Xcalibur 3.1 Data Acquisition and Processing User Guide Version A

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Sequence Setup View

Use the Sequence Setup view of the Home Page window to set up a sequence table for acquiring, processing, or acquiring and processing a sample set containing unknown samples, calibration standard samples, quality control samples, and blank samples.

Contents

Sequence Setup View Features

Sequence Setup Menus

Sequence Editor Toolbar

Sequence Setup View Dialog Boxes

For information about creating and modifying sequences, see Chapter 4, “Creating and

Modifying Sequences.”

For information about running and batch reprocessing sequences, see

Chapter 5, “Running and Batch Reprocessing Sequences.”

Sequence Setup View Features

Clicking the Sequence Setup icon on the Roadmap view or the Sequence View icon on the

Home Page View toolbar, or choosing View > Sequence Setup view from the Home Page window menu opens the sequence table and the Sequence Editor toolbar.

Each sample injection to be acquired or raw data file to be reprocessed is defined by the

settings of its sequence row as described in Table 31

.

You can enter the sample information into each row manually or you can use the New

Sequence Template dialog box to enter the sample information semi-automatically. For more

information about creating and modifying sequences, see Chapter 4, “Creating and

Modifying Sequences.”

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Sequence Setup View Features

Tip For a quantitative analysis, the Xcalibur data system organizes the sample data into brackets. Each bracket contains two sample categories. The calibration standards make up one category. The other sample types including unknowns, blanks, and QC samples make up the other category.

The Xcalibur data system provides four options for sequence bracketing: None, Open,

Overlapped, and Non-Overlapped. Only the None option for sequence bracketing allows the use of more than one processing method per sequence. Because the sequence table editor allows only Open sequence bracketing, you must use the New Sequence Template dialog box to set up the other bracketing options.

Table 31

describes the columns in the Sequence Setup table.

Table 31. Sequence table parameters (Sheet 1 of 8)

Parameter

Sample Type

Description

Specifies the type of sample described by the sequence row. The sample type defines how the data system processes the sample data. These sample types are available for all bracket types:

Unknown, Blank, and QC. The available standard sample types depend on the bracket type and include the following: Std Clear, Std Update, Start Bracket., and End Bracket.

Unknown

Blank

An Unknown is a sample with an unknown amount of the analyte or analytes

A Blank is a sample matrix or solvent blank.

QC

Std Clear

Std Update

Start Bracket

A QC is a quality control sample that contains known amounts of the analyte or analytes in a sample matrix or solvent blank.

Standard Clear is available with the None bracketing option.

When the data system processes a Std Clear sample, it clears the data for all of the calibration levels in the calibration file and populates the associated calibration level with data from the current data file. A calibration file can contain data for multiple named components (analytes) and multiple calibration levels.

Standard Update is available with the None bracketing option.

When the data system processes a Std Update sample, it updates the associated calibration level with additional data from the current data file.

Start Bracket is available only with the Overlapping and

Non-Overlapping bracketing options. The Start Bracket sample type defines the beginning of the current bracket. When the data system encounters the Start Bracket sample type during post-acquisition processing, it clears the calibration data for the associated calibration level.

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Sequence Setup View Features

Table 31. Sequence table parameters (Sheet 2 of 8)

Parameter

End Bracket

Description

End Bracket is available with the Non-Overlapping bracketing option. The End Bracket sample type defines the end of the current bracket. With the Non-Overlapping bracketing option, each bracket must begin with the Start Bracket sample type for each calibration level and end with the End Bracket sample type for each calibration level. During post-acquisition processing, the data system processes the standard sample types first and then calculates the calibration curve for each target component

(analyte) by using the information from the Start Bracket and End

Bracket sample types for the current bracket. After the data system calculates the calibration for each analyte, it processes all of the sample types in the current bracket.

Tip To select the sample type for a sequence row, click the

Sample Type column, and then click the down arrow that appears to display the list of sample types.

File Name

For more information about sample types and sequence

bracketing, see “Step 2: Selecting the Bracket Type” on page 71

.

Specifies the name of the file that contains the sample data. The

File Name is a combination of the Base File Name prefix and a sequential sequence number.

• If you use the New Sequence Template dialog box to create a sequence, you define the base file name in the Base File Name box and the starting number for the sequence in the Starting

Number box.

• If you use the default Starting Number of 1, the suffix for the first sample is 01, the suffix for the second sample is 02, and so on.

• If you change the Starting Number to a value of 10 or higher, the suffix for the first sample is the Starting Number, and subsequent rows in the sequence are incremented by 1. For example, if the Starting Number is 10, the suffix for the first sample is 10, the suffix for the second sample is 11, and so on.

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Sequence Setup View Features

Table 31. Sequence table parameters (Sheet 3 of 8)

Parameter

Sample ID

Description

Specifies identifying text for each sample. To change the current

ID, type a new alphanumeric value in the Sample ID box. The sample ID value does not have to be a unique identifier.

Path

If you use the New Sequence Template dialog box to create the sequence, you can use the Base Sample ID box to enter an alphanumeric prefix to the Sample ID that the data system applies to each sample in the new sequence. If the instrument configuration includes an autosampler, the data system uses the sample vial or microwell position as the suffix for each sample. For information about the position notation, refer to the Help for your autosampler.

Specifies the path to the raw file or files that the Xcalibur data system creates for the sample data. The data system creates these files with a (.raw) extension. A path contains the drive and one or more folders. A typical path can look like C:\Xcalibur\DATA.

Instrument Method

To find and select the path, double-click the Path box. The Select

Directory dialog box opens. The data system enters the path in the

Path box. You can also type the path in the Path box.

Specifies the path and file name of the instrument method to be used to control the instruments of the mass spectrometry system during a sample run. A path contains the drive and one or more folders. A typical path for an instrument method file named

ABC.meth can look like C:\Xcalibur\methods\ABC.meth.

To find and select the path and file name, double-click the Inst

Meth box. The Select Instrument Method dialog box opens. The data system enters the path and file name in the Inst Meth box.

You can also type the path and file name in the Inst Meth box.

You can select up to one instrument method per injection.

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Table 31. Sequence table parameters (Sheet 4 of 8)

Parameter

Processing Method

Description

Specifies the path and file name of the processing method to be used to process the samples. A path contains the drive and one or more folders. A typical path for a processing method file named

ABC.pmd can look like C:\Xcalibur\methods\ABC.pmd.

Calibration File

To find and select the path and file name, double-click the

Processing Method box. The Select Processing Method dialog box opens. The data system enters the path and file name in the

Processing Method box. You can also type the path and file name in the Processing Method box.

With the Open, Overlapping, and Non-Overlapping bracketing options, you can select only one processing method for the entire sequence. When you create the sequence manually, the data system defines the bracketing option as Open.

Specifies the calibration file to be used for an unbracketed sequence (None bracket type). To quantitatively process an unbracketed sequence, you must specify a calibration file.

A typical path for a calibration file named ABC.xcal can look like this C:\Xcalibur\methods\ABC.xcal.

To find and select the path and file name, double-click the

Calibration File box. The Select Calibration File dialog box opens. The data system enters the path and file name in the Cal

File box. You can also type the path and file name in the Cal File box.

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Sequence Setup View Features

Table 31. Sequence table parameters (Sheet 5 of 8)

Parameter

Position

Description

Specifies the vial or microwell position in the autosampler. To change the position, type a value in the Position box.

For information about the tray, microwell plate, and vial notation, refer to the Help for your autosampler.

If you use the New Sequence Template dialog box to create your sequence, you can use the following parameters in the Samples area to set up the vial positions:

• Type the initial vial position in the Initial Vial Position box.

• If the Select Vials button is available, you can click it to open a graphical representation of the autosampler tray that you can use to select the vial positions.

• Select the Re-Use Vial Positions check box to set up the sequence to makes replicate injections from the same vial position.

Injection Volume Specifies the injection volume in microliters of sample to be injected. To change the volume, type the new volume in the Inj

Vol box.

If you are using an autosampler, you can set the default injection volume in the instrument method. The minimum and maximum injection volumes that you can use depend on the autosampler you select. The usable range depends on the injection mode and might be smaller than the range displayed in the status bar. For more details, consult your autosampler manual.

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Sequence Setup View Features

Table 31. Sequence table parameters (Sheet 6 of 8)

Parameter

Level

Description

Specifies the calibration level for a standard sample type or the quality control level for a QC sample.

Sample Weight

Sample Volume

To specify the calibration level for a standard or QC sample type, you must first add a processing method to the sequence. After you add a processing method to the sequence, the level list appears when you double-click the Level column for a standard or QC sample type.

Specifies the amount of a component that has been placed in the sample. The processing method specifies the unit for this sample weight. The unit is included in Xcalibur reports. The data system does not convert units. To change the sample weight, type the weight in the Sample Weight box.

Specifies the volume of a component that has been placed in the sample. The processing method specifies the unit for this volume.

The unit is only included in Xcalibur reports. The data system does not convert units. To change the sample volume, type the sample volume in the Sample Volume box.

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Sequence Setup View Features

Table 31. Sequence table parameters (Sheet 7 of 8)

Parameter

ISTD Correction

Amount

Description

Specifies the ISTD correction amount. If the value in this box is not 0.000, the value is used in an algorithm to automatically correct for the case where the internal standard amounts specified in the active processing method are correct, but where the amount of internal standard actually in one or more samples is different from the amount specified in the processing method.

Dilution Factor

Comment

This correction eliminates the necessity of remaking the samples to the internal standard concentrations or amounts specified in the processing method and re-running the samples.

For each component defined as an internal standard, you can apply a bulk adjustment factor to the base response of each internal standard defined in the processing method. If no correction is required, confirm that a value of 0.000 is entered in the Sequence Setup ISTD Corr Amt box. If a correction is required, enter the sum of all internal standard amounts or concentrations actually in the sample into the Sequence Setup

ISTD Corr Amt box for the sample row or rows requiring adjustment. The value entered uses the same units as specified in the processing method. Do not type the units into the box. For example, for 20 ng, type 20.

Specifies the dilution factor that was used to prepare the sample.

The valid range is 0.000 to 10 000.000. The data system interprets a value of 0.000 as no dilution. If for example, you type a value of 2 in the Dil Factor column for the Unknown sample types, the data system multiplies the calculated amount by a factor of 2.

To change the dilution factor, type a value in the Dil Factor box.

Use this box to add comments about the sample.

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Table 31. Sequence table parameters (Sheet 8 of 8)

Parameter

Sample Name

Heading 1

[Study]

Description

Specifies the sample name for the sample.

Use these columns to convey additional information about the sample to others or as a reminder to yourself.

Heading 2

[Client]

Heading 3

[Laboratory]

For information about changing the column heading labels, see

“Customizing the User Labels for a Sequence” on page 90 .

Heading 4

[Company]

Heading 5

[Phone]

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Sequence Setup Menus

Sequence Setup Menus

The menu bar of the Sequence Setup view contains the following menus from left to right:

File, Edit, Change, Actions, View, GoTo, and Help. This section describes the following menus:

“File Menu – Sequence Setup View,” on this page

“Edit Menu – Sequence Setup View” on page 212

“Change Menu – Sequence Setup View” on page 213

“Actions Menu – Sequence Setup View” on page 214

For information about the View, GoTo, and Help menus, see

“Home Page Menus” on page 168 .

File Menu – Sequence Setup View

Table 31

lists the File menu commands for the Sequence Setup view of the Home Page window.

Table 32. File menu – Sequence Setup commands (Sheet 1 of 2)

Icon or button

Command Description

New

Open

Opens the New Sequence Template dialog box that you use to create a new sequence.

Opens the Open dialog box that you use to open an existing sequence file.

Save

Save As

Opens the File Summary Information dialog box, where you can enter an auditable comment about the sequence. After you save the comment by clicking

OK, the Save As dialog box opens.

Opens the File Summary Information dialog box, where you can enter an auditable comment about the sequence. After you save the comment by clicking

OK, the Save As dialog box opens.

Summary Information Opens the File Summary Information dialog box, where you can view, change, or delete the comment about the current file.

Import Sequence Opens the Import Sequence dialog box that you can use to locate (drive and directory) and import one or more columns of a stored sequence.

Export Sequence

For more information, see “Import Sequence Dialog Box” on page 233

.

Opens the Export Sequence dialog box that you can use to export one or more columns of the current sequence to a new location and with a new name.

For more information, see “Export Sequence Dialog Box” on page 230 .

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Sequence Setup Menus

Table 32. File menu – Sequence Setup commands (Sheet 2 of 2)

Icon or button

Command

Change Dataset Name

Description

Opens the Dataset Name Selector dialog box. Use this dialog box to select a dataset name from a predefined list of names.

View Audit Trail

Print

Print Preview

Page Setup

Recently Used Files

Exit

The text of this menu item might be different if the administrator chose to use another name for a dataset. For example, this menu item might be Change Job

Name or Change Study Name.

For more information, see “Study Name Selector Dialog Box” on page 412

.

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

Opens the Print Selection dialog box that you can use to print a sequentially numbered vial position list from the current sequence, selected rows in a sequence, or currently displayed columns of the current sequence.

Opens the Print Selection dialog box. After you click OK to close the Print

Selection dialog box, the data system displays a preview of the text to be printed.

Opens the Page Setup dialog box, where you can select the following printing options: paper, orientation, margins, and printer.

View the paths and names of the four most recently used files. These are located above the Exit command. The Xcalibur data system displays both open and closed files. Click a displayed file to load it. If the selected file was closed, the data system opens it.

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

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Sequence Setup Menus

Edit Menu – Sequence Setup View

The Edit menu is available only in the Sequence Setup view of the Home Page window.

Table 33

describes the Edit menu commands.

Table 33. Edit menu commands

Button or icon

Command Description

Undo Cancels your previous action.

– Clear

Copy

Paste

Insert Row

Delete Row

Go To Row

Fill Down

Browse File

Name

Removes the text in selected sequence table cells or entire sequence rows. The data system clears the text from the selected boxes. When you clear and entire row, the data system replaces the previously selected sample type in the Sample Type column with the

Unknown sample type. For more information, see

“Using the Edit Commands” on page 86

.

Copies the selected rows or columns from the sequence to the Clipboard.

Pastes copied sequence rows or columns from the Clipboard to the sequence table.

Inserts a row above the selected row. For more information, see

“Using the Edit

Commands” on page 86 .

Deletes one or more adjacent rows from the sequence. For more information, see

“Using the Edit Commands” on page 86

.

Opens the Go to Row dialog box. Use this dialog box to move the cursor in the current sequence to a specified row number. This action is extremely useful when you are reviewing or modifying a long sequence. For more information, see

“Go To Line Number

Dialog Box” on page 233

and “Going to a Sequence Row” on page 91 .

Copies information from a sample row to a series of rows and avoid repetitive cut-and-paste operations.

For more information, see “Fill Down Dialog Box” on page 232

and “Filling Down

Sequence Parameters” on page 92 .

Depending on the selected file type, this command does the following:

• When you select a cell in the File Name column, this command opens the Select Data

File dialog box, where you can browse to and select a data file.

• When you select a cell in the Inst Meth column, this command opens the Select

Instrument Method dialog box, where you can browse to and select an instrument method.

• When you select a cell in the Proc Meth column, this command opens the Select

Processing Method dialog box, where you can browse to and select a processing method.

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Change Menu – Sequence Setup View

Table 34

describes the Change menu commands that are available in the Sequence Setup view of the Home Page window. This menu is not available from the other Home Page views.

Table 34. Change menu commands

Icon Command

User Labels

Description

Opens the User Labels dialog box, where you can change the column headings of five columns in the Sequence

Setup view. The default headings are Study, Client,

Laboratory, Company, and Phone.

– Tray Name

For more information, see “User Labels Dialog Box” on page 255 .

Opens the Tray Selection dialog box, where you can select the autosampler tray type for the current sequence. This dialog box is not available for all autosamplers.

For more information, see “Tray Selection Dialog Box” on page 254 .

Column Arrangement Opens the Column Arrangement dialog box, where you can select the columns that you want to display for the current sequence.

Transfer Row Info

For more information, see “Column Arrangement Dialog

Box” on page 228 .

Opens the Transfer Row Info dialog box. Use this dialog box to copy information from one sample row of the sequence to other rows in the sequence that have either the same position in the autosampler tray or the same sample ID.

For more information, see “Transfer Row Information

Dialog Box” on page 253 .

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Sequence Setup Menus

Actions Menu – Sequence Setup View

Table 35

describes the Actions menu commands for the Sequence Setup view of the Home

Page window.

Table 35. Actions menu – Sequence Setup commands (Sheet 1 of 4)

Icon

Command

Check Disk Space

Run This Sample

Run Sequence

Batch Reprocess

Open [Method] File

Description

Opens the Disk Space dialog box, where you can determine how much available disk space you have on a disk drive.

Opens the Run Sequence dialog box with a selection of one sequence row in the

Run Rows box. Use the Run Sequence dialog box to set up the run parameters.

Opens the Run Sequence dialog box with a selection all the sequence rows. Use the

Run Sequence dialog box to set up the run parameters.

Opens the Batch Reprocess dialog box, where you can set up the reprocessing options for the current sequence and start the batch reprocessing process.

Opens either an instrument method or a processing method selected from the sequence table in the Sequence Setup view.

• When you select an instrument method in the Inst Meth column of the sequence and then select this command, the data system opens the Instrument

Setup window and displays the selected file so that you can edit the parameters.

• When you select a processing method in the Proc Meth column of the sequence and then select this command, the data system opens the Processing

Setup window and displays the selected file so that you can edit the parameters.

This command is only active when you select an instrument method or a processing method.

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Table 35. Actions menu – Sequence Setup commands (Sheet 2 of 4)

Icon Command

Start Analysis

Description

Starts the sequence run manually.

By default, the Start When Ready check box is selected. If you want to make automated injections with an autosampler, do not clear this check box. For information about connecting the contact closure signal between the mass spectrometer and the autosampler, see the Getting Connected Guide for your mass spectrometer. For information about specifying the start instrument, see

“Running a Single Sample or Multiple Samples” on page 101

.

When you clear the Start When Ready check box in the Start Options area of the

Run Sequence dialog box, you must do one of the following to start each sample run:

• Choose Actions > Start Analysis in the menu bar.

Stop Analysis

–or–

• Click the Start Analysis icon, , in the toolbar.

Before you send the Start Analysis command, make sure that the data system is in the Ready state.

For more information, see “Starting Each Run Manually” on page 106 .

Stops the current sample run.

When you choose Stop Analysis, the following actions occur:

• The Pause/Resume Sequence Queue icon goes to the resume sequence queue state; that is, it appears depressed, .

• The data system immediately stops the current run and acquires the raw data file.

• On the Info view – Status page, the Sequence readback under Run Manager displays PAUSED.

To resume the sequence, click the Pause/Resume Sequence Queue icon,

The data system resumes the sequence at the next sample in the queue.

For more information, see “Stopping the Current Sample Run or Pausing the

Sequence Queue” on page 105

.

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Sequence Setup Menus

Table 35. Actions menu – Sequence Setup commands (Sheet 3 of 4)

Icon Command

Pause Analysis

Description

Pauses the current sequence after the current sample run ends.

When you choose Pause Analysis, the following actions occur:

• A check appears to the left of the Pause Analysis command.

• The Pause/Resume Sequence Queue icon goes to the resume sequence queue state; that is, it appears depressed, .

• The data system continues to acquire data for the current sample until the run time specified in the instrument method expires. At the end of the run, the data system acquires the raw data file.

• At the end of the current run, the data system enters the Paused state as indicated by the PAUSED text for the Sequence readback under Run Manager on the Information view – Status page.

To restart a paused sequence

Devices On

Devices Standby

The data system resumes the sequence with the next sample in the queue.

Places the system in the On state when the current sequence is completed. In this state, all power and flows are maintained at operational levels. Set the data system in the On state to run another sequence without waiting.

This option has the same effect as choosing the On option in the After Sequence

Set System area in the Run Sequence dialog box in the Sequence Setup view.

Places the system in the Standby state when the current sequence is completed. Set the data system in the Standby state to run another sequence with only a short delay of time. Depending on the instrument, this state turns gas and liquid flows off but maintains heaters and other subsystems in an On state so that there is no warm-up time required when you change to the On state.

This option has the same effect as choosing the Standby option in the After

Sequence Set System area in the Run Sequence dialog box.

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Table 35. Actions menu – Sequence Setup commands (Sheet 4 of 4)

Icon

Command

Devices Off

Description

Places the system in the Off state when the current sequence is completed. The Off state indicates that all power to the instrument that can be controlled by the data system is turned off. This action includes power to all heaters and most subassemblies, but in some cases it might not include all subassemblies.

This option has the same effect as choosing the Off option in the After Sequence

Set System area in the Run Sequence dialog box.

CAUTION The Off state does not guarantee that all voltages are turned off, nor does it indicate that all heated components are at room temperature. To perform maintenance on an instrument, refer to the hardware maintenance manual.

Automatic Devices On Sets the Xcalibur data system to automatically turn on all devices controlled by the data system before starting a data acquisition.

If this command has a check mark to its left, the data system automatically turns on all devices that are in the Off or Standby state.

Reinstate Warnings

If this command does not have a check mark to its left, the Xcalibur data system posts the following message if you have one or more devices in a Standby or Off state:

One or more devices to be used by this sequence are not ‘On’. The sequence will not start until all the requested devices are ready. Do you want all the devices to be switched ‘On’? Press ‘Yes’ to switch devices On, or ‘No’ to continue with devices in the ‘Off ’ or in ‘Standby’ state. If you select ‘No’ you will need to select the Devices On command from the Actions menu before the sequence will proceed.

Restores the display of messages that you have turned off by selecting the Don’t Ask

Again check box.

Periodically, the data system displays a message or dialog box that includes the following:

Don’t ask again.

If you select this option when you see it, the data system does not display this message again until you turn warnings back on using the Reinstate Warnings command.

To turn off warnings, select this check box:

Don’t ask again

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Sequence Editor Toolbar

Sequence Editor Toolbar

Table 36

lists the buttons in the Sequence Editor toolbar of the Home Page window.

Table 36. Sequence Editor toolbar buttons (Sheet 1 of 4)

Icon or

Button

Command Description

New Sequence

Open

Opens the New Sequence Template dialog box that you can use to create a new sequence.

Opens the Open dialog box that you use to open an existing sequence file.

Save

Print

Copy

Opens the File Summary Information dialog box, where you can enter an auditable comment about the sequence. After you save the comment by clicking OK, the

Save As dialog box opens.

Opens the Print Selection dialog box that you can use to print a sequentially numbered vial position list from the current sequence, selected rows in a sequence, or currently displayed columns of the current sequence.

Copies selected rows or columns from the sequence to the Clipboard.

Paste

Undo

Pastes copied sequence rows or columns from the Clipboard to the screen.

Cancels your previous action.

Fill Down Copies information from a sample row to a series of rows to avoid repetitive cut-and-paste operations.

For more information, see “Fill Down Dialog Box” on page 232

and “Filling Down

Sequence Parameters” on page 92 .

Browse File Name Depending on the selected file type, this command does the following:

• When you select a cell in the File Name column, this command opens the

Select Data File dialog box, where you can browse to and select a data file.

• When you select a cell in the Inst Meth column, this command opens the

Select Instrument Method dialog box, where you can browse to and select an instrument method.

• When you select a cell in the Proc Meth column, this command opens the

Select Processing Method dialog box, where you can browse to and select a processing method.

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Sequence Editor Toolbar

Table 36. Sequence Editor toolbar buttons (Sheet 2 of 4)

Icon or

Button

Command Description

User Labels Opens the User Labels dialog box, where you can change the column headings of five columns in the Sequence Setup view. The default headings are Study, Client,

Laboratory, Company, and Phone.

Column

Arrangement

For more information, see “User Labels Dialog Box” on page 255 .

Opens the Column Arrangement dialog box, where you can select the columns that you want to display for the current sequence.

For more information, see “Column Arrangement Dialog Box” on page 228

.

Transfer Row Info Opens the Transfer Row Info dialog box. Use this dialog box to copy information from one sample row of the sequence to other rows in the sequence that have either the same position in the autosampler tray or the same sample ID.

Disk Space

Run Sample

Run Sequence

Batch Reprocess

For more information, see “Transfer Row Information Dialog Box” on page 253 .

Opens the Disk Space dialog box, where you can determine how much available disk space you have on your disk drive or drives.

Opens the Run Sequence dialog box. If you do not select a sequence row before clicking this icon, the Run Rows box lists row 1. If you select a sequence row before clicking this icon, the Run Rows box lists the selected row number.

Opens the Run Sequence dialog box. If you do not select a range of sequence rows, the Run Rows box lists the entire sequence range. If you select a range of rows, the

Run Rows box lists the selected range.

Opens the Batch Reprocess Setup dialog box. If you do not select a range of sequence rows before clicking this icon, the Process Rows box lists the entire sequence range.

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Sequence Editor Toolbar

Table 36. Sequence Editor toolbar buttons (Sheet 3 of 4)

Icon or

Button

Command Description

Start Analysis Starts the sequence run manually.

By default, the Start When Ready check box is selected. If you want to make automated injections with an autosampler, do not clear this check box. For information about connecting the contact closure signal between the mass spectrometer and the autosampler, see the Getting Connected Guide for your mass spectrometer. For information about specifying the start instrument, see

“Running a Single Sample or Multiple Samples” on page 101

.

When you clear the Start When Ready check box in the Start Options area of the

Run Sequence dialog box, you must do one of the following to start each sample run:

• Choose Actions > Start Analysis in the menu bar.

Stop Analysis

–or–

• Click the Start Analysis icon, , in the toolbar.

Before you send the Start Analysis command, make sure that the data system is in the Ready state.

For more information, see “Starting Each Run Manually” on page 106 .

Stops the current sample run.

When you click the Stop Analysis icon, the following actions occur:

• The Pause/Resume Sequence Queue icon goes to the resume sequence queue state; that is, it appears depressed, .

• The data system immediately stops the current run and acquires the raw data file.

• On the Info view – Status page, the Sequence readback under Run Manager displays PAUSED.

To resume the sequence, click the Pause/Resume Sequence Queue icon,

The data system resumes the sequence at the next sample in the queue.

For more information, see “Stopping the Current Sample Run or Pausing the

Sequence Queue” on page 105

.

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Sequence Editor Toolbar

Table 36. Sequence Editor toolbar buttons (Sheet 4 of 4)

Icon or

Button

Command Description

Pause/Resume

Sequence Queue

Pauses the current sequence after the current sample run ends.

When you click the Pause/Resume Sequence Queue icon, the following actions occur:

• A check appears to the left of the Pause Analysis command.

• The Pause/Resume Sequence Queue icon goes to the resume sequence queue state; that is, it appears depressed, .

• The data system continues to acquire data for the current sample until the run time specified in the instrument method expires. At the end of the run, the data system acquires the raw data file.

• At the end of the current run, the data system enters the Paused state as indicated by the PAUSED text for the Sequence readback under Run Manager on the Information view – Status page.

Help

To restart a paused sequence

Click .

The data system resumes the sequence with the next sample in the queue. You can review the sample list queue at any time using the Acquisition Queue page of the

Home Page Information view.

Opens Xcalibur Help and displays the contents window for the Sequence Setup view.

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Sequence Setup View Dialog Boxes

You can open these dialog boxes in the Sequence Setup view. This list is in alphabetical order.

Batch Reprocess Setup Dialog Box

Change Instruments In Use Dialog Box

Column Arrangement Dialog Box

Export Sequence Dialog Box

Fill Down Dialog Box

Go To Line Number Dialog Box

Import Sequence Dialog Box

New Sequence Template Dialog Box

Page Setup Dialog Box

Print Selection Dialog Box

Run Sequence Dialog Box

Transfer Row Information Dialog Box

Tray Selection Dialog Box

User Labels Dialog Box

Batch Reprocess Setup Dialog Box

Use the Batch Reprocess Setup dialog box to select batch processing settings for the sequence rows displayed in the Process Rows box. You can use the check boxes to activate options in the processing method. Whether you are processing or reprocessing the data, the results are the same. This user guide refers to processed data whether the action is processing or reprocessing.

The Xcalibur data system requires that you select a valid processing method for each sample that you want to include in the batch reprocess. To change the processing method, double-click the Proc Meth [Processing Method] column for the sample row of interest. The

Select Processing Method dialog box opens so that you can browse to and select a processing method for batch processing. If you do not select a valid processing method, the data system posts a message describing the problem.

For information about using the Batch Reprocess Setup dialog box, see “Batch Reprocessing a

Sequence” on page 116

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This table describes the parameters in the Batch Reprocess Setup dialog box.

Table 37. Batch Reprocess Setup dialog box (Sheet 1 of 3)

Parameter

Process Rows

Process Rows

Description

Specifies the sequence rows that have been selected for batch processing. To change the range, either select the rows in the sequence before opening the Batch Reprocess Setup dialog box or type the sample (row number) or sample range (first row through last row) in the Process Rows box using the following format:

FirstRowNumber–LastRowNumber. For example, to process sample rows 10 through 22, type10–22.

Processing Actions

Quan

Peak Detection &

Integration

(Quan)

Selecting this check box enables these check boxes for quantitative processing: Peak Detection & Integration, Calibration, and

Quantitation processing.

Selecting this check box turns on peak detection and integration processing for the samples selected from the current sequence and displayed in the Process Rows box.

Calibration

(Quan)

Define the peak detection and integration parameters in the quantitative section of the processing method.

The sequence must include a valid processing method and valid raw data files.

Selecting this check box turns on calibration processing for the samples selected from the current sequence and displayed in the

Process Rows box.

Quantitation

(Quan)

The processing method defines the calibration settings.

To update the calibration during batch reprocessing, the selected sequence rows must include a valid processing method, valid raw data files, and the appropriate calibration level selections in the

Level column of the sequence table.

Selecting this check box turns on quantitation processing for the samples selected from the current sequence and displayed in the

Process Rows box.

The processing method defines the quantitative processing parameters.

For quantitative processing, the selected sequence rows must include a valid processing method and valid raw data files.

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Table 37. Batch Reprocess Setup dialog box (Sheet 2 of 3)

Parameter

Qual

Peak Detection &

Integration

(Qual)

Description

Selecting this check box makes the following check boxes available for qualitative processing: Peak Detection & Integration,

Spectrum Enhancement, and Library Search.

Selecting this check box turns on peak detection and integration for the samples selected from the current sequence and displayed in the Process Rows box.

Spectrum

Enhancement

(Qual)

Library Search

(Qual)

Define these parameters in the qualitative section of the processing method.

For qualitative processing, the selected sequence rows must include a valid processing method and valid raw data files.

Selecting this check box turns on spectrum enhancement processing for the samples selected from the current sequence and displayed in the Process Rows box.

Set up spectrum enhancement in the processing method by

defining the parameters on the Spectrum Enhancement Page for

Qual View in the Processing Setup window.

To perform spectrum enhancement, the selected sequence rows must include a valid processing method and valid raw data files.

Selecting this check box turns on library searches for the samples selected from the current sequence and displayed in the Process

Rows box.

Set up library searches in the processing method by defining the

library search parameters on the Library Search Constraints Page for Qual View

in the Processing Setup window.

Reports

To run library searches, the selected sequence rows must include a valid processing method and valid raw data files.

Selecting this check box makes these check boxes available: Print

Sample Reports and Print Summary Reports.

Print Sample Reports Selecting this check box turns on printing for sample reports.

Set up sample reports in the processing method by defining the sample report parameters in the Reports view of the Processing

Setup window.

To print sample reports, the selected sequence rows must include a valid processing method and valid raw data files.

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Table 37. Batch Reprocess Setup dialog box (Sheet 3 of 3)

Parameter

Print Summary

Reports

Description

Selecting this check box turns on printing for summary reports.

Set up summary reports in the processing method by defining the summary report parameters in the Reports view of the Processing

Setup window.

Programs

To print summary reports, the selected sequence rows must include a valid processing method and valid raw data files.

Selecting this check box turns on the Programs that the processing method specifies.

Create Quan Summary

Spreadsheet

Running programs requires a valid processing method.

When you select this check box, the data system creates a spreadsheet that you can open in Excel after batch reprocessing is complete.

Advanced Options

Replace Sample Info Selecting this check box removes sequence data in the raw data files and replaces it with the active sequence data

To use the data in the current raw file, make sure the check box is clear.

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Change Instruments In Use Dialog Box

Use the Change Instruments In Use dialog box to select the instruments that you are using to run the current sequence and the start instrument that triggers data acquisition for each run.

If you change the Foundation instrument configuration after running the previous sequence, this dialog box automatically appears.

For more information about using the Change Instruments In Use dialog box, see “Running a

Single Sample or Multiple Samples” on page 101 .

To add an instrument to the list

1. Click Cancel to close the Change Instruments In Use dialog box.

2. Close down all running Xcalibur programs.

3. Choose Start > Programs > Thermo Foundation x.x > Instrument Configuration.

The Instrument Configuration view opens.

4. Select and configure the instrument.

When you reopen the Change Instruments In Use dialog box, the newly configured instrument appears on the Instrument list.

To select the start instrument

1. In the row of the instrument that you want to use as the start instrument, click the Start

Instrument column to change the blank entry to Yes.

2. Click OK to accept the changes and close the dialog box.

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This table describes the columns in the Change Instruments in Use dialog box.

Table 38. Change Instruments In Use dialog box parameters

Parameter

Instrument

Description

Displays the list of instruments that have been configured for operation as Xcalibur devices.

In Use

Start Instrument

To change the entries in the Instrument column, you must use the

Instrument Configuration window.

Specifies whether the instrument is in use for this sequence run.

The rows in this list display either Yes (in use) or a blank entry

(not in use). When you configure an instrument using the

Instrument Configuration window, its default status is Yes. If you do not want to use the instrument for the current sequence run, click the Yes entry to change it to a blank entry. Instruments with a blank entry are not available for the current sequence.

For example, if a sample is to be manually injected by syringe into a mass spectrometer or MS detector, the In Use entries for all instruments, except the mass spectrometer or MS detector, must be blank.

Specifies the Start Instrument.

This list can either have one Yes in one of the instrument rows or all blanks for all instrument rows (no Yes entries).

The autosampler is usually selected to be the Start Instrument because this is the instrument that controls when a run starts. In this case, a Yes appears for all instruments to be used for the sequence submission, including the autosampler, because they are waiting for a contact closure event to start operation. When all devices used in the run achieve this status, the Start Instrument initiates the run.

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Sequence Setup View Dialog Boxes

Column Arrangement Dialog Box

Use the Column Arrangement dialog box to select which columns to display and the position or order of the columns in the current sequence.

This table describes the parameters in the Column Arrangement dialog box. For information about using the Column Arrangement dialog box, see

“Adding, Removing, and Arranging the

Sequence Columns” on page 88 .

This table describes the parameters in the Column Arrangement dialog box.

Table 39. Column Arrangement dialog box parameters (Sheet 1 of 2)

Parameter

Available Columns

Description

Displays the columns that do not currently appear in the

Sequence Setup view but that you can add. Possible columns include the following:

• Sample Type

• File Name

• Sample ID

• Path

• Inst Meth

• Proc Meth

• Position

• Inj Vol

• Cal File

• Level

• Sample Wt

• Sample Vol

• ISTD Corr Amt

• Dil Factor

• Comment

• SampleName

• User Labels 1-5

Displayed Columns

To set up the User Labels column heading, use the

User

Labels Dialog Box

.

Displays the columns that currently appear in the

Sequence

Setup View Features . The left-to-right order of the columns

for a particular sequence corresponds to the top-to-bottom order in the Displayed Columns list.

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Table 39. Column Arrangement dialog box parameters (Sheet 2 of 2)

Parameter

Buttons

Add

Description

Remove

Move Up

To add a column to the sequence, select the column in the

Available Columns list box. Click Add to move the column name to the Displayed Columns list. The Sequence Setup view displays the columns listed in the Displayed Columns list.

To remove a sequence column from the current display, select the column from the Displayed Columns list. Click Remove to move the column name to the Available Columns list.

To change the column order in the current sequence, click

Move Up and Move Down. To move a displayed column to the left in the sequence, select the column in the Displayed

Columns list, and click Move Up.

Move Down

The data system displays only the columns that are listed in the Displayed Columns list. The left-to-right order of the columns for a particular sequence corresponds to the top-to-bottom order in the Displayed Columns list.

To change the column order in the current sequence, click

Move Up and Move Down. To move a displayed column to the right in the sequence, select the column in the Displayed

Columns list, and click Move Down.

The data system displays only the columns that are listed in the Displayed Columns list. The left-to-right order of the columns for a particular sequence corresponds to the top-to-bottom order in the Displayed Columns list.

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Export Sequence Dialog Box

Use the Export Sequence dialog box to select the columns of the sequence that you want to export and to designate the path and file name of the exported file. The Xcalibur data system creates an exported comma-separated-value text file with a (.csv) file extension by inserting a column separator character between each sequence field. This file format can be read by a text editor program or a spreadsheet program.

The list separator character used for an exported sequence file is specified in the Regional

Options page of the Settings Properties dialog box.

To change the list separator character

1. Choose Start > Settings > Control Panel.

The Control Panel window opens.

2. Double-click Regional and Language Options.

The Regional and Language Options dialog box opens.

3. On the Regional Options page, click Customize. Click the Numbers tab.

4. Type a comma in the List Separator box.

Each country has a default list separator. For example, the list separator for the United States is the comma. In this case, the data system places a comma between each sequence field in the exported file. You can change the list separator to any alphanumeric character. However, avoid using characters that cannot be distinguished from characters used in the sequence text fields, such as alphabetic characters, because they result in unreadable (invalid) files. The most common list separators are the comma (,) and the semicolon (;).

Because you can modify the Study, Client, Laboratory, Company, and Phone columns using the User Labels dialog box, the data system changes these fields in the exported file to User

Label 1, User Label 2, User Label 3, User Label 4, and User Label 5, respectively.

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The Export Sequence dialog box provides check boxes so that you can include any, all, or none of the sequence columns.

For more information about using the Export Sequence dialog box, see

“Exporting a

Sequence” on page 127

.

This table describes the parameters in the Export Sequence dialog box.

Table 40. Export Sequence dialog box parameters

Parameter

Export to File

Description

Specifies the destination path and file name for the exported file. The data system saves the file with a (.csv) extension.

Select Columns to Export This area contains check boxes that correspond to columns in

the Sequence Setup View Features . To include the data in a

column, select the corresponding check box. You can choose from the following columns:

• Sample Type

• File Name

• Sample ID

• Path

• Inst Meth

• Proc Meth

• Position

• Inj Vol

• Level

• Sample Wt

• Sample Vol

• ISTD Corr Amt

• Dil Factor

• Comment

• Sample Name

• User Labels 1-5

All

Clear

Click All to select all the check boxes.

Click Clear to clear all the check boxes.

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Fill Down Dialog Box

Use the Fill Down dialog box to fill selected rows of selected columns with duplicate text entries or appropriately sequenced number entries. Select the cells in the row that you want to copy from as well as all of the cell rows that you want to copy to. The Xcalibur data system highlights the cells that you select.

For information about using the Fill Down dialog box, see “Filling Down Sequence

Parameters” on page 92

.

Note The rows that you select must be contiguous (neighboring rows in the sequence).

The row that you want to copy from must be the top row of the cells selected. The Fill

Down command on the Edit menu and the Fill Down icon in the toolbar become available.

The data system performs its fill down function on any sequence columns or headings that you select.

This table describes the parameters in the Fill Down dialog box.

Table 41. Fill Down dialog box parameters

Parameter

Select Columns

Description

This area lists the sequence columns. When you make a selection in the sequence table and click the Fill Down icon in the toolbar or choose Edit > Fill Down from the menu bar, the Fill Down dialog box opens with the check boxes for the corresponding column selected. You can change the selection by selecting or clearing the check boxes.

Click All to select all the check boxes.

All

Clear

Fill Rows X to __ using row Y

Click Clear to clear all the check boxes.

This box indicates which row you are using to fill down (Y) and which rows will be filled (X to the value that you enter).

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Go To Line Number Dialog Box

Use the Go To Line Number dialog box to go to a specified row of the current sequence. This feature is extremely useful if you are reviewing or modifying a long sequence.

This table describes the parameters in the Go To Line Number dialog box.

Table 42. Go To Line Number dialog box parameters

Parameter

Row

Description

Type the row number of the sequence that you want to display. To move to a specific row, type the row number (the number of the leftmost column of the sequence) in the Row box, and click OK.

The data system moves the focus to the selected row.

Import Sequence Dialog Box

Use the Import Sequence dialog box to select the columns of the sequence that you want to import and to designate the path and file name of the imported file. The Xcalibur data system only reads comma-separated-value text files with a (.csv) file extension. This file format can be read by a text editor program or a spreadsheet program. If you try to import any other file extension or file type, the data system generates an invalid file message.

In addition, the list separator character used in the file that you import must be the same as the current list separator character set in your computer operating system.

Each country has a default list separator. For example, the default list separator for the United

States is the comma. In this case, the data system places a comma between each sequence field in the exported CSV file. You can change the list separator to any alphanumeric character.

However, avoid using characters that cannot be distinguished from the characters used in the sequence text fields, such as alphabetic characters, because they result in unreadable (invalid) files. The most common list separators are the comma (,) and the semicolon (;).

Use the Import From File box or the Browse button to designate the path and file name of the imported sequence file.

The Import Sequence dialog box provides check boxes so that you can include any, all, or none of the sequence columns in the imported list. Click All to select all the column check boxes. Click Clear to clear all the column check boxes.

For information about checking the list separator, see

“Changing the List Separator

Character” on page 123

. For more information about using the Import Sequence dialog box, see

“Importing a Sequence” on page 125 .

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This table describes the parameters in the Import Sequence dialog box.

Table 43. Import Sequence dialog box parameters

Parameter Description

Import From File Specifies the path and file name of the imported CSV file.

Select Columns to Import This area contains check boxes that correspond to columns in the

Sequence Setup View Features . To include the data in a column,

select the corresponding check box. You can choose from the following columns:

• Sample Type

• Name

• Sample ID

• Path

• Inst Meth

• Proc Meth

• Position

• Inj Vol

• Level

• Sample Wt

• Sample Vol

• ISTD Corr Amt

• Dil Factor

• Comment

• Sample Name

• User Labels 1-5

All

Clear

Click All to select all the check boxes.

Click Clear to clear all the check boxes.

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New Sequence Template Dialog Box

The New Sequence Template dialog box provides a quick and simple way to create a new sequence. Select the following options in the General, Samples, Bracket Type, Calibration, and QC areas. The Xcalibur data system creates a new sequence for you and displays it in the

Sequence Setup View Features .

For information about using the New Sequence Template dialog box to create a sequence

semi-automatically, see “Creating a Sequence Semi-Automatically” on page 69 .

This table describes the parameters in the New Sequence Template dialog box.

Table 44. New Sequence Template dialog box parameters (Sheet 1 of 9)

Parameter

General

Base File Name

Description

Starting Number

Path

Specifies the base file name that the data system uses when it creates the raw file for the sequence. The data system places additional information describing a specific sample at the end of this name so that each sample in your list has a unique identification. This file is stored in the location defined in the

Path box. To assign a base file name that is used for all samples in the new sequence, type the name in the Base File Name box.

Type a number for the data system to add as a suffix to the name you entered into the Base File Name box. The file name of the raw data files consists of the base file name and the starting number suffix. For example, if the Base File Name is ABC and you enter

50 into the Starting Number box, the data system creates the new sequence with File Name ABC50 as the first file name.

Specifies the path to the raw data files. A path contains the drive and one or more folders. A typical path can look like

C:\Xcalibur\DATA.

To find and select the path, double-click Browse to the right of the Path box. The Select Data Directory dialog box opens. The data system enters the path in the Path box. You can also type the path in the Path box.

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Table 44. New Sequence Template dialog box parameters (Sheet 2 of 9)

Parameter

Instrument Method

Description

Specifies the path and instrument method for the samples in the sequence. A path contains the drive and one or more folders. A typical path for an instrument method file named ABC can look like C:\Xcalibur\methods\ABC.meth.

Processing Method

Calibration File

To find and select the path, double-click Browse to the right of the Instrument Method box. The Select Instrument Method dialog box opens. The data system enters the path and file name in the Inst Method box for you. You can also type the path and file name in the Instrument Method text box.

Specifies the path and processing method for the samples in the sequence. A path contains the drive and one or more folders. A typical path for a processing method file named ABC can look like

C:\Xcalibur\methods\ABC.

To find and select the path, double-click Browse to the right of the Processing Method box. The Select Processing Method dialog box opens. The data system enters the path and file name in the

Processing Method box. You can also type the path and file name in the Processing Method box.

Specifies the location for the calibration file. This box is only active if you select the None option in the Bracket Type area. If you select None as a bracket type, a Calibration File column is included in the sequence. This column contains the full path and name of the current default calibration file. A path contains the drive and one or more directories. A typical path for a calibration file named ABC can look like this C:\Xcalibur\methods\ABC.

Enter the path and file name of the calibration files that you want to use to process the samples in the current sequence using bracket type None.

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Table 44. New Sequence Template dialog box parameters (Sheet 3 of 9)

Parameter

Calibration File

(continued)

Description

To use a calibration file, follow these procedures:

To append the new calibration data to a previously created calibration file

1. Click Browse located to the right of the Calibration File box.

The Select Calibration File dialog box opens.

2. From this dialog box, browse to the calibration file.

3. Click OK.

The data system enters the path and file name (without the file extension) in the Calibration File box. When you create a new sequence, the data system includes this path and calibration file name in the Cal File column of the sequence.

To display the calibration file column

1. Choose Change > Column Arrangement.

2. In the Available Columns list, select Cal File. Then click Add.

3. Click OK to close the dialog box.

To create a new calibration file

Type the path and calibration file name that you want the data system to create during batch processing. Do not include the

(.xcal) file extension.

Samples

Number of Samples Specifies the number of Unknown samples for the data system to include in the new sequence. The data system divides and orders these samples among the number of calibration sets or brackets that you select. For example, if you specify two calibration sets and five samples, The data system orders the new sequence as follows:

• Calibration Standard Samples (Set 1)

• Unknowns (3 Samples)

• Calibration Standard Samples (Set 2)

• Unknowns (2 Samples)

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Table 44. New Sequence Template dialog box parameters (Sheet 4 of 9)

Parameter Description

Tray Type Specifies the tray type that must be installed in your autosampler when the current sequence is used. To change the tray type, click the arrow to display the list of vial tray type options. Select one of the vial tray types. The data system displays your new selection in the Tray Type list.

Injections Per Sample Specifies the number of replicate injections per sample position.

Initial Vial Position Specifies the first vial position in the new sequence.

The vial or microwell plate notation depends on the configured autosampler. The default position is the first position for the configured vial tray or microwell plate.

To start at another position, do one of the following:

• Type the position in the Initial Vial Position box.

• Interactively select the position as follows (not available for some autosamplers): a. Click Select Vials to open the Vial Selection dialog box. b. Select the initial vial position by clicking the graphic. c.

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

d. Click Cancel to make the Number of Samples box available.

Re-Use Vial Numbers Specifies whether to reuse the vial positions for replicate samples.

If you select the Re-Use Vial Positions check box, the data system creates a sequence where the replicate Calibration, QC, Blank, and Unknown samples are drawn from the same vial. If you clear the Re-Use Vial Positions check box, the data system creates a sequence in which each sample is drawn from a different vial.

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Table 44. New Sequence Template dialog box parameters (Sheet 5 of 9)

Parameter

Base Sample ID

Description

Specifies the prefix for the sample identification. Type an alphanumeric prefix in the Base Sample ID box that the data system applies to each sample in the new sequence. If the instrument configuration includes an autosampler, the data system appends the row position to the sample ID prefix and starts sample ID numbering at the initial vial position. For example, if you type Assay in the Base Sample ID box, and the initial vial position for the sequence is A:1, the data system numbers the first five samples as follows:

• AssayA:1

• AssayA:2

• AssayA:3

• AssayA:4

• AssayA:5

Bracket Type

None If you select this option, the data system creates a sequence with no brackets. The Xcalibur data system processes the samples in the sequence in the order they are submitted. Real-time samples are processed before reprocessed samples. The data system orders your

Unknown, Blank (optional), Calibration (optional), and QC

(optional) samples in the following repetitive sequence:

• Calibration Blank Sample

• Calibration Samples

• Calibration Blank Sample

• QC Samples

• QC Blank Sample

• Unknown Samples

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Table 44. New Sequence Template dialog box parameters (Sheet 6 of 9)

Parameter

Open

Description

If you select this option, the data system creates a sequence with one open bracket. You can place samples and calibrants in any order. Calibration samples are processed before Unknown and QC samples. The data system orders your Unknown, Blank (optional),

Calibration (optional), and QC (optional) samples in the following repetitive sequence:

• Blank Sample

• Calibration Samples

Non-Overlapped

• Blank Sample

• QC Samples

• QC Blank Sample

• Unknown Samples

• Calibration Blank Sample

• Calibration Samples

• Calibration Blank Sample

If you select this option, the data system creates a sequence with one or more non-overlapped brackets. The data system orders your Unknown, Blank (optional), Calibration (optional), and QC

(optional) samples in the following repetitive sequence:

• Calibration Blank Sample

• Calibration Samples

• Calibration Blank Sample

• QC Samples

• QC Blank Sample

• Unknown Samples

• Calibration Blank Sample

• Calibration Samples

• Calibration Blank Sample

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Table 44. New Sequence Template dialog box parameters (Sheet 7 of 9)

Parameter

Overlapped

Description

If you select this option, the data system creates a sequence with one or more overlapped brackets. The data system orders your

Unknown, Blank (optional), Calibration (optional), and QC

(optional) samples in the following repetitive overlapping-bracket sequence:

• Calibration Blank Sample [Bracket 1]

• Calibration Samples [Bracket 1]

• Calibration Blank Sample [Bracket 1]

• QC Samples [Bracket 1]

• QC Blank Sample [Bracket 1]

• Unknown Samples [Bracket 1]

• Calibration Blank Sample [Bracket 1, 2]

• Calibration Samples [Bracket 1, 2]

• Calibration Blank Sample [Bracket 1,2]

• QC Samples [Bracket 2]

• QC Blank Sample [Bracket 2]

• Unknown Samples [Bracket 2]

• Calibration Blank Sample [Bracket 2, 3]

• Calibration Samples [Bracket 2, 3]

• Calibration Blank Sample [Bracket 2, 3]....

Calibration

Add Standards Selecting this check box makes the parameters in the Calibration area available and the data system adds calibration standards to the sequence table. When you select this check box, you must also select a processing method that contains defined calibration levels.

If you select the Add Standards check box without selecting a valid processing method for the sequence, the data system displays a warning message when you click OK to close the dialog box and creates a sequence with only Unknown sample types.

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Table 44. New Sequence Template dialog box parameters (Sheet 8 of 9)

Parameter

Number of Calibration

Sets

This box is available when you select the None option in the

Bracket Type area. Type the number of calibration sets that you want in your new sequence. The valid range of values is 1 to 10.

Number of brackets

Description

This box is available when you select the Non-Overlapped option or the Overlapped option in the Bracket Type area. Enter the number of brackets that you want in your new sequence. The valid range of values is 1 to 10.

Injections Per Level

Add Blanks

Fill In Sample ID for

Standards

Specifies the number of replicate calibration standard samples that are to be run at each defined calibration level. The data system groups replicate calibration samples in the new sequence. The valid range of values is 1 to 10.

Selecting this check box add blanks to your sequence. If you select this check box, the data system places one blank before and one blank after each series of calibration standard samples in the new sequence.

If you select this check box, the data system populates the Sample

ID column in the new sequence for each standard sample type. If you type a name in the Base Sample ID box in the Samples area, the data system uses the name as the prefix and the vial position as the suffix to provide a sample ID for the standard samples. If you leave the Sample ID box empty, the data system uses the vial position to provide a sample ID for the standard samples. If you clear this check box, the data system leaves the Sample ID column empty for standard sample types. By default, the Fill In Sample ID for Standards check box is selected.

QC

Add QCs

After First Calibration

Only

Selecting this check box makes the parameters in the QC area available, and the data system adds QC samples to the sequence table. When you select this check box, you must also select a processing method that contains defined QC levels. If you select the Add QCs check box without selecting a valid processing method for the sequence, the data system displays a warning message when you click OK to close the dialog box and creates a sequence without QC levels.

When you select this option, the data system adds a quality control sample only after the first group of calibration samples in the new sequence. The data system does not follow subsequent calibration sample sets with a quality control sample. This option is available if you select the Add QCs check box.

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Table 44. New Sequence Template dialog box parameters (Sheet 9 of 9)

Parameter

After Every Calibration When you select this option, the data system adds a quality control sample after every calibration sample set in the new sequence. This option is available if you select the Add QCs check box.

Add Blanks

Description

Fill In Sample ID for

QCs

Selecting this check box adds Quality Control (QC) blanks to your sequence. If you select this check box, the data system places one blank after each series of quality control samples in the new sequence.

If you select this check box, the data system populates the Sample

ID column in the new sequence for each QC sample type. If you type a name in the Base Sample ID box in the Samples area, the data system uses the name as the prefix and the vial position as the suffix to provide a sample ID for the QC samples. If you leave the

Sample ID box empty, the data system uses the vial position to provide a sample ID for the QC sample types. If you clear this check box, the data system leaves the Sample ID column empty for QC sample types. By default, the Fill In Sample ID for QCs check box is selected.

Page Setup Dialog Box

Use the Page Setup dialog box to set up the page layout for reports printed from the Qual

Browser window, Sequence Setup view, or the XReport application.

The page setup settings for the Qual Browser window, Sequence Setup view, and XReport application are independent of each other.

Figure 90 shows the Page Setup dialog box that opens from the Qual Browser window or the

Sequence Setup view.

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Sequence Setup View Dialog Boxes

Figure 90. Page Setup dialog box

To open the Page Setup dialog box

Do one of the following:

• From the menu bar of the Qual Browser window, Sequence Setup view, or XReport application, choose File > Page Setup.

–or–

• In the XReport application, set up the page breaks for the report template as follows: i.

Drag the Page Break object to the template pane. ii. Right-click the Page Break object and choose Properties from the shortcut menu.

The Page Setup dialog box opens.

To setup the print properties

1. Open the Page Setup dialog box.

2. Set up the following properties: a. In the Paper area, do the following:

• Select the paper size.

• Select the paper source.

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Sequence Setup View Dialog Boxes b. In the Orientation area, select the Portrait or Landscape option.

c.

In the Margins area, type the appropriate margins in the Left, Right, Top, and

Bottom boxes.

The range of valid values depends on the paper size and page orientation.

d. (XReport only) In the Heights area, do the following:

• Type the appropriate value for the placement of the header in the Header box.

• Type the appropriate value for the placement of the footer in the Footer box.

As you change the properties, the graphic at the top of the dialog box displays the effect of the changes.

3. Click OK to accept the changes and return to the template pane.

Table 45

describes the parameters in the Page Setup dialog box.

Table 45. Page Setup dialog box parameters

Parameter

Paper

Size

Description

Specifies the paper size for printing.

Source

Default selection: Letter

Specifies the paper source. Some printers have multiple paper trays.

Default selection: Automatically Select

Orientation

Portrait

Landscape

Margins (inches)

Selecting this option prints pages vertically.

Selecting this option prints pages horizontally.

Left, Right, Top, and

Bottom

Adjusts the space between the edge of the document and the corresponding edge of the page.

Heights (inches) XReport application only

Header

Footer

Buttons

Specifies the distance of the header from the top of the page.

Specifies the distance of the footer from the bottom of the page.

OK

Cancel

Accepts the new settings and closes the dialog box.

Cancels the new settings and closes the dialog box.

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Print Selection Dialog Box

Use the Print Selection dialog box to print a vial or sequence list. For information about using the Print Selection dialog box, see

“Printing a Vial or Sequence List” on page 95

.

This table describes the parameters in the Print Selection dialog box.

Table 46. Print Selection dialog box parameters

Parameter

Select the Printing Output

Description

Vial Position List

All Columns

Displayed Columns

Only

Select this option to print a sequentially numbered vial position list from the active sequence. The vial position list summarizes the sequence settings for each vial. A vial position list is useful when you are setting up the autosampler tray vial sequence.

Select this option to print selected rows in a sequence.

Select this option to print the currently displayed columns of the active sequence.

To change the sequence columns displayed, choose Change >

Column Arrangement.

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Run Sequence Dialog Box

Use the Run Sequence dialog box to select acquisition options and processing action options for the sequence.

The list of rows selected from the sequence must be consecutive. For example, you can run samples 1 through 10 by using the Run Sequence dialog box once. To skip sample 4, run samples 1 through 3 and samples 5 through 10 by using the Run Sequence dialog box twice.

The first time, select samples 1 through 3. The second time, select samples 5 through 10.

For more information about using the Run Sequence dialog box, see “Running a Single

Sample or Multiple Samples” on page 101 . For information about modifying the instrument

configuration, see “Setting Up the Instrument Configuration in the Foundation Platform” on page 157 .

This table describes the parameters in the Run Sequence dialog box.

Table 47. Run Sequence dialog box parameters (Sheet 1 of 6)

Parameter

Acquisition Options

Instrument

Description

Start Instrument

(read-only)

Displays the instruments that you configured for operation as

Xcalibur devices in the Instrument Configuration window of the

Foundation platform.

A Yes in this column specifies that the instrument starts the run.

For an LC/MS system, the Start Instrument is typically the autosampler because the autosampler triggers data acquisition when it injects the sample into the chromatograph.

Start When Ready

You can change the start instrument and the instruments in use by

opening the Change Instruments In Use Dialog box (see “Change

Instruments In Use Dialog Box” on page 226 ).

Determines whether the Xcalibur data system automatically starts a sequence run when the instruments are in the Ready state. By default, this check box is selected. Clear this check box if you want to start the sequence run manually.

When the Start When Ready check box is selected, the data system places the sequence in the processing queue as soon as you click OK and starts each sequence run when the instruments are in the Ready state.

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Table 47. Run Sequence dialog box parameters (Sheet 2 of 6)

Parameter

Start When Ready

(continued)

Description

If you clear the Start When Ready check box, the data system waits until you do one of the following to start each sequence run:

• Click the Start Analysis icon, .

–or–

Change Instruments

Choose Actions > Start Analysis.

Opens the Change Instruments In Use dialog box, where you can change the status of the instruments in use or select a different start instrument.

Instrument Method

Start Up/Browse

Shut Down/Browse

Specifies the instrument method (METH) file that runs before the sequence run starts.

Specifies the instrument method (METH) file that runs after the sequence run finishes.

Programs

Pre Acquisition/

Browse

Post Acquisition/

Browse

Run Synchronously

Specifies the executable (EXE or BAT program) that runs before data acquisition.

Specifies the EXE or BAT program that runs after data acquisition.

Run Pre Acquisition and Post Acquisition programs either synchronously (in series) or asynchronously (in parallel) with data acquisition.

To run programs synchronously, the Run Manager waits until they can be run before acquisition, after acquisition, or both.

To run programs asynchronously, the Xcalibur data system runs the program at the same time as data acquisition. For example, you can perform file conversions with XConvert.exe while you are taking data. In this case, the Pre Acquisition and Post Acquisition terminology does not apply.

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Table 47. Run Sequence dialog box parameters (Sheet 3 of 6)

Parameter

Pre Acquisition/ Post

Acquisition

Description

Runs the Pre Acquisition program displayed in the Pre Acquisition box either synchronously (in series) or asynchronously (in parallel) with data collection.

If you select the Pre Acquisition check box, the data system runs the program synchronously. In this case, the Run Manager waits until data system can run the Pre Acquisition program before data acquisition. For example, to switch the divert valve before a run, you can select a synchronous Pre Acquisition program; or, to convert data from one data type to another data type while you are acquiring data, you can program and select a Post Acquisition program.

If you clear the Pre Acquisition check box, the data system runs the program asynchronously. For example, you can use the

XConvert.exe program to perform file conversions from one data type to another data type during processing. If the Post

Acquisition check box is clear, the program displayed in the Post

Acquisition box is run asynchronously. For example, you can perform operations that do not involve taking data.

To change the current program or macro name in the command line, double-click the Program or Macro Name box to open the

Open dialog box and select a program or macro. The data system displays the new program or macro name. You can also type the command line.

You can use the following macros in the command line:

%R: Provides the current raw file

%I: Provides the instrument method name

%S: Provides the sequence name

%V: Provides the vial (or well) number in the Position column of the sequence

%%: Provides a single % character in the run line

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Table 47. Run Sequence dialog box parameters (Sheet 4 of 6)

Parameter

Pre Acquisition/ Post

Acquisition

(continued)

Description

You can run the XConvert.exe program during a sequence run.

To convert the current file (myfile.raw) from the Xcalibur (.raw) file format to the ANDI (.cdf ) file format and copy it to the current default data directory, use the following command line:

XConvert /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 Xcalibur RAW file

(L).

%R is the macro argument for the current RAW file.

For more examples, see Appendix F, “Executable Programs and

Command Line Arguments.”

After Sequence Set System

You can include a command line argument that launches a program and prints a specified file to the default printer (/p) or a specified printer (/pt).

The On option is the default selection in this area.

On Select the On option to leave the system in the On state when the current sequence is completed. Select the On state to run another sequence without waiting. All power and flows are maintained at operational levels.

Standby

This option has the same effect as choosing Actions > Devices On from the Home Page window.

Select the Standby option to place the system in the Standby state when the current sequence is completed. Select the Standby state to run another sequence with only a short delay of time.

Depending on the instrument, this state turns gas and liquid flows off but maintains heaters and other subsystems in an On state so that there is no warm-up time required when you change to the

On state.

This option has the same effect as choosing Actions > Devices

Standby from the Home Page window.

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Table 47. Run Sequence dialog box parameters (Sheet 5 of 6)

Parameter

Off

Description

Select the Off option to place the system in the Off state when the current sequence is completed. The Off state indicates that all power to the instrument, which can be controlled by Xcalibur software, is turned off. This power shutoff includes power to all heaters and most but not all subassemblies.

User

Run Rows

Priority Sequence

This option has the same effect as choosing Actions > Devices Off from the Home Page window.

CAUTION The Off state does not guarantee that all voltages are turned off, nor does it indicate that all heated components are at room temperature. To perform maintenance on an instrument, refer to the hardware manual for your instrument.

By default, this box lists the name of the data system computer user. You can type a name in this box with up to 24 alphanumeric characters to identify the operator who submitted the sequence.

Specifies the currently selected sequence rows. You can also enter a different row or a new range in the box. The range can only include contiguous sample rows. To enter a range, type the first row number, a hyphen, and the last row number, firstrow-lastrow.

If you select this check box, the data system processes the selected sequence as soon as possible or after the last sequence in the current queue. If the data system is processing a sample, the priority sequence is run next, ahead of all other samples in the processing queue. If the data system is not processing a sample, the priority sequence runs immediately. The data system does not cancel a currently running sample or sequence to accommodate a priority sequence.

When you open the Run Sequence dialog box, this check box is clear. To make sure the selected priority sequence runs as soon as possible, select the Priority Sequence check box.

Processing Actions

Quan Selecting this check box makes the quantitative processing actions that the processing method defines available. Define the quantitative processing actions for a processing method in the

Quan view of the Processing Setup window (see “Setting Up the

Quantitative Processing Parameters” on page 21

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Table 47. Run Sequence dialog box parameters (Sheet 6 of 6)

Parameter

Qual

Reports

Programs

Description

Selecting this check box makes the qualitative processing actions that the processing method defines available. Define the qualitative processing actions for a processing method in the Qual

view of the Processing Setup window (see “Setting Up the

Qualitative Processing Parameters” on page 50 ).

Selecting this check box makes the report actions that the processing method defines available. Define the reporting options for a processing method in the Reports view of the Processing

Setup window (see “Adding Report Templates to Processing

Methods” on page 59 ).

Selecting this check box launches software programs that the processing method defines for the samples selected from the current sequence and displayed in the Process Rows box.

Define the programs for a processing method in the Programs

view of the Processing Setup window (see “Adding Programs or

Macros to Processing Methods” on page 64 ).

Enabling programs requires a valid processing method and a valid raw file.

Create Quan Summary Creates a summary of the quantitation data. Select the Create

Quan Summary check box to print a summary.

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Transfer Row Information Dialog Box

Use the Transfer Row Information dialog box to copy information from one sample row of the sequence to other rows in the sequence that have either the same position in the autosampler tray or the same Sample ID. The sequence list is scanned from top to bottom.

When the Xcalibur data system finds repeated Sample IDs or position numbers in the list, it copies the row information from the first occurrence of the Sample ID or position to all rows with same sample ID or position number. The File Name and Sample Type columns are not affected.

Table 48

describes the parameters in the Transfer Row Information dialog box.

Table 48. Transfer Row Information dialog box parameters

Parameter Description

Match by Sample ID Select this option to copy the row information from the first occurrence of a Sample ID to all rows that have the same Sample

ID.

Match by Position Select this option to copy the row information from the first occurrence of a position to all rows that have the same position.

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Tray Selection Dialog Box

You can use the Tray Selection list to correct the vial position numbering sequence or to select the appropriate tray type. The tray types displayed in the list are all of those that are available for the currently configured autosampler.

Use the Tray Selection dialog box to select a tray for the currently configured autosampler.

Note If the configured autosampler does not provide a selection of sample trays, this dialog box is not available; instead, the following message appears:

The configured autosampler does not offer any selection of trays.

Tray types are associated with and are a part of each sequence method. If you change your autosampler, the following message appears:

Invalid autosampler vial position. A valid example vial position would be [ ].

The format inserted in the [ ] above corresponds to the currently configured autosampler.

Table 49

describes the parameters in the Tray Selections dialog box.

Table 49. Tray Selection dialog box parameter

Parameter

Select Tray Type with which to Validate

Sequence

Description

View or change the currently selected autosampler tray. To use a different tray, click the down arrow to display all available trays for the currently configured autosampler. Click the tray that you want to use to select it. The data system displays the selected tray in the list box.

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User Labels Dialog Box

Use the User Labels dialog box to define the column headings for the user-specific information in the sequence table. These column headings are stored with the sequence. In addition to the sequence table, these column headings also appear in the Export Sequence dialog box, Import Sequence dialog box, Fill Down dialog box, and Column Arrangement dialog box.

You can return the headings to their default values by clicking Default Headings. The default column headings are as follows:

• Heading 1: Study

• Heading 2: Client

• Heading 3: Laboratory

• Heading 4: Company

• Heading 5: Phone

To change a heading, select the current heading and type over it. If you do not want to use a heading, delete the text and leave the box blank. When all of the heading captions are correct, click OK.

For more information about using the User Labels dialog box, see

“Customizing the User

Labels for a Sequence” on page 90

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