, the expected target ion ratio range is 30 to 70%. (With the Relative option this range would be 40 to

60%.) If the qualifier ion peak-to-quantitation peak ratio is outside this range, the ion ratio confirmation test fails, and the data system sets the IRC Flag to False. If the qualifier ion peak-to-quantitation peak ratio is within range, the ion ratio confirmation test passes, and the data system sets the IRC Flag to

True. The response of all specified qualifier ions must be inside the respective ratio ranges for IRC to succeed.

In assessing a target ion ratio range, the data system truncates the range at 0% to avoid negative values.

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Table 98. Avalon Peak Detection parameters for the gas chromatography (GC) mode (Sheet 6 of 6)

Parameter Description

Qualifier Ion

Coelution

Specifies the Qualifier Ion Coelution window.

Before it runs the ion ratio confirmation test, the data system generates a mass chromatogram for each specified qualifier ion.

Each of these chromatograms must feature a peak matching that of the quantitation mass or masses. If the retention time of the qualifier ion peak apex lies outside of the Qualifier Ion Coelution window (centered on the quantitation peak), the data system rejects the quantitation peak.

The data system tests quantitation peaks with matching qualifier ion peaks (in the coelution window) for ion ratio confirmation.

Genesis Detection Page for Quan View

Use the Genesis Detection page of the Quan view to view or specify the peak detection and integration criteria for the Genesis peak detection algorithm.

After selecting Genesis as the peak detection algorithm on the Identification page of the Quan view, this page appears when you open the Detection page of the Quan view.

Note Click Advanced to open the Genesis Advanced Detection Options dialog box where you can set up the advanced detection parameters for the Genesis algorithm.

These topics describe the parameters on the Genesis Detection page for the Processing Setup

– Quan view:

Quan View – Genesis Detection Page Buttons

Genesis Peak Integration Parameters

Genesis Peak Detection Parameters – LC Mode

Genesis Peak Detection Parameters – GC Mode

For information about changing the chromatography mode, see

Chromatography Options

Dialog Box

.

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Quan View – Genesis Detection Page Buttons

Table 95

describes the buttons at the bottom of the Qual view – Detection page.

Table 99. Buttons at the bottom of the Quan view – Detection page for the Genesis algorithm

Parameter

Save As Default

Advanced

Description

Validates and saves the settings on the current page as default settings. The Processing Setup application uses these settings for all new components and all new processing methods. This option guarantees that the settings for the components are consistent and valid. The application writes over the previous default values and cannot recover them.

For the Genesis peak detection algorithm, this button opens the

Genesis Advanced Detection Options dialog box, where you can set up the advanced parameters for the Genesis algorithm.

Flags

For information about the Genesis Advanced Detection Options dialog box, see

Genesis Advanced Detection Options Dialog Box .

Opens the Data Flags dialog box, where you can set peak area and peak height threshold values. The data system reports these data flags in result files, printed reports, and Quan Browser.

For information about the Data Flags dialog box, see

Data Flags

Dialog Box

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Genesis Peak Integration Parameters

Table 100

describes the parameters in the Genesis Peak Integration area on the Detection page of the Quan view.

Table 100.Genesis peak integration parameters

Parameter

Genesis Peak Integration

Description

Smoothing Points Specifies the degree of data smoothing to be performed on the active chromatogram before peak detection and integration.

S/N Threshold

Enable Valley

Detection

To change this value, type a value in the Smoothing Points box.

Default: 7

Range: odd integers from 1 (no smoothing) through 15

(maximum smoothing)

Specifies the signal-to-noise threshold for peak integration. The data system only integrates peaks with a signal-to-noise value that is greater than this value.

To change this value, type a value in the S/N Threshold box.

Default: 0.5

Range: 0.0–999.0

Selecting this check box turns on the valley detection integration algorithm and activates the Expected Width parameter. This integration algorithm drops a vertical line from the apex of the valley between unresolved peaks to the baseline. The intersection of the vertical line and the baseline defines the end of the first peak and the beginning of the second peak.

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Table 100.Genesis peak integration parameters

Parameter Description

Expected Width (sec) Specifies the expected peak width, in seconds, for valley detection.

This parameter controls the minimum peak width for a peak when the valley detection algorithm is turned on. Selecting the

Enable Valley Detection check box makes this box available.

When valley detection is turned on, the data system ignores a valley (local minima) that is within the following window: peak apex ± expected width/2

When the data system finds a valley outside the expected peak width window, it terminates the peak at that point. The data system always terminates a peak when the signal reaches the baseline, independent of the value set for the expected peak width.

To enter a value for this parameter, select the Enable Valley

Detection check box. Then type a value in the Expected Width box.

Range: 0.0–999.0

Constrain Peak Width Selecting this check box turns on the constrain peak width integration algorithm and activates the Peak Height (%) and

Tailing Factor boxes.

Peak Height (%) Specifies the percent of the total peak height (100%) that determine the start and end points for the peak. To integrate the area under a peak, the data system drops a vertical line to the baseline at these points. The integrated area of a peak is constrained to the peak width between these points.

To enter a value for this parameter, select the Constrain Peak

Width check box. Then type a value in the Peak Height (%) box.

Tailing Factor

Range: 0.0–100.0

Controls how the data system integrates the tail of a peak. The tailing factor is the maximum ratio of the trailing edge to the leading edge of a constrained peak.

To enter a value for this parameter, select the Constrain Peak

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

Range: 0.5–9.0

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Table 100.Genesis peak integration parameters

Parameter

Min

(graphical representation)

Description

Displays a representative drawing of the minimum value for the selected parameter. The location of the cursor defines the selected parameter.

Max

(graphical representation)

For example, if you click the Smoothing Points box, the graphic shows the typical result obtained with the minimum number of smoothing points: a peak with reduced noise.

The number in the upper left corner of the graphic is a representative low value for the active parameter. It is not necessarily the minimum value for the parameter.

Displays a representative drawing of maximum value for the selected parameter. The location of the cursor defines the selected parameter.

For example, if you click the Smoothing Points box, the graphic shows the typical result obtained with a high number of smoothing points: a peak without noise.

The number in the upper left corner of the graphic is a representative high value of the active parameter. It is not necessarily the maximum value for the parameter.

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Genesis Peak Detection Parameters – LC Mode

Table 101

describes the parameters in the Genesis Peak Detection area for the liquid chromatography (LC) mode.

Table 101. Genesis Peak Detection parameters for the liquid chromatography (LC) mode

Parameter

Genesis Peak Detection

Description

Highest Peak

Nearest RT

When you select this option, the data system uses the highest peak in the chromatogram within the specified retention time window for component identification.

When you select this option, the data system uses the peak with the nearest retention time in the chromatogram to the expected retention time for component identification.

Minimum Peak Height

(S/N)

Specifies the minimum peak height on the basis of the signal-to-noise ratio that a peak must meet before the data system recognizes it as a possible chromatographic peak for the selected component.

To identify the chromatographic peak for the selected component, the data system ignores chromatographic peaks with a peak height that is less than the specified signal-to-noise threshold value.

Range: 0.0–999.0

Genesis Peak Detection Parameters – GC Mode

Table 102

describes the parameters in the Genesis Peak Detection area on the Detection page of the Quan view for the GC mode and mass spectral data.

Table 102. Genesis Peak Detection parameters for the gas chromatography (GC) mode (Sheet 1 of 6)

Parameter Description

Genesis Peak Detection (GC mode)

Spectrum This option is only available in the GC chromatography mode for the data acquired with an MS detector.

When you select this option, the data system uses the user-defined reference spectrum for component identification. The data system attempts to match the reference spectrum with a series of unknown spectra and calculates a score value for each comparison.

When you select the Spectrum option, a mass intensity list and the

Thresholds area appear (see Additional parameters for the

Spectrum option (Genesis)

).

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Table 102. Genesis Peak Detection parameters for the gas chromatography (GC) mode (Sheet 2 of 6)

Parameter

Highest Peak

Description

When you select this option, the data system uses the highest peak in the chromatogram within the specified retention time window for component identification, and the Ion Ratio Confirmation window appears.

Nearest RT

You can use the parameters in the Ion Ratio Confirmation area to confirm the identify of the chromatographic peak on the basis of spectral information (see

Ion Ratio Confirmation (Genesis)

).

When you select this option, the data system uses the peak with the nearest retention time in the chromatogram to the expected retention time for component identification, and the Ion Ratio

Confirmation window appears.

You can use the parameters in the Ion Ratio Confirmation area to confirm the identify of the chromatographic peak on the basis of spectral information (see

Ion Ratio Confirmation (Genesis)

).

Minimum Peak Height

(S/N)

Specifies the minimum peak height on the basis of the signal-to-noise ratio that a peak must meet before the data system recognizes it as a possible chromatographic peak for the selected component.

To identify the chromatographic peak for the selected component, the data system ignores chromatographic peaks with a peak height that is less than the specified signal-to-noise threshold value.

Range: 0.0–999.0

Additional parameters for the Spectrum option (Genesis)

Mass intensity list for the Spectrum option

Enter mass-to-charge [m/z] and intensity percentages for up to 50 spectrum peaks. The data system uses this data to identify the component. For information about interactively using

the spectrum in a representative raw data file to enter the spectral data in the list, see “To enter data in the spectrum table by using an open raw data file” on page 38 .

m/z

Each m/z value in this column specifies the mass-to-charge [m/z] value for one spectral peak in the reference spectrum. The adjacent Intensity (%) box specifies the intensity percentage for this m/z value.

Range: 0.5–999 999

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Table 102. Genesis Peak Detection parameters for the gas chromatography (GC) mode (Sheet 3 of 6)

Parameter

Intensity

Description

Each intensity percentage in this column specifies the relative intensity for one spectral peak in the reference spectrum. The adjacent m/z box specifies the m/z value for the spectral peak.

Range: 0–100

Thresholds (Spectrum option)

The Thresholds area appears when you select the Spectrum option in the GC mode.

Forward Specifies a threshold value for forward comparisons between the reference spectrum and candidates in the chromatogram. A forward search is a direct matching algorithm comparing unknowns against the reference spectrum in the peak identification table. The match is scored on a scale of 0 to 999. A perfect match results in a score of 999. As a general guide, 900 or greater is an excellent match; 800 to 900, a good match; 700 to

800, a fair match. Less than 600 is a poor match. Unknown spectra with many peaks tend to score lower than similar spectra with fewer peaks.

Reverse

Range: 0–1000

Specifies a threshold value for reverse comparisons between the reference spectrum and candidates in the chromatogram. A reverse search ignores any peaks in the unknown that are not in the reference spectrum in the peak identification table. The match is scored on a scale of 0 to 999. A perfect match results in a score of

999. As a general guide, 900 or greater is an excellent match; 800 to 900, a good match; 700 to 800, a fair match. Less than 600 is a poor match. A spectrum with many peaks tends to score more highly in a reverse match than in a forward match.

Match

Range: 0–1000

Specifies a threshold value for match comparisons between the reference spectrum and candidates in the chromatogram. The match threshold is scored on a scale of 0 to 999. The match algorithm is a complex probability factor that is based on the differences between the forward factors of all the candidates. If one candidate has a forward matching factor of 900 and the next best is only 300, the probability of the component being correctly identified is high and so the match factor is scored highly for the first candidate. If the forward factors for all the candidates are similar, whether high or low, the match factor is low.

Range: 0–1000

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Table 102. Genesis Peak Detection parameters for the gas chromatography (GC) mode (Sheet 4 of 6)

Parameter Description

Ion Ratio Confirmation (Genesis)

This area appears when you select the Highest Peak or Nearest RT option in the GC mode for data from an MS detector.

Use the parameters in this area to specify up to five qualifier ions to confirm the detection of a target analyte. You can also set the coelution window and select a method for calculating the target ion ratio window and tolerance.

Enable Selecting this check box activates the parameters in the Ion Ratio

Confirmation area.

Ion Ratio Using: Area or Height

(read-only)

Qualifier ion table

This read-only parameter shows the currently selected peak quantitation method: area or height. The data system uses the same method to calculate the qualifier ion peak response and then the target ratio. You can change this parameter by selecting the

Area or Height options in the Response area on the Calibration page.

Use this table to enter mass-to-charge [m/z] and target ratio tolerances [Window (±%)] data for up to five qualifier ions.

m/z

Target Ratio (%)

If you select Area response, the data system integrates each qualifier ion peak and calculates a ratio using the integrated qualifier ion peak and the quantitation peak area. It then compares this ratio with your specified target ratio. If the calculated ratio is outside of the target ratio by more than your specified tolerance [Window(±%)], it rejects the quantitation peak.

If you select Height response, the data system calculates a ratio using the qualifier ion peak height with the height of the quantitation peak. It then compares this ratio with your specified target ratio. If the calculated ratio is outside of the target ratio by more than your specified tolerance [Window(±%)], it rejects the quantitation peak.

The value in this column specifies the mass-to-charge [m/z] value for a qualifier ion.

Range: 0.5–999 999

The value in this column specifies the Target Ratio (%) value for a qualifier ion.

Range: 0.00–1 000 000 for a manual target ratio for the qualifier ion

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Table 102. Genesis Peak Detection parameters for the gas chromatography (GC) mode (Sheet 5 of 6)

Parameter

Window (±%)

Description

The value in this column specifies the Target Ratio tolerance for a qualifier ion.

Range: 0.00–100.00

Window%

Relative Selecting this option specifies that the target ratio tolerance values in the Window (±%) column of the qualifier ion table are relative values.

For example, if you set the target ratio to 50% and the Window

(±%) parameter to 20%, the expected target ion ratio range is 40 to 60%. (With the Absolute option this range would be 30 to

70%.) If the ion ratio is outside this range, the ion ratio confirmation test fails, and the data system sets the IRC Flag to

False. If the qualifier ion peak-to-quantitation peak ratio is within range, the ion ratio confirmation test passes, and the data system sets the IRC Flag to True. The response of all specified qualifier ions must be inside the respective ratio ranges for IRC to succeed.

Absolute

In assessing a target ion ratio range, the data system truncates the range at 0% to avoid negative values.

Selecting this option specifies that the target ratio tolerance values in the Window (±%) column of the qualifier ion table are absolute values.

For example, if you set the target ratio to 50% and the Window

(±%) parameter to 20%, the expected target ion ratio range is 30 to 70%. (With the Relative option this range would be 40 to

60%.) If the qualifier ion peak-to-quantitation peak ratio is outside this range, the ion ratio confirmation test fails, and the data system sets the IRC Flag to False. If the qualifier ion peak-to-quantitation peak ratio is within range, the ion ratio confirmation test passes, and the data system sets the IRC Flag to

True. The response of all specified qualifier ions must be inside the respective ratio ranges for IRC to succeed.

In assessing a target ion ratio range, the data system truncates the range at 0% to avoid negative values.

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Table 102. Genesis Peak Detection parameters for the gas chromatography (GC) mode (Sheet 6 of 6)

Parameter Description

Qualifier Ion

Coelution

Specifies the Qualifier Ion Coelution window.

Before it runs the ion ratio confirmation test, the data system generates a mass chromatogram for each specified qualifier ion.

Each of these chromatograms must feature a peak matching that of the quantitation mass or masses. If the retention time of the qualifier ion peak apex lies outside of the Qualifier Ion Coelution window (centered on the quantitation peak), the data system rejects the quantitation peak.

The data system tests quantitation peaks with matching qualifier ion peaks (in the coelution window) for ion ratio confirmation.

ICIS Detection Page for Quan View

Use the ICIS Detection page to specify peak integration and detection criteria for the ICIS peak detection algorithm.

After selecting ICIS as the peak detection algorithm on the Identification page of the Quan view, this page appears when you open the Detection page of the Quan view.

Note Click Advanced to open the ICIS Advanced Parameters dialog box where you can set up the advanced detection parameters for the ICIS algorithm.

These topics describe the parameters on the ICIS Detection page for the Processing Setup –

Quan view:

Quan View – ICIS Detection Page Buttons

ICIS Peak Integration Parameters

ICIS Peak Detection Parameters – LC Mode

ICIS Peak Detection Parameters – GC Mode

For information about changing the chromatography mode, see

Chromatography Options

Dialog Box

.

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Table 103

describes the buttons at the bottom of the Qual view – Detection page for the ICIS peak detection algorithm.

Table 103. Buttons at the bottom of the Quan view – Detection page for the Genesis algorithm

Parameter

Save As Default

Advanced

Description

Validates and saves the settings on the current page as default settings. The Processing Setup application uses these settings for all new components and all new processing methods. This option guarantees that the settings for the components are consistent and valid. The application writes over the previous default values and cannot recover them.

For the ICIS peak detection algorithm, this button opens the ICIS

Advanced Parameters dialog box, where you can set up the advanced parameters for the Genesis algorithm.

Flags

For information about the ICIS Advanced Parameters dialog box, see

ICIS Advanced Parameters Dialog Box .

Opens the Data Flags dialog box, where you can set peak area and peak height threshold values. The data system reports these data flags in result files, printed reports, and Quan Browser.

For information about the Data Flags dialog box, see

Data Flags

Dialog Box

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ICIS Peak Integration Parameters

Table 104

describes the parameters in the ICIS Peak Integration area on the Detection page of the Quan view.

Table 104. ICIS Detection page for Quan view parameters (Sheet 1 of 2)

Parameter

ICIS Peak Integration

Smoothing Points

Description

Specifies the number of points in the moving average used to smooth the data.

Baseline Window

Default: 7

Range: 1–15

The ICIS peak detection algorithm uses this value.

Specifies the number of scans to review for a local minima.

Default: 40

Range: 1–500

The ICIS peak detection algorithm uses this value.

Area Noise Factor

Peak Noise Factor

Specifies the noise-level multiplier used to determine the peak edges after the data system determines the start and end points of a possible peak for the selected component. As you increase this value, the integrated peak area decreases.

Default: 5

Range: 1–500

The ICIS peak detection algorithm uses this value.

Specifies the noise-level multiplier used to determine the potential peak signal threshold.

Default: 10

Range: 1–1000

The ICIS peak detection algorithm uses this value.

Constrain Peak Width Select this check box to constrain the integrated area of a component peak by specifying a peak height threshold and a tailing factor.

When you select the Constrain Peak Width check box, the Peak

Height (%) and Tailing Factor boxes become available.

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Table 104. ICIS Detection page for Quan view parameters (Sheet 2 of 2)

Parameter

Peak Height (%)

Description

Specifies the percent of the total peak height (100%) that a signal must be above the baseline before the data system turns integration on or off.

Tailing Factor

To enter a value for this parameter, select the Constrain Peak

Width check box. Then type a value in the Peak Height (%) box.

Range: 0.0–100.0

Specifies a tailing factor that controls how the data system integrates the tail of a peak. This factor is the maximum ratio of the trailing edge to the leading edge of a constrained peak.

To enter a value for this parameter, select the Constrain Peak

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

Min

(graphical representation)

Max

(graphical representation)

Range: 0.5–9.0

Displays a representative drawing of the minimum value for the selected parameter. The location of the cursor defines the selected parameter.

For example, if you click the Smoothing Points box, the graphic shows the typical result obtained with the minimum number of smoothing points: a peak with reduced noise.

The number in the upper left corner of the graphic is a representative low value for the active parameter. It is not necessarily the minimum value for the parameter.

Displays a representative drawing of maximum value for the selected parameter. The location of the cursor defines the selected parameter.

For example, if you click the Smoothing Points box, the graphic shows the typical result obtained with a high number of smoothing points: a peak without noise.

The number in the upper left corner of the graphic is a representative high value of the active parameter. It is not necessarily the maximum value for the parameter.

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ICIS Peak Detection Parameters – LC Mode

Table 105

describes the parameters in the ICIS Peak Detection area for the liquid chromatography (LC) mode.

Table 105. Genesis Peak Detection parameters for the liquid chromatography (LC) mode

Parameter

Genesis Peak Detection

Description

Highest Peak

Nearest RT

When you select this option, the data system uses the highest peak in the chromatogram within the specified retention time window for component identification.

When you select this option, the data system uses the peak with the nearest retention time in the chromatogram to the expected retention time for component identification.

Minimum Peak Height

(S/N)

Specifies the minimum peak height on the basis of the signal-to-noise ratio that a peak must meet before the data system recognizes it as a possible chromatographic peak for the selected component.

To identify the chromatographic peak for the selected component, the data system ignores chromatographic peaks with a peak height that is less than the specified signal-to-noise threshold value.

Range: 0.0–999.0

ICIS Peak Detection Parameters – GC Mode

Table 106

describes the parameters in the ICIS Peak Detection area on the Detection page of the Quan view for the GC mode and mass spectral data.

Table 106. ICIS Peak Detection parameters for the gas chromatography (GC) mode (Sheet 1 of 6)

Parameter Description

Genesis Peak Detection (GC mode)

Spectrum This option is only available in the GC chromatography mode for the data acquired with an MS detector.

When you select this option, the data system uses the user-defined reference spectrum for component identification. The data system attempts to match the reference spectrum with a series of unknown spectra and calculates a score value for each comparison.

When you select the Spectrum option, a mass intensity list and the

Thresholds area appear (see Additional parameters for the

Spectrum option (ICIS) ).

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Table 106. ICIS Peak Detection parameters for the gas chromatography (GC) mode (Sheet 2 of 6)

Parameter

Highest Peak

Description

When you select this option, the data system uses the highest peak in the chromatogram within the specified retention time window for component identification and the Ion Ratio Confirmation window appears.

Nearest RT

You can use the parameters in the Ion Ratio Confirmation area to confirm the identify of the chromatographic peak on the basis of spectral information (see

Ion Ratio Confirmation (ICIS)

).

When you select this option, the data system uses the peak with the nearest retention time in the chromatogram to the expected retention time for component identification and the Ion Ratio

Confirmation window appears.

You can use the parameters in the Ion Ratio Confirmation area to confirm the identify of the chromatographic peak on the basis of spectral information (see

Ion Ratio Confirmation (ICIS)

).

Minimum Peak Height

(S/N)

Specifies the minimum peak height on the basis of the signal-to-noise ratio that a peak must meet before the data system recognizes it as a possible chromatographic peak for the selected component.

To identify the chromatographic peak for the selected component, the data system ignores chromatographic peaks with a peak height that is less than the specified signal-to-noise threshold value.

Range: 0.0–999.0

Additional parameters for the Spectrum option (ICIS)

Mass intensity list for the Spectrum option

Enter mass-to-charge [m/z] and intensity percentages for up to 50 spectrum peaks. The data system uses this data to identify the component. For information about interactively using

the spectrum in a representative raw data file to enter the spectral data in the list, see “To enter data in the spectrum table by using an open raw data file” on page 38 .

m/z

Each m/z value in this column specifies the mass-to-charge [m/z] value for one spectral peak in the reference spectrum. The adjacent Intensity (%) box specifies the intensity percentage for this m/z value.

Range: 0.5–999 999

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Table 106. ICIS Peak Detection parameters for the gas chromatography (GC) mode (Sheet 3 of 6)

Parameter

Intensity

Description

Each intensity percentage in this column specifies the relative intensity for one spectral peak in the reference spectrum. The adjacent m/z box specifies the m/z value for the spectral peak.

Range: 0–100

Thresholds (Spectrum option)

The Thresholds area appears when you select the Spectrum option in the GC mode.

Forward Specifies a threshold value for forward comparisons between the reference spectrum and candidates in the chromatogram. A forward search is a direct matching algorithm comparing unknowns against the reference spectrum in the peak identification table. The match is scored on a scale of 0 to 999. A perfect match results in a score of 999. As a general guide, 900 or greater is an excellent match; 800 to 900, a good match; 700 to

800, a fair match. Less than 600 is a poor match. Unknown spectra with many peaks tend to score lower than similar spectra with fewer peaks.

Reverse

Range: 0–1000

Specifies a threshold value for reverse comparisons between the reference spectrum and candidates in the chromatogram. A reverse search ignores any peaks in the unknown that are not in the reference spectrum in the peak identification table. The match is scored on a scale of 0 to 999. A perfect match results in a score of

999. As a general guide, 900 or greater is an excellent match; 800 to 900, a good match; 700 to 800, a fair match. Less than 600 is a poor match. A spectrum with many peaks tends to score more highly in a reverse match than in a forward match.

Match

Range: 0–1000

Specifies a threshold value for match comparisons between the reference spectrum and candidates in the chromatogram. The match threshold is scored on a scale of 0 to 999. The match algorithm is a complex probability factor that is based on the differences between the forward factors of all the candidates. If one candidate has a forward matching factor of 900 and the next best is only 300, the probability of the component being correctly identified is high and so the match factor is scored highly for the first candidate. If the forward factors for all the candidates are similar, whether high or low, the match factor is low.

Range: 0–1000

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Table 106. ICIS Peak Detection parameters for the gas chromatography (GC) mode (Sheet 4 of 6)

Parameter Description

Ion Ratio Confirmation (ICIS)

This area appears when you select the Highest Peak or Nearest RT option in the GC mode for data from an MS detector.

Use the parameters in this area to specify up to five qualifier ions to confirm the detection of a target analyte. You can also set the coelution window and select a method for calculating the target ion ratio window and tolerance.

Enable Selecting this check box activates the parameters in the Ion Ratio

Confirmation area.

Ion Ratio Using: Area or Height

(read-only)

Qualifier ion table

This read-only parameter shows the currently selected peak quantitation method: area or height. The data system uses the same method to calculate the qualifier ion peak response and then the target ratio. You can change this parameter by selecting the

Area or Height options in the Response area on the Calibration page.

Use this table to enter mass-to-charge [m/z] and target ratio tolerances [Window (±%)] data for up to five qualifier ions.

m/z

Target Ratio (%)

If you select Area response, the data system integrates each qualifier ion peak and calculates a ratio using the integrated qualifier ion peak and the quantitation peak area. It then compares this ratio with your specified target ratio. If the calculated ratio is outside of the target ratio by more than your specified tolerance [Window(±%)], it rejects the quantitation peak.

If you select Height response, the data system calculates a ratio using the qualifier ion peak height with the height of the quantitation peak. It then compares this ratio with your specified target ratio. If the calculated ratio is outside of the target ratio by more than your specified tolerance [Window(±%)], it rejects the quantitation peak.

Specifies the mass-to-charge [m/z] value for a qualifier ion.

Range: 0.5–999 999

Specifies the Target Ratio (%) value for a qualifier ion.

Range for a manual target ratio for the qualifier ion:

0.00–1 000 000

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Table 106. ICIS Peak Detection parameters for the gas chromatography (GC) mode (Sheet 5 of 6)

Parameter

Window (±%)

Description

The value in this column specifies the Target Ratio tolerance for a qualifier ion.

Range: 0.00–100.00

Window%

Relative Selecting this option specifies that the target ratio tolerance values in the Window (±%) column of the qualifier ion table are relative values.

For example, if you set the target ratio to 50% and the Window

(±%) parameter to 20%, the expected target ion ratio range is 40 to 60%. (With the Absolute option, this range would be 30 to

70%.) If the ion ratio is outside this range, the ion ratio confirmation test fails, and the data system sets the IRC Flag to

False. If the qualifier ion peak-to-quantitation peak ratio is within range, the ion ratio confirmation test passes, and the data system sets the IRC Flag to True. The response of all specified qualifier ions must be inside the respective ratio ranges for IRC to succeed.

Absolute

In assessing a target ion ratio range, the data system truncates the range at 0% to avoid negative values.

Selecting this option specifies that the target ratio tolerance values in the Window (±%) column of the qualifier ion table are absolute values.

For example, if you set the target ratio to 50% and the Window

(±%) parameter to 20%, the expected target ion ratio range is 30 to 70%. (With the Relative option, this range would be 40 to

60%.) If the qualifier ion peak-to-quantitation peak ratio is outside this range, the ion ratio confirmation test fails, and the data system sets the IRC Flag to False. If the qualifier ion peak-to-quantitation peak ratio is within range, the ion ratio confirmation test passes, and the data system sets the IRC Flag to

True. The response of all specified qualifier ions must be inside the respective ratio ranges for IRC to succeed.

In assessing a target ion ratio range, the data system truncates the range at 0% to avoid negative values.

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Table 106. ICIS Peak Detection parameters for the gas chromatography (GC) mode (Sheet 6 of 6)

Parameter Description

Qualifier Ion

Coelution

Specifies the Qualifier Ion Coelution window.

Before it runs the ion ratio confirmation test, the data system generates a mass chromatogram for each specified qualifier ion.

Each of these chromatograms must feature a peak matching that of the quantitation mass or masses. If the retention time of the qualifier ion peak apex lies outside of the Qualifier Ion Coelution window (centered on the quantitation peak), the data system rejects the quantitation peak.

The data system tests quantitation peaks with matching qualifier ion peaks (in the coelution window) for ion ratio confirmation.

Calibration Page for Quan View

The Calibration page consists of a Calibration settings page and a Components list:

• The Calibration settings page consists of Component Type, Target Compounds, Internal

Standard, Weighting, Origin, and Response.

• The Components list is located at the far right of the page where you can view and select component names that are defined for the active processing method.

For information about using the Calibration page, see

“Setting Up the Calibration

Parameters” on page 41

.

Table 107

describes the parameters on the Quan view – Calibration page.

Table 107. Calibration page for Quan view parameters (Sheet 1 of 5)

Parameter

Component Type

Target Compound

Description

Specifies that the selected component is a target compound. This button is only active if you have defined at least one component as an internal standard and selected another component as

Component Type: Target Compound.

To select a component as a target compound type

1. Select a component.

2. Select the Target Compound option and click OK.

The data system activates the options in the Target

Compound area.

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Table 107. Calibration page for Quan view parameters (Sheet 2 of 5)

Parameter

ISTD

Description

Specifies that the selected component is an internal standard.

To select a component as an internal standard compound type

1. Select a component in the Component list.

2. Select the Internal Standard option and click OK.

When you choose the ISTD option:

• The ISTD area becomes active.

• The Target Compounds area is unavailable.

• The Levels page becomes unavailable.

The ISTD option is unavailable if you have selected the External

Standard option in the Calibration Options Dialog Box

.

ISTD

Amount

Units

Specifies the amount of the selected component that is added to each sample to provide an internal standard. You can enter amounts with up to three decimals of precision. Select the ISTD

Component Type to activate this box.

Specifies the units used for the internal standard amount. For example, ng (nanograms). Select the ISTD Component Type to enable this box.

Target Compounds

Target Compounds

ISTD

Specifies the calibration curve parameters for the selected target compound.

Lists the components identified as internal standard components.

This list is available when you select the internal standard calibration technique, identify one or more components as internal standard components, and select a target component in the Components list.

To select an internal standard component for a target component

1. Select the target component of interest in the Components list.

2. Select an internal standard component in the ISTD list.

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Table 107. Calibration page for Quan view parameters (Sheet 3 of 5)

Parameter

Isotope (%) button

Calibration Curve

Description

Opens the Correction for Isotope Contribution dialog box, where you can set up the calibration corrections for isotope contributions of the internal standard to the target compound and the target compound to the internal standard.

Specifies the calibration curve type.

Units

The available selections are as follows:

• Linear

• Quadratic

• Linear Log-Log

• Quadratic Log-Log

• Average RF (response factor)

• Point-to-Point

• Cubic Spline

• Locally Weighted

Specifies the label used for the x coordinate in the calibration curve plot when it appears on the Calibration page of the Quan view. Enter any alphanumeric string.

Weighting

Equal

1/X

1/X^2

1/Y

1/Y^2

Weights all calibration data points equally during the least-squares regression calculation of the calibration curve.

Specifies a weighting of 1/X for all calibration data points during the least-squares regression calculation of the calibration curve.

Calibrants are weighted by the inverse of their quantity.

Specifies a weighting of 1/X^2 for all calibration data points during the least-squares regression calculation of the calibration curve. Calibrants are weighted by the inverse of the square of their quantity.

Specifies a weighting of 1/Y for all calibration data points during the least-squares regression calculation of the calibration curve.

Calibrants are weighted by the inverse of their response (or response ratio).

Specifies a weighting of 1/Y^2 for all calibration data points during the least-squares regression calculation of the calibration curve. Calibrants are weighted by the inverse of the square of their response (or response ratio).

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Table 107. Calibration page for Quan view parameters (Sheet 4 of 5)

Parameter

1/s^2

Description

Specifies a weighting of 1/s^2 for all calibration data points during the least-squares regression calculation of the calibration curve.

Calibrants at a given level are weighted by the inverse of the standard deviation of their responses (or response ratios). For this weighting factor to be used, there must be two or more replicates at each level. If only one calibrant is available for any level, 1/s^2 weighting cannot be used.

Origin

Ignore

Force

Include

Select the Ignore option to exclude the origin as a valid point in your calibration curve. If you select this option, the calibration curve might or might not pass through the origin.

Select the Force option to make sure that the calibration curve passes through the origin of the data point plot.

Select the Include option to include the origin as a single data point in the calculation of the calibration curve. If you select this option, the calibration curve might or might not pass through the origin.

Response

Area

Height

Specifies that the data system use the area of the target compound peak (or the ratio of the areas for the target compound peak and the internal standard compound peak) for the calibration.

Specifies that the data system use the height of the target compound peak (or the ratio of heights for the target compound peak and the internal standard compound peak) for the calibration.

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Table 107. Calibration page for Quan view parameters (Sheet 5 of 5)

Parameter

Component

Component List

Description

Lists the component names for the active processing method. This list is located in the Components pane at the far right of the

Processing Method window and contains all of the component names that you have defined for the active processing method.

To add a new component to the list

1. Replace <New > in the Name box with the name of the component.

2. Click OK.

The new component name appears in the Name box and

Component List.

To delete a component from the list

1. Click the component name in the Component List.

2. Choose Options > Delete Component.

Buttons

Save As Default

Flags

Validates and saves the settings on the current page as default settings. The Processing Setup application uses these settings for all new components and all new processing methods. This option guarantees that the settings for the components are consistent and valid. The application writes over the previous default values and cannot recover them.

Opens the Calibration and Quantitation Flags dialog box. The data system reports these data flags in result files, printed reports,

and Quan Browser. For more information, see Calibration and

Quantitation Flags Dialog Box

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Levels Page for Quan View

Use the Levels page to define calibration and QC levels for Target compounds. You can use

the Standard Dilution Dialog Box to create calibration level information for all components

quickly and easily. This page is not available for ISTD component types.

For information about setting up the calibration and QC levels, see “Setting Up the

Calibration and QC Levels” on page 47

.

Table 108

describes the parameters on the Levels page.

Table 108. Levels page for Quan view parameters (Sheet 1 of 2)

Parameter

Readout

Units

Description

Displays the units set on the Calibration page. The units are also used in reports and in Quan Browser.

Calibration Levels

Calibration levels shortcut menu

Delete Rows

Insert Row

Calibration levels table

Cal Level

Amount

Use this shortcut menu to make changes to the Cal Levels table.

This shortcut menu contains the following commands: Delete

Rows, Insert Rows, and Copy Levels to All Target Components.

Deletes the currently selected row of the Cal Levels table.

Inserts a new row in the Cal Levels table.

Copy Levels to All

Target

Components

Copies the current Cal Levels table to all target components. This action ensures that all target components contain exact duplicates of the current Cal Levels table.

Specifies the calibration level names. The data system can accommodate up to 50 calibration levels. To enter a calibration level, type the new name in the appropriate Cal Level box. To delete a Cal level row, click to the left of the row. The data system highlights the row. Then press DELETE.

For each target component, specifies the amounts for each calibration level. You can enter amounts with up to three decimals of precision. To enter a calibration amount, type the value in the

Amount box at the appropriate level.

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Table 108. Levels page for Quan view parameters (Sheet 2 of 2)

Parameter

QC Levels

QC Levels Shortcut

Menu

Delete Rows

Insert Row

Copy Levels to All

Target

Components

QC levels table

QC Level

Amount

% Test

Description

Use this shortcut menu to make changes to the QC Levels table.

This shortcut menu contains the following commands: Delete

Rows, Insert Rows, and Copy Levels to All Target Components.

Deletes the currently selected row of the QC Levels table.

Inserts a new row in the QC Levels table.

Copies the current QC Levels table to all target components. This action ensures that all target components contain exact duplicates of the current QC table.

Enter the QC (quality control) level names, amounts, and %test values. Use QC samples containing known amounts of a component to check the accuracy of an analysis. The data system determines the amount of the target components in the QC samples in the same manner as unknown samples and then determines the difference between the specified amount and the calculated amount.

The data system can accommodate up to 50 QC levels. To enter a quality control level, type a name in the appropriate QC Level box. To delete a QC level row, click to the left of the row. The data system highlights the row. Then press DELETE.

For the selected target component, type the amount for each QC level component.

Type a value for the acceptable difference (as a percent) between the specified amount and the calculated amount for each QC level.

Buttons

Save As Default Validates and saves the settings on the current page as default settings. The Processing Setup application uses these settings for all new components and all new processing methods. This option guarantees that the settings for the components are consistent and valid. The application writes over the previous default values and cannot recover them.

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System Suitability Page for Quan View

Use the System Suitability page to carry out a sequence of automated chromatographic checks that assign a pass or fail qualification to a target peak. These checks are based on an analysis of the quantitation peak and, if ion ratio confirmation is enabled, all qualifier ion peaks in the retention time window. System suitability flags are reported in Sample and Summary reports and in Quan Browser.

For information about setting up the system suitability parameters, see

“Setting Up the

System Suitability Parameters” on page 50 .

Table 109

describes the parameters on the System Suitability page.

Table 109. System Suitability page for Quan view parameters (Sheet 1 of 5)

Parameter

Resolution Parameters

Enable

Description

Selecting this check box activates the Resolution Threshold (%) box. Resolution testing is based on a comparison of the peak height to the adjacent valley height in the quantitation window.

Resolution Threshold

(%)

If the endpoint of a peak is not detected as a valley, the peak always passes the Resolution Threshold test, regardless of the set threshold value or the presence of overlapping peaks.

Specifies the resolution threshold. The default value is 90%, and the valid range is 0 to 100%. Resolution threshold is defined as the ratio:

100 × V/P where:

V = The horizontal asymptote extended from the target peak’s apex to the lowest point in the valley between the target peak and a neighboring peak

P = The height of the target peak

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Table 109. System Suitability page for Quan view parameters (Sheet 2 of 5)

Parameter

Symmetry Parameters

Enable

Description

Selecting this check box activates the system suitability check of peak symmetry. Symmetry is determined at a specified peak height and is a measure of how even-sided a peak is about a perpendicular dropped from its apex.

The data system determines symmetry at the peak height specified in the Peak Height (%) box. For the purposes of the test, a peak is considered symmetrical if:

(Lesser of L and R) × 100 / (Greater of L and R) > Symmetry

Threshold (%) where:

L = distance from the left side of the peak to the perpendicular, dropped from the peak apex

R = The distance from the right side of the peak to the perpendicular, dropped from the peak apex

Peak Height (%)

Measurements of L and R are taken from the raw data file without smoothing.

Specifies the peak height where the data system measures the symmetry of target peaks.

Default: 50%

Range: 0–100%

Specifies the symmetry threshold value. Symmetry Threshold

(%)

Default: 90%

Range: 0–100%

Peak Classification Parameters

Enable Selecting this check box activates the peak classification parameters.

Detect Peak Width

Peak Height (%) Specifies the peak height where the data system tests the width of target peaks.

Default: 50%

Range: 0–100%

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Table 109. System Suitability page for Quan view parameters (Sheet 3 of 5)

Parameter Description

Min Peak Width (sec) Specifies the minimum peak width at the specified peak height for the peak width suitability test.

Default: 1.80

Range: 0.06–29.99

Max Peak Width (sec) Specifies the maximum peak width at the specified peak height for the peak width suitability test.

Default: 3.60

Range: 1.01–30.00

Detect Tailing

Tailing is calculated at the value defined in the Peak Height (%) box. For the purposes of the test, a peak is considered to be excessively tailed if:

R / L > Threshold (%) where:

L = The distance from the left side of the peak to the perpendicular, dropped from the peak apex

R = distance from the right side of the peak to the perpendicular, dropped from the peak apex

Measurements of L and R are taken from the raw data file without smoothing.

Peak Height (%) Specifies the Peak Height where the data system measures the tailing of target peaks.

Failure Threshold

Default: 10%

Range: 0–100%

Specifies the failure threshold for the tailing suitability test.

Default: 2.0

Range: 1.0–50.0

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Table 109. System Suitability page for Quan view parameters (Sheet 4 of 5)

Parameter

Detect Column Overload

Description

A peak is considered to be overloaded if:

L / R > Failure Threshold (%) where:

L = The distance from the left side of the peak to the perpendicular, dropped from the peak apex

R = The distance from the right side of the peak to the perpendicular, dropped from the peak apex

Measurements of L and R are taken from the raw data file without smoothing.

Peak Height (%) Specifies the peak height at which the data system measures column overloading.

Failure Threshold

Default: 50%

Range: 0–100%

Specifies the failure threshold value for the column overload suitability test.

Default: 1.5

Range: 1.0–20.0

Detect Baseline Clipping

Number of Peak

Widths for Noise

Detection

Type a number in the Number of Peak Widths for Noise

Detection box for the baseline clipping system suitability test.

A peak is considered to be baseline clipped if there is no signal

(zero intensity) on either side of the peak in the specified number of peak widths. The range is truncated to the quantitation window if the specified number of peak widths extends beyond the window’s edge.

Default: 1.0

Range: 0.1–10.0

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Table 109. System Suitability page for Quan view parameters (Sheet 5 of 5)

Parameter Description

Detect Minimum Signal-To-Noise Ratio

Signal-To-Noise Ratio Specifies the minimum signal-to-noise ratio. The data system calculates the signal-to-noise ratio in the quantitation window using only the baseline signal and excludes any extraneous, minor, detected peaks from the calculation.

Default: 3

Range: 1–500

Buttons

Save As Default Validates and saves the settings on the current page as default settings. The Processing Setup application uses these settings for all new components and all new processing methods. This option guarantees that the settings for the components are consistent and valid. The application writes over the previous default values and cannot recover them.

Peak Purity Page for Quan View

Use the Peak Purity page to specify the values of the peak purity parameters to include in a quantitative processing method for the PDA detector type only. When you specify the processing method in a sequence, you can then apply the parameters to your quantitative

PDA analysis as you acquire data. Use a raw data file of PDA data in Quan Browser to specify the values for peak purity parameters that you want to use in the processing method.

Table 110

describes the parameters on the Peak Purity page. The parameters on the Peak

Purity page are the same in the Qual and Quan views.

Figure 96 on page 347

shows the Peak

Purity page in the Qual view.

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Table 110. Peak Purity page for Quan view parameters

Parameter

Purity Parameters

Description

Enable Selecting this check box activates the Scan Threshold (mAU) and

Peak Coverage (%) parameters.

Scan Threshold (mAU) Specifies a minimum value of intensity for wavelength scans in milliabsorbance units (mAU). A peak purity calculation starts with the scan at the apex of the peak, and then collects wavelength data from scans on both sides of the apex until the specified Scan

Threshold (mAU) is reached. Use scan threshold for either symmetrical or asymmetrical peaks.

Peak Coverage (%)

Default: 50 mAU

Range: 0–1000 mAU (or 1 AU)

In a sample with high background or noise, consider starting with a value of 40 mAU.

Specifies a maximum percent value of the width of the integrated peak. A peak purity calculation starts with the scan at the apex of the peak and then collects wavelength data from scans on both sides of the apex until the specified Peak Coverage (%) is reached.

Use peak coverage for symmetrical peaks.

Limit Scan Wavelength Selecting this check box activates the Range (nm) box. Select this check box to limit the number of wavelengths to include in the peak purity calculation. Then enter a range in the Wavelength

Range box.

Range (nm)

Default: 95%

Range: 0.0–100.0%

Specifies a range of UV-Vis scans (in nanometers). A peak purity calculation starts with the scan at the apex of a peak and collects wavelength data from scans on both sides of the apex until all the wavelengths in the range are included. Use wavelength range for either symmetrical or asymmetrical peaks.

To activate this box, select the Limit Scan Wavelength check box.

The default wavelength range is the full width of the scan.

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Programs View

Use the Programs view of the Processing Setup window to compile a list of programs or macros to be run by the data system after the analysis of a sample and the processing of the resulting data. The data system runs the programs in the listed order.

For more information about adding programs and macros to a processing method, see

“Adding Programs or Macros to Processing Methods” on page 66 .

For information about the Programs view toolbar, see

Reports and Programs Views Toolbar

.

For information about the OK, Cancel, and Save As Default buttons, see

OK, Cancel, and

Save As Default Buttons . For information about using the Programs view, see

“Enabling and

Setting Up a Program or Macro” on page 67 .

The Programs table lists the programs to be run by the data system during post processing.

For information about using the programs table, see Table 111 and these topics:

Column Headings

Macro Arguments

Printing Raw Files and Layout Files

To activate a program or macro

1. For the program or macro that you want to activate, click the Enable column.

A check box appears.

2. Select the check box.

When you click elsewhere in the view, the box displays a Yes value.

To select a sample type

1. Click the table cell.

A check box appears.

2. Select the check box.

When you click elsewhere in the view, the box displays a Yes value.

To change the status of a table cell from Yes to blank

1. Click the cell.

A check box appears.

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2. Do one of the following:

• To change the status to Yes, select the check box.

• To change the status to blank (inactive), clear the check box.

Table 111

describes the parameters for the Programs table in the Program view.

Table 111. Programs table (Sheet 1 of 2)

Parameter

Programs

Description

Specifies post processing programs or macros to be run after the processing of a bracketed or non-bracketed sequence. Each row in the Programs table consists of eight columns.

[Row Number] Each numbered row represents an item in the table. The asterisk

(*) indicates the last unused row in the table. Use this row to enter a new item.

Enable Selecting this check box activates the program or macro. When the program or macro is available, the box displays a Yes value. If it is unavailable, the box is blank.

Sample Type

Std

QC

Unk

Other

Action

Specifies the availability of the report for Standard Sample types. If the report is available, the box displays a Yes value. If it is unavailable, the box is blank.

Specifies the availability of the report for QC sample types. If the report is available, the box displays a Yes value. If it is unavailable, the box is blank.

Specifies the availability of the report for Unknown sample types.

If the report is available, the box displays a Yes value. If it is unavailable, the box is blank.

Specifies the availability of the report for sample types other than

Standard, QC, or Unknown. If the report is available, the box displays a Yes value. If it is unavailable, the box is blank.

Specifies the action that occurs when a program is run. To change the current action, click the Action list to display the action options. Then select one of the following actions: Run Excel

Macro or Run Program.

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Table 111. Programs table (Sheet 2 of 2)

Parameter

Program or Macro

Name

Description

Specifies the full path of the program or macro that the data system uses during post-processing. You can type the full path in the box or browse for the program or macro in the Browse for

Program dialog box. Double-click the Program or Macro Name box to display the Browse for Program dialog box. Or right-click the cell and select Browse from the context menu.

To change the current program or macro name in the command line, double-click the Program or Macro Name box to activate the

Open dialog box so that you can select your program or macro.

The data system displays the new program or macro name. You can also type on the command line.

Here is an example using the XConvert.exe program:

Sync

Parameters

To convert the current file (myfile.raw) from Xcalibur (RAW) file format to ANDI (CDF) file format and copy it to the current default data directory, use the following command line:

Convert /DA /SL %R where:

DA indicates that the destination file (D) is to be ANDI format (A).

SL indicates that the source file (S) is an LCQ™ raw file (L).

%R is the macro argument for the current raw data file.

See Command Line Arguments

or

ExcelExp.exe

for more examples.

Specifies whether to run the selected program synchronously or asynchronously. The data system initiates asynchronous programs simultaneously but starts synchronous programs only when the previous program is finished. To change the current action, click the box and then select or clear the check box as required.

Specifies any command parameters for the selected program. See

the Program or Macro Name

box for examples.

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Column Headings

Table 112

describes the column headings in the Programs table and their use. The Programs table is part of the Programs view in the Processing Setup window.

Table 112. Column headings in the Programs table

Column heading

Enable

Save As

Std

QC

Unk

Other

Action

Program Name

Sync

Parameters

Use

Enables a program.

Provides you with various options for exporting the specified summary report.

Determines whether the data system runs a program after a

Standard sample analysis.

Determines whether the data system runs the program after a QC sample analysis.

Determines whether the data system runs the program after an

Unknown sample analysis.

Determines whether the data system runs the program after any other type of sample analysis.

Provides two options: Run Program or Run Excel Macro.

Displays the full path of the program or macro to be run by the data system during post processing.

Determines whether the selected program runs synchronously or asynchronously. The data system initiates asynchronous programs simultaneously. A synchronous program starts only when the previous program is terminated.

Specifies any command parameters for the selected program. If an

Export Only action is selected, the cell lists the available export file types: XLS, TXT, or CSV. The data system exports a Report File formatted according to the selected file name extension.

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Macro Arguments

You can use the following macros in the command line.

Table 113. Macro arguments

Macro arguments

%R

%F

%%

%X

Macro parameter replacement

Provides the current raw data file.

Provides the current result file.

Provides a single (%) character in the run line.

If the previous custom report was generated using Actions >

Export Only, the (%X) macro provides the result file name with the extension that was selected from the Export Type list.

%S

If you convert a file and select an .xls file name extension, the data system uses the converted raw data file with a .crf file name extension. It does not change the file name extension if you select a .txt or .csv extension.

If the previous custom report was generated using Actions: Run

Excel Macro, the (%X) macro provides the result file name with an .xls file name extension.

Passes the current sequence file (SLD file type) and the current row number. The row number is zero-based: 0 denotes the first sample, 1 refers to the second sample, and so on.

Printing Raw Files and Layout Files

You can include a command line argument that launches an application and prints a specified file to the default printer (/p) or a specified printer (/pt).

Reports View

Use the Reports view of the Processing Setup window to specify how the data system produces reports for samples and sequences. The data system provides several standard report formats.

You can also design custom reports in XReport, the Xcalibur report designer. The data system exports results in a number of file formats, including XLS and HTML.

For more information about adding reports to a processing method, see “Adding Report

Templates to Processing Methods” on page 61 .

The Reports view consists of a menu bar, a toolbar, and two report tables. For information

about the Reports view toolbar, see Reports and Programs Views Toolbar . For information

about the OK, Cancel, and Save As Default buttons, see

OK, Cancel, and Save As Default

Buttons

.

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The Reports view displays two tables:

• Sample Reports list the reports to be produced for processed samples in a sequence.

• Summary Reports list the reports to be produced for sequences or brackets.

Table 114

and these topics describe the parameters in the Reports view:

Sample Report Column Headings

Summary Reports Column Headings

Valid File Types for Sample and Summary Reports

Table 114. Reports view tables (Sheet 1 of 2)

Parameter

Sample Reports

Description

This table specifies sample reports to be issued for each sample in a sequence. Each row in the Sample Reports table consists of seven columns. Refer to the XReport User Guide for more information about generating reports.

Row Number

Each numbered row represents an item in the table. The asterisk

(*) indicates the last unused row in the table. Use this row to enter a new item.

Enable column Specifies the report status. If the report is available, the box displays a Yes value. If it is unavailable, the box is blank. When you click the box, a check box appears. Clicking the check box activates the row. When you click anywhere else on the page, the data system replaces the selected check box with the text Yes.

Sample Type columns

Std

QC

Unk

Specifies the report availability for Standard Sample types. If the report is available, the box displays a Yes value. If it is unavailable, the box is blank. When you click the box, a check box appears so you can change the status.

Specifies the report availability for QC sample types. If the report is available, the box displays a Yes value. If it is unavailable, the box is blank. When you click the box, a check box appears so you can change the status.

Specifies the report availability for Unknown sample types. If the report is available, the box displays a Yes value. If it is unavailable, the box is blank. When you click the box, a check box appears so you can change the status.

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Table 114. Reports view tables (Sheet 2 of 2)

Parameter

Other

Save As

Description

Specifies the report availability for sample types other than

Standard, QC, or Unknown. If the report is available, the box displays a Yes value. If it is unavailable, the box is blank. When you click the box, a check box appears so you can change the status.

Specifies the file export option for the sample report.

Report Template Name Specifies the name and location of the report template that the processing method uses to generate the report. You can type the full path in the box or browse for the template in the Browse for

Sample Report Template dialog box. Double-click a Report

Template Name box to display the Browse for Sample Report

Template dialog box. Or right-click the cell and select Browse from the context menu.

Summary Reports

The data system saves the exported file with the sample file name and the correct extension in the folder where it stores the result files (see

Valid File Types for Sample and Summary Reports ).

This table specifies Summary reports to be issued after processing of a bracketed or non-bracketed sequence. Each row in the Summary Reports table consists of three columns.

Row Number

Each numbered row represents an item in the table. The asterisk

(*) indicates the last unused row in the table. Use this row to enter a new item.

Enable

Save As

Specifies the report status. If the report status is available, the box displays a Yes value. If it is unavailable, the box is blank. When you click the box, a check box appears so you can change the status.

Specifies the file export option for the summary report. The data system saves the exported file with the sample file name and the appropriate extension in the data folder where result files are stored.

Report Template Name Specifies the name and location of the report template that the processing method uses to generate the report. You can type the full path in the box or browse for the template in the Browse for

Summary Report Template dialog box. Double-click a Report

Template Name box to display the Browse for Summary Report

Template dialog box. Or right-click the cell and select Browse from the context menu.

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Sample Report Column Headings

The following table defines columns for sample reports.

Column heading

Enable

Std

QC

Unk

Other

Save As

Report Template Name

Use

Enables a sample report.

Specifies the report for a Standard sample type.

Specifies the report for a QC sample type.

Specifies the report for an Unknown sample type.

Specifies the report for all other sample types.

Specifies the file type for saved report.

Specifies the full path of the template that the data system uses in generating the sample report.

Summary Reports Column Headings

The following table defines columns for summary reports.

Column heading

Enable

Save As

Report Template Name

Use

Enables a summary report.

View or change various options for exporting the specified summary report.

View or change the full path of the template that the data system uses in generating the summary report.

Valid File Types for Sample and Summary Reports

The following table lists the valid files types.

Export type

None

Text

Doc

HTML

PDF

RTF

XLS

Description

Print only, no exported file

ASCII plain text file (TXT)

Microsoft Word document (DOC)

Hypertext markup language file (HTML)

Portable document format file (PDF)

Rich text format file (RTF)

Microsoft Excel spreadsheet (XLS)

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