xcalibur 2.0 xreport user guide version ctools.thermofisher.com/content/sfs/manuals/man-xcali... ·...

For Research Use OnlyNot for use in Diagnostic Procedures

Xcalibur®

Getting Productive:Designing and Generating Custom Reports with XReport

XCALI-97105 Revision C June 2006

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Contents

Preface .............................................................................................ixAbout This Guide ...................................................................... ixRelated Documentation ............................................................. ixSafety and Special Notices.......................................................... ixContacting Us.............................................................................x

Assistance .................................................................................xChanges to the Manual and Online Help.................................x

Chapter 1 Introduction to XReport......................................................................1Overview of XReport ..................................................................2

What is XReport?.....................................................................2The XReport Window .............................................................3Configuring XReport Objects ..................................................4

Using XReport ............................................................................7Starting XReport ......................................................................7Creating and Generating Reports with XReport.......................8Exiting XReport .....................................................................10

Overview of Report Templates..................................................11Report Template ....................................................................11Sections..................................................................................11Report Objects .......................................................................12Data Source Files ...................................................................15Report (Resolved Document).................................................15

Chapter 2 Creating a Template .........................................................................17Step 1 - Add, Order, and Configure Sections ............................18

Adding, Deleting, or Re-ordering Sections .............................18Resizing Sections....................................................................18Configuring a Repeating Section............................................19

Thermo Electron Corporation Xcalilbur: Getting Productive with XReports v

Contents

Step 2 - Add and Configure Report Objects..............................20Adding, Deleting, Repositioning, and Resizing Objects .........20Aligning Objects ....................................................................21Centering Objects ..................................................................21Using the Report Template Grid............................................22Using Columns ......................................................................23Using Page Breaks ..................................................................23Configuring Objects ..............................................................24Changing Font Settings..........................................................24Changing Page Layout ...........................................................25

Step 3 - Preview and Save the Template ....................................26

Chapter 3 Generating a Report ......................................................................... 29Creating a Report Within XReport ...........................................30

Choosing Data Sources for a Template ..................................30Resolving, Saving, and Printing a Report ...............................31

Creating a Report from Xcalibur ...............................................32Sample Reports and Summary Reports ..................................32Generating a Report From Sequence Setup ............................32Generating a Report From Quan Browser..............................36Creating a Signed Report .......................................................39

Chapter 4 Configuring Objects and Sections ................................................ 45Configuring a Repeating Section...............................................46Configuring a Text Object ........................................................50

Configuring Text Fields .........................................................51Adding Custom Text Fields ...................................................52Configuring Text Attributes...................................................53Setting Text Fonts..................................................................54

Configuring an Annotation Object ...........................................56Configuring a Table Object ......................................................58

Choosing Table Columns ......................................................59Configuring Custom (User) Columns....................................59Specifying Table Sort Order...................................................62Setting Table Fonts ................................................................63Setting Additional Table Properties........................................64

Configuring a Bitmap Object....................................................73

vi Xcalilbur: Getting Productive with XReports Thermo Electron Corporation

Contents

Configuring a Chromatogram...................................................74Use Container Supplied Quan Peak Page...............................76Use Container Supplied Qual Peak Page................................77Select Chromatogram Type Page ...........................................78Select Demo File Page............................................................79Select the Quan Peak Page .....................................................83Select the Qual Peak Page ......................................................85Select Mass Spectrum Quan Traces to Display Page...............86Configure How the Peak Window Will Look Page ................87Select Plot Details Page ..........................................................88Select Enhance Details Page ...................................................91Select Chromatogram Style Page............................................92Select the Peak Labeling Page.................................................94Select How the Chromatogram Axes Will

Be Configured Page ............................................................98Configure Normalization for the Chromatogram Page.........100Finishing the Chromatogram Wizard...................................101

Configuring a Component Calibration Curve.........................102Configuring a Spectrum..........................................................104

Options Page .......................................................................105Plot Type Page .....................................................................106Enhance Page.......................................................................107Style Page.............................................................................109Labels Page...........................................................................110Axis Page..............................................................................111Normalization Page..............................................................113Peak Page .............................................................................115

Configuring Columns .............................................................116Sample Repeat Option .........................................................117Summary Repeat Option .....................................................118

Appendix A Example XReport Template Files .................................................121

Appendix B Report Objects .................................................................................123

Appendix C Sample Report .................................................................................129

Index..................................................................................................135

Thermo Electron Corporation Xcalilbur: Getting Productive with XReports vii

Thermo Electron Corporation Xcalilbur: Getting Productive with XReports ix

Preface

About This Guide Welcome to XReport, the custom reports application of Xcalibur®!

XReport is part of Xcalibur, the Thermo Electron mass spectrometry data system.

RelatedDocumentation

In addition to this guide, Thermo Electron provides the following documents for Xcalibur 2.0:

• Administrator’s Guide: Configuring Xcalibur Software for Compliance with 21 CFR Part 11

• Getting Productive: Processing Setup and the Analysis of Quantitation Data

• Getting Productive: Quantitative Analysis

• Getting Productive: Designing and Generating Custom Reports with XReport

• Getting Productive: Creating and Searching Libraries

• Help available from within the software

Safety and SpecialNotices

Make sure you follow the precautionary statements presented in this guide. The safety and other special notices appear in boxes.

Safety and special notices include the following:

CAUTION Highlights hazards to humans, property, or the environment. Each CAUTION notice is accompanied by an appropriate CAUTION symbol.

IMPORTANT Highlights information necessary to avoid damage to software, loss of data, invalid test results, or information critical for optimal performance of the system.

Note Highlights information of general interest.

Tip Helpful information that can make a task easier.

PrefaceContacting Us

Contacting Us There are several ways to contact Thermo Electron.

Assistance For new product updates, technical support, and ordering information, contact us in one of the following ways:

Visit Us on the Web

www.thermo.com/finnigan

Contact Technical Support

Phone: 1-800-685-9535Fax: [email protected]

Contact Customer Service

In the US and Canada for ordering information:Phone: 1-800-532-4752Fax: 1-561-688-8731

International contacts for ordering information: Visit www.thermo.com/finnigan for the current listing.

Changes to the Manualand Online Help

To suggest changes to this guide or to the Help, use either of the following methods:

• Fill out a reader survey online at www.thermo.com/lcms-techpubs

• Send an e-mail message to the Technical Publications Editor at [email protected]

x Xcalilbur: Getting Productive with XReports Thermo Electron Corporation

mailto:[email protected]


mailto:[email protected]



www.thermo.com/lcms-techpubs

Chapter 1 Introduction to XReport

XReport is part of Xcalibur®, the Thermo Electron mass spectrometry data system.

Read this manual to get productive with XReport, the built-in tool of Xcalibur for designing and generating customized reports.

This chapter contains the following sections:

• Overview of XReport

• Using XReport

• Overview of Report Templates

Thermo Electron Corporation Xcalilbur: Getting Productive with XReports 1

1 Introduction to XReportOverview of XReport

Overview of XReport This section provides an overview of the fundamental features of XReport.

This section includes the following topics:

• What is XReport?

• The XReport Window

• Configuring XReport Objects

What is XReport? XReport is the name given to the custom reports application of Xcalibur. Use XReport to create customized reports containing all of the results and important information produced with Xcalibur. Create Xcalibur reports containing the following:

• Textual information (for example, sample information)

• Tabulated information (for example, a calibration file table)

• Graphical information (for example, a spectrum or a chromatogram)

In addition, use XReport to format a report to a style, print the report, and save the report in text (.txt file), Word document (.doc file), Excel workbook (.xls file), rich text (.rtf file), .pdf file, or web page (.htm or .html file) formats. Use these options to e-mail reports or display them on the Internet.

2 Xcalilbur: Getting Productive with XReports Thermo Electron Corporation


The XReport Window The XReport window is split into four different panes:

• Sections pane

• Objects pane

• Template pane

• Report Template Outline pane

See Figure 1, which illustrates the location of the panes.

The Sections pane lists the available sections for the selected application (for example, Xcalibur). To add a section to a report, drag it from the Sections pane to the Template pane.

Figure 1. XReport window

Template Outline Pane

Template Pane

Sections Pane

Objects Pane



The Objects pane lists the objects that are available for the currently selected section. To add an object to a report, drag it from the Objects pane to the currently selected section in the Template pane.

Use the Template pane to configure a report layout by dragging and arranging objects. To configure a report object, right-click it and choose Properties from the shortcut menu. To configure a repeating section, right-click the QL or QN icon in the left margin of the page at the top of the section and choose Properties from the shortcut menu. The size of the page in this pane corresponds to the size of a standard 8.5" by 11" piece of paper in either portrait or landscape mode. Adjust the height of sections by dragging the bottom border of the section downward. A selected section has a bright blue border around it.

The Report Template Outline pane lists the sections that are in the current report. You can un-dock this pane and reposition it on the screen or close it. Un-dock it by dragging the top gray portion away from the pane. To redisplay the pane, choose View > Report Template Outline pane.

To delete a section from a template, click it in the Report Template Outline pane and press DELETE. To move a section, drag it up or down in the Report Template Outline pane list. You cannot move the header and footer sections. To select and scroll to a section, double-click it.

Configuring XReportObjects

Use the Template pane of the XReport window to configure objects by right-clicking on them and choosing Properties from the shortcut menu. Set parameters in the configuration dialog box that appears. You can configure nearly all items in XReport, including:

• Repeating sections

• Tables

• Chromatograms

• Spectra

• Component Calibration Curves

• Text objects

Chapter 4 provides specific information on configuring each object.



Repeating Section Configuration Use the Repeating Section Configuration dialog box to specify the following:

• The type of repeating section - either Qual or Quan

• Whether to exclude Internal Standards or Target Compounds from a Quan repeating section

• The order in which peaks and components are repeated

• Any limit on number of peaks to be reported

• How the individual peaks or components are split across pages in the final report

Table Configuration Use the Table Configuration wizard to do the following:

• Specify the columns to be included in the table

• Define and customize table columns

• Specify an order for the table

Chromatogram Wizard Use the Chromatogram Wizard to do the following:

• Select Chromatogram Type and Peak Type

• Use a demonstration (demo) file

• Select plot details

• Select smoothing parameters

• Use MS Quan traces

• Configure the Chromatogram display, style, labeling, axes, and normalization methods



Component Calibration CurveConfiguration

Use the Component Calibration Curve Wizard to specify the name of the component for which a non-repeating Component Cal Curve report object is plotted in a report.

Data Source Browser Use the Data Source Browser to select data files that can be used to generate reports from within XReport.

Shipped XReport Templates An XReport template is an XReport document (.xrt file) with XReport objects embedded within it. You do not have to create personal XReport templates. XReport comes complete with customized report templates, ready-built for you to use. Appendix A provides full details of these report templates.


1 Introduction to XReportUsing XReport

Using XReport This section describes how to use XReport and contains the following topics:

• Starting XReport

• Creating and Generating Reports with XReport

• Exiting XReport

Starting XReport Start XReport as follows:

From the Microsoft Windows® XP taskbar, choose Start > Programs > Xcalibur > XReport or double-click the XReport icon on the desktop.

When more than one application uses XReport for reporting installed (for example, both Xcalibur 2.0 and LCquan 2.5), the Template Configuration dialog box appears (see Figure 2). Select the application for the report template and click OK.

Figure 2. Template Configuration dialog box



XReport opens and creates a new template (see Figure 3).

Creating and GeneratingReports with XReport

There are two distinct stages in the process of producing a customized Xcalibur report using XReport:

• Creating a Report Template

• Generating a Report Using a Report Template

These stages are outlined in the following topics, and discussed in detail in Chapter 2 and Chapter 3.

Figure 3. XReport window, showing a new template

Note Xcalibur ships with several XReport templates (.xrt file with XReport objects embedded within it) ready for you to use. These are located in the Xcalibur\templates folder. Details of these report templates are given in Appendix A.



Creating a Report Template Use XReport to create a customized report template (.xrt file) that defines how the final report looks and defines the specific information in the report. A report template is created by the following generalized steps:

1. Start XReport as described in the previous topic, Starting XReport.

A new XReport document is created and appears in the report window (see Figure 3).

2. Use XReport to add sections and report objects to the report template by dragging items from the Available Sections and Available Objects panes to the report preview pane.

3. Use XReport to configure the sections and report objects (adjust their properties to customize their output) included in the report template.

Right-click on objects and sections to configure and choose Properties from the shortcut menu. Set parameters in the configuration dialog boxes and use the menus, toolbars, or mouse to align, resize, and reposition objects.

4. Save the report template.

Chapter 2 and Chapter 4 of this manual provide more detailed information on how to create and configure a report template.

Generating a Report Using aReport Template

After creating a report template, generate a report (or resolved document) by combining (resolving) a report template with one or more data source files (for example, Xcalibur .pmd, .raw, .rst, .sld, and .xcal files).

There are three ways to generate a report:

• From a report template open in XReport— search for the required data source files and combine (resolve) the data with the template to generate a report. Preview, print, and save the report in .txt, .doc, .xls, .rtf, .pdf, or .htm format.

• From a data processing application (for example, Xcalibur)— associate the data you produce in the application with a report template (for example, do this in Quan Browser) and combine the data with the template to generate a single report.

• From a data processing application (for example, Xcalibur)— insert the name of the template into a processing method (such as Processing Setup) and generate reports automatically when you batch process data (such as in Sequence Setup).



Exiting XReport Save the report template or report before exiting XReport.

To exit XReport, complete or cancel any active dialog boxes and choose File > Exit.

Note Chapter 3 provides more detailed information on how to generate a report from within Xcalibur.


1 Introduction to XReportOverview of Report Templates

Overview of ReportTemplates

This section defines the basic terminology used throughout the software and this manual for new users of XReport and Xcalibur. This section defines the following key terms, some of which have already been introduced:

• Report Template

• Sections

• Report Objects (see Appendix B for full details.)

• Data Source Files (.pmd, .raw, .rst, .sld, .xcal)

• Report (Resolved Document)

Report Template An XReport template is an XReport document (.xrt file) that defines the content, layout and style of a report. Use the template to include sections and report objects (for example, graphs, tables, annotation text, or graphics) in a report template. The software generates an Xcalibur report after combining a report template with Xcalibur data (data source files).

XReport ships with several example report templates that are ready to use. These are located in the Xcalibur\Templates folder. Appendix A provides details of these pre-configured report templates.

Sections Divide the report template into section to hold report objects. Add sections into a report template using the Sections pane in the XReport window.

The basic types of section used in XReport are as follows:

• Header or footer

• Quan Repeating section

• Qual Repeating section

• Non-repeating section

A report object that is placed in a repeating section can behave differently from the same report object placed in a non-repeating section when the software combines a report template with data. See Appendix B for information on how a report object functions when it is placed inside or outside a repeating section.

Note See the other Xcalibur manuals or the Xcalibur online Help for additional information relating to Xcalibur.



Header or Footer Sections A header or footer section is a section of the report that is automatically repeated at the top and bottom of each page in the resolved report. Header and footer sections can contain objects such as a company logo, report information, page numbers, and date stamps.

Repeating Sections A repeating section is a section of a report template that is automatically repeated for every component or peak in a resolved document. Change the properties of a repeating section to customize its behavior.

Two types of repeating section can be used in an XReport template:

Non-Repeating Sections A non-repeating section usually displays static details associated with data or methods that apply once and globally within the system (for example, processing method settings, instrument method settings, filename, confirmation ion information, and so on).

Report Objects Report objects are customized tables, graphics, or text that indicate what kind of data appears in the report.When Xcalibur combines a report template with data, it replaces the report objects in the report template with data to generate a report.

Report objects include the following:

• Text Objects

• Table Objects

• Graphic Objects

• Formatting Objects

See Appendix B for a descriptive listing of XReport objects.

Qual repeating section Use a Qual repeating section to display details relating to a single Qual peak within some data. The section is repeated for all Qual peaks found.

Quan repeating section Use a Quan, or component, repeating section to display details relating to a single Quan peak in some data or a component configured in a processing method. The section is repeated for all Quan peaks or components.



Text Objects Text objects contain static text labels and associated customized data fields. Customize which specific fields are displayed by right-clicking on the object and choosing Properties from the shortcut menu to open the Configuration dialog box. When the software combines a template with data to generate a report, it replaces the text object fields with textual information (static text).

The following Xcalibur text objects are available in XReport:

• Annotation

• Component Ident/Detect/Cal Settings

• Component ISTD Settings Summary

• Component Settings Summary

• Component Sys Suit/Flags Settings

• Instrument Method

• Processing Method - General

• Processing Method - Qual

• Quan ISTD Peak Summary

• Quan Peak Summary

• Report Info

• Sample Header



Table Objects When Xcalibur combines a template with data, it replaces table objects with tabulated information (populated data table). Configure or change the properties of a table object to customize its output. XReport provides the following table objects:

• Avalon Qual Events Table

• Avalon Quan Events Table

• Calibration File Table

• Component Cal Level Table

• Component QC Level Table

• Component Spectrum Table

• Dilution Factor Table

• Electronic Signature

• Ion Ratio Confirmation Results Table

• IRC Settings Table

• IRC Summary Table

• Lib. Search Graph Table

• Lib. Search Results Table

• Proc. Method Programs Table

• Proc. Method Sample Reports Settings Table

• Proc. Method Summary Reports Settings Table

• Qual Peak Table

• Qual Summary Table

• Quan Peak Table

• Quan Summary Table

• Sample Table (Quan Results)

• Sequence Table

• Spectrum Candidate Results Table

• Spectrum List Table



Graphic Objects When Xreport combines a report template with data, it replaces graphic objects with graphical information. Configure or change the properties of a graphic object to customize its output. The following graphic objects are available in XReport:

• Bitmap• Chromatogram• Component Cal (Calibration) Curve• Spectrum

Formatting Objects Formatting objects available in XReport include:

• Columns• Page Break

These objects serve to format the report only.

Data Source Files Data source files are those files that contain acquired data. For example, there are five types of Xcalibur data source files: processing method (.pmd), raw (.raw), result (.rst), sequence (.sld), and calibration (.xcal).

Report (ResolvedDocument)

Generate a report (or resolved document) using a report template. In an Xcalibur report, the software combines (or resolves) the report objects in the report template with Xcalibur data. Save and present reports in standard Microsoft Word document format (.doc file), or in text (.txt file), Microsoft Excel workbook (.xls file), rich text (.rtf file), PDF (.pdf file) or web page (.htm or .html file) format.


Chapter 2 Creating a Template

This chapter explains how to create a personal report template. After creating a report template, save the template and use it to generate an Xcalibur report (described in Chapter 3).

When you start XReport, XReport creates a new template that includes header and footer sections (see Figure 4). Work with this new template or choose File > Open to open an existing template and select an XReport template (.xrt) file.

When you create a template, go through the following steps:

• Step 1 - Add, Order, and Configure Sections

• Step 2 - Add and Configure Report Objects

• Step 3 - Preview and Save the Template

These steps are described in the topics below.

Figure 4. XReport window, showing a new templates


2 Creating a TemplateStep 1 - Add, Order, and Configure Sections

Step 1 - Add, Order,and Configure

Sections

In Step 1, select which sections to include in the report template. Choose to include Quan-based or Qual-based Repeating sections or non-repeating sections in a report template. For a description of the different section types and how repeating sections work, see “Configuring a Repeating Section” on page 46.

This topic contains the following subtopics:

• Adding, Deleting, or Re-ordering Sections

• Resizing Sections

• Configuring a Repeating Section

Adding, Deleting, orRe-ordering Sections

To add a section to the report, drag it from the Sections pane (upper left) to the Template pane (center). Add only one section to the template at a time.

To delete a section from the report, click it in the Report Template Outline pane (far right) and press DELETE. The system prompts you to confirm the deletion. You cannot delete the header or footer sections. When the Report Template Outline pane is not visible, choose View > Report Template Outline or right-click in a section and choose Delete Section from the shortcut menu.

To re-order the sections in the template, click and drag them in the Report Template Outline pane. Header and footer sections must remain at the top and bottom of the list, respectively.

Resizing Sections To automatically remove the extra space at the top and bottom of a section, click in the section to select it, and choose Layout > Shrink Wrap.

To automatically add one half page of extra space at the bottom of a section, click in the section to select it, and choose Layout > Expand.

To manually add or remove extra space at the bottom of a section, click and drag the bottom border of a section up or down.


2 Creating a TemplateStep 1 - Add, Order, and Configure Sections

Configuring a RepeatingSection

To configure a Qual or Quan repeating section

1. Scroll to where you can see the QL or QN icon at the top left edge of the section in the Template pane. Right-click it and choose Properties from the shortcut menu. The Repeating Section Properties dialog box appears (see Figure 5).

2. Set the parameters and click OK. See “Configuring a Repeating Section” on page 46 for more information about the individual parameters in this dialog box.

Figure 5. Repeating Section Properties dialog box


2 Creating a TemplateStep 2 - Add and Configure Report Objects

Step 2 - Add andConfigure Report

Objects

In Step 2, select the report objects to include in a specified section of the report template. Select from these options: text objects, table objects, graphic objects, and text, depending on the selections you made in Step 1.

XReports displays the objects that are available for the currently selected section in the Objects pane (lower right). The contents of this pane changes when you select different sections.

This topic contains the following subtopics:

• Adding, Deleting, Repositioning, and Resizing Objects

• Aligning Objects

• Centering Objects

• Using the Report Template Grid

• Using Columns

• Using Page Breaks

• Configuring Objects

• Changing Font Settings

• Changing Page Layout

Adding, Deleting,Repositioning, and

Resizing Objects

To add an object to the report, drag it from the Objects pane (lower left) to the currently selected section (boxed in blue) in the Template (center) pane. Add only one object to the template at a time.

To delete an object from the report, click it in the Template (center) pane to select it (blue handlebars on each side and at each corner become visible) and press DELETE.

To reposition an object, click it to select it and drag it to the preferred location.

To resize an object, click it to select it, and drag one of the corner handles (small blue squares) until the object is the preferred size.



To make two or more objects the same size

1. Click the first object to size. The size of the first object selected determines the size of subsequent objects.

2. Press SHIFT and click each other object to resize.

3. Click the button on the toolbar that corresponds to the dimension to resize: Height, Width, or Both.

To resize the columns in a table object, double-click the table. Handles (small blue boxes) appear on the interior column borders. Click and drag the handles to resize the columns.

Aligning Objects To align one or more objects

1. Click the first object to align. The position of the first object selected determines how subsequent objects are aligned.

2. Press <Shift> and click each other object to align.

3. Click the button on the toolbar that corresponds to the edge to align: Left, Right, Top, Bottom or click Auto Align to snap all objects to the nearest grid line. Choose View > Report Template Grid to view the grid lines. Choose Layout > Preferences to open the Preferences dialog box (Figure 6) and adjust the grid settings.

Centering Objects To center one or more objects

1. Click the first object to center. Press <Shift> and click each other object to center.

2. Click the Center Horizontally or Center Vertically button on the toolbar to center the objects on the page.



Using the Report TemplateGrid

The Template pane has a grid built into it. Choose View > Report Template Grid to view the grid lines.

Choose Layout > Preferences (see Figure 6) to open the Preferences dialog box and adjust the grid settings. Set the spacing between grid lines and whether to snap objects to the grid as they are added to the Template pane.

Figure 6. Preferences dialog box



Using Columns Add columns to arrange other reporting objects so that they appear in a columnar format. To add a column to the template, drag the column object from the Objects pane into the Template pane.

After adding a column object in the template, resize, reposition, and configure it. To configure a column object, right-click it and choose Properties from the shortcut menu to open the Column Properties dialog box (see Figure 7). See “Configuring Columns” on page 116 for more information on how to configure columns and how columns work with different repeat types.

You can resize the entire column object (click it to select it, and drag the corner handles), but the columns within the column object remain equal in size.

After you have finished configuring the columns, drag objects into the columns.

Using Page Breaks To add a page break to the template, drag the Page Break object from the Objects pane into the Template pane. After adding a page break in the template, reposition it by clicking on it and dragging.

If you do not manually insert page breaks, objects automatically shift to a new page when there is not enough room on the current page. Preview where these automatic breaks occur by choosing Layout > Preferences to display the Preferences dialog box (Figure 6), and then select the Show Page End check box.

Figure 7. Column Properties dialog box



Configuring Objects To configure an object, right-click it and choose Properties from the shortcut menu to open the Properties dialog box. See Chapter 4 for information on how to configure each of the specific objects, and Appendix B for a description of each object, including which section(s) each object can be used in.

Changing Font Settings Use XReport to change font settings for text and table objects globally or locally. When you change the font settings globally, each object added from that point on appears in the new fonts (objects that are already in the template are not updated). When you change font settings locally, only the selected objects reflect the new font settings.

To change the font settings for a single object

1. Either right-click the object and choose Properties from the shortcut menu to open the Properties dialog box and display the Font page, or select the object and click the Font button on the toolbar to open the Font dialog box. Both of these pages provide the same settings.

2. Update the settings and click OK.

To change the font settings for more than one text or table object at a time:

1. Click the first object. Press and hold SHIFT while you click the other objects.

2. Click the Font button on the toolbar to open the Font dialog box.


To globally change the font settings used for each new object that is added to the template

1. Click in any section and confirm that no objects are selected.

2. Click the Font button on the toolbar to open the Font dialog box.




Changing Page Layout To change the page layout, including header/footer section heights, switch between portrait/landscape pages, or change the margins, choose File > Page Setup to open the Page Setup dialog box (see Figure 8)

Figure 8. Page Setup dialog box


2 Creating a TemplateStep 3 - Preview and Save the Template

Step 3 - Preview andSave the Template

To preview template appearance by simulating the creation of a report with default data

1. Choose File > Simulate Report to open the Preview window (see Figure 9).The Preview window shows the report with the default data.

2. When the report is correct, click Close to close the preview window.

3. Choose File > Save to save the template. (Or Save As when working with a locked template. See below.)

Figure 9. Preview window



Use XReport to lock a template so that it can never be modified and saved with the same filename. After you lock a template, modify it by saving it with a different filename. Choose File > Open to open a locked template the same way you open any other template.

Note The default data set used by XReport is the steroid example data that is shipped with Xcalibur. It consists of the following files:

• steroid.pmd

• steroids02.raw

• steroids02.RST

• steroid.sld

When the template is designed for a very different type of data set than the default data, you might not see the results you expect when you preview the template. In that case, choose appropriate data sources for the template and create the report as described in “Creating a Report Within XReport” on page 30.



To lock the template

1. Choose File > Save As to open the Save As dialog box (see Figure 10).

2. Give the report template an appropriate name and save it in a suitable location. Save the customized report templates in the Xcalibur\templates folder with the templates that ship with Xcalibur.

3. Select the Lock Template check box and click Save.

Figure 10. Save As dialog box, showing XReport Templates


Chapter 3 Generating a Report

This chapter describes how to generate an Xcalibur report. Generate an Xcalibur report (or resolved document) by combining (resolving) a report template with one or more Xcalibur data source files (.pmd, .raw, .rst, .sld, .xcal files). There are two ways to generate reports:

• Creating a Report Within XReport— use the XReport Data Source Browser to automatically search for the required data source files and resolve the data to generate a report. A single report is generated by this method.

• Creating a Report from Xcalibur— associate the data you produced in Xcalibur with a report template and combine the data with the template to generate a report. You can generate multiple reports from Xcalibur.


3 Generating a ReportCreating a Report Within XReport

Creating a ReportWithin XReport

Creating a report within XReport involves the following steps:

• Choosing Data Sources for a Template

• Resolving, Saving, and Printing a Report

Choosing Data Sources fora Template

The process of generating a report from an XReport template involves using the Data Source dialog box to search for the required data source files. The data source file(s) required to generate a report depends on the content (sections and report objects) of the report template. See Appendix B for information on which data files are needed for each type of report object.

To resolve a template with data

1. Choose File > Open in XReport to open the template (.xrt file), select the template, and click Open.

2. Choose Report > Data Sources to open the Data Sources dialog box (see Figure 11).

3. In each of the boxes, enter or search for a data file.

Figure 11. Data Sources dialog box


3 Generating a ReportCreating a Report Within XReport

4. Click OK.

Resolving, Saving, andPrinting a Report

To create a report using the selected data sources (see the previous topic)

1. Choose File > Resolve Report in XReport to open the Preview window (see Figure 12). The Preview window shows a report combined with chosen data sources.

2. Click Save to save the report in the following formats: Word file (.doc), Excel file (.xls), Web page (.htm or .html), rich text (.rtf ), PDF (.pdf ), or text (.txt).

3. Click Print to print the report.

4. Click Close to return to the XReport window.

Note If you specify an .rst file that references a .raw file, and that .raw file does not exist or is in the wrong folder, XReport sends an error message. Confirm the .raw file is in the correct folder.

Figure 12. Preview window


3 Generating a ReportCreating a Report from Xcalibur

Creating a Reportfrom Xcalibur

Reports are generated from Xcalibur by associating the data that you produced in Xcalibur with a report template. Xcalibur combines the data with the specified report template to generate a report. You can generate multiple reports from Xcalibur.

Generate a report from the following areas of Xcalibur:

• Generating a Report From Sequence Setup—Running a Sample or Sequence and Batch Reprocessing

• Generating a Report From Quan Browser—Reports dialog box

In addition, when generating reports from Xcalibur, create reports containing Electronic Signature information.

Sample Reports andSummary Reports

To set up reporting options in Xcalibur, either in Processing Setup or Quan Browser, select two types of reports: Sample Reports and Summary Reports. Use Sample Reports to print reports that give information about individual samples. Use Summary Reports to print reports that give summary information about an entire sequence or set of samples.

Table 2 describes the example template files included with XReport and indicates the specific templates to use to generate Sample Reports or to generate Summary Reports.

Generating a Report FromSequence Setup

To generate reports from the Sequence Setup window, create a processing method that includes the necessary report options in the Reports Page of the method.

Use the Sequence Setup window to generate reports when:

• Running a Sample or Sequence

• Batch Reprocessing a Sequence

Each of these are discussed below.

Note A basic understanding of Xcalibur is presumed for this section. See Xcalibur Getting Productive manuals or the Xcalibur online Help for more information.

Note Close the report template in XReport before using it to generate a report from Xcalibur.



Setting up Report Options inProcessing Setup

To set up report settings in the Processing Setup window

1. Open the Processing Setup window and set up the processing method as normal.

2. Choose View > Reports to display the Reports view.

3. Add one or more reports to either the Sample or Summary report tables:

The Sample table lists the reports to be produced for processed samples in a sequence. The Summary table lists the reports to be produced for sequences or brackets.

a. Click in the Enable column to display a check box and select the check box to enable the report.

b. To create a Sample table, set the Std, QC, Unk, and Other check boxes.

c. Select the output for the report in the Save As column. Choose from none (this prints the report, but does not save it), or .txt, .doc, .html, .pdf, .rtf, or .xls (these save the report in the selected format).

Xcalibur saves reports created from the processing method in the same directory as the source data files and names files in the format [data file name][template name].xxx, where

• [data file name] is the name of the data file from which the report was generated

• [template name] is the name of the template used to generate the report• xxx is the suffix (for example, .doc or .pdf ) indicating the file typeWhen more than one report is generated from the same data file and template, XReport adds a date stamp before the suffix.

d. Double-click in the Report Name column to select an XReport template (.xrt file) to use for this report.

4. Save the processing method.

Generating Reports whenRunning a Sample or Sequence

To generate reports when running a sample or a sequence

1. Confirm that you have report options set in a processing method as described in the earlier topic, Setting up Report Options in Processing Setup.

2. In Xcalibur’s Sequence Setup window, open the sequence.



3. Enter the processing method created earlier that includes all of the report options in the Proc Meth column.

4. When running a sequence, specify the rows to be processed from the current sequence by clicking and dragging in the left-most column. Xcalibur highlights the selected rows.

When running a sample, click in the left-most column of the sample row to select it.

5. Choose Actions > Run This Sequence or Actions > Run This Sample to open the Run Sequence or Run Sample dialog box (see Figure 13).

Xcalibur displays the sequence rows or sample selected in step 3 in the Process Rows box.

6. Select the Reports check box in the Processing Actions area.

7. Set all of the other parameters.

8. Click OK. Xcalibur starts processing the selected sample or samples.

Figure 13. Run Sequence dialog box



Generating Reports when BatchReprocessing a Sequence

To generate reports when batch reprocessing a sequence

1. Set report parameters in the processing method as described in the earlier topic (see “Setting up Report Options in Processing Setup” on page 33).

2. In Xcalibur’s Sequence Setup window, open the sequence.

3. Enter the processing method created earlier that includes all of the report options in the Proc Meth column.

4. Specify the rows to be reprocessed from the current sequence by clicking and dragging in the left-most column. Xcalibur highlights the selected rows.

5. Choose Actions > Batch Reprocess (see Figure 14) to open the Batch Reprocess Setup dialog box.

Xcalibur displays the sequence rows selected in step 1 in the Process Rows box.

Figure 14. Batch Reprocess dialog box



6. If necessary, change the rows to be reprocessed by entering the first and last row to be reprocessed in the Process Rows box. The format is either [Row] for one sample or [First Row - Last Row] for multiple samples.

7. Select Quan and Qual processing actions.

8. Select XReport processing actions:

a. Select the Reports check box to create reports while batch processing.

b. Select the Print Sample Reports check box to print reports for the samples displayed in the Process Rows box.

You defined the Sample report parameters in the Reports view of the Processing Setup window.

c. Select the Print Summary Reports check box to print reports for the samples that are displayed in the Process Rows box.

You defined the Summary report parameters in the Reports view of the Processing Setup window.

d. Select Programs, Spreadsheet, and Advanced actions.

9. Click OK. Xcalibur initiates batch reprocessing of the selected samples.

Generating a Report FromQuan Browser

To generate a report from the Quan Browser window

1. Open the Quan Browser window. Xcalibur displays the Open dialog box.

2. Select a sequence by selecting the file of type .sld that contains the samples to print reports for and click Open.

3. Choose View > Reports Dialog (see Figure 15) to open the Reports dialog box.



4. Make a row of the Sample Reports area active by clicking on the Enable box in the first row and click the Enable box again. A check box appears in the box.

5. Select the check box. When you click again, Xcalibur displays the word Yes in the Enable box to indicate that the entire row of options is selected.

6. Select the report type to print by clicking on one of the following boxes to select reports for that sample type: Stds, QCs, Unks, or Other. A check box control appears.

7. Select the check box. When you click again, Xcalibur displays the word Yes in the Enable box to indicate that reports are to be printed for all selected samples of this sample type.

8. Repeat steps 6 and 7 for all sample types to print reports for.

9. Display the Open Report Template dialog box by double-clicking in the Report Template Name box. Select the previously prepared Report

Figure 15. Quan Browser window - Reports dialog box



Template document and click Open. Xcalibur displays the full path and the name of the Report Template document of type .xrt in the Report Template Name box.

10. Repeat steps 5 through 10 for the next row for each Report Template document to use to print reports.

11. Select the Include Sample Reports check box at the bottom of the Reports dialog box to make all of the sample reports you have selected for printing available. Similarly, select the Include Summary Report check box to make summary reports available.

12. Open the Select Report Samples dialog box by clicking Select Samples. The samples available from the .sld file opened in step 2 appear in the Sample Choices box (see Figure 16).

13. To print a report, select the samples.

• For a group of contiguous samples, click the first of the sequence, scroll until you see the last sample in the sequence, and hold down SHIFT while you click. Xcalibur highlights the selected sequence.

• For a group of non-contiguous samples, hold down CTRL while you click each sample to select/deselect it. Xcalibur highlights the selected samples.

14. Click Add to copy the selected samples to the Selected Samples area.

Figure 16. Select Report Samples dialog box



15. Click OK to return to the Reports dialog box.

16. Click Print Reports to print reports. Prior to printing reports, Xcalibur:

• Displays the Printer Activity icon at the bottom of the Quan Browser window.

• Resolves the data in the sample file with the selected Report Template document.

• Adds the report printing task(s) to the processing queue and displays the Printing message box.

After the reports print, Xcalibur returns you to the Quan Browser window.

Xcalibur saves reports created from Quan Browser in the same directory as the source data files and names files in the format [data file name][template name].xxx, where

• [data file name] is the name of the data file from which the report was generated

• [template name] is the name of the template used to generate the report• xxx is the suffix (for example, .doc or .pdf ) indicating the file type

When more than one report is generated from the same data file and template, a date stamp is added before the suffix.

Creating a Signed Report When generating reports from Quan Browser or by Batch Reprocessing in Sequence Setup, create signed reports containing electronic signatures.

To creating a signed report

1. Create a report template containing the Electronic Signature table object or choose one of the pre-configured templates supplied with XReport. All of the pre-configured templates contain the Electronic Signature table object in the footer.

2. Confirm that the Xcalibur Authorization Manager settings are set to require electronic signatures at the report generating step. See “Configuring Authorization Manager Settings for Signed Reports” on page 40.

3. Generate the report.



Configuring AuthorizationManager Settings for Signed

Reports

In order to produce signed reports with electronic signatures, Configure the Xcalibur Authorization Manager Settings to require signatures. Xcalibur administrators should perform this configuration.

To configure Authorization Manager settings for signed reports

1. Choose Start > All Programs > Xcalibur > Authorization Manager. The Authorization Manager window appears.

2. Set permissions for producing signed reports from Sequence Setup:

a. Expand the Home Page entry and expand the Sequence Operations entry in the permission level pane.

b. Select Batch Reprocess from the list of operations underneath the Sequence Operations entry.

c. Select Signature List in the Permission Level area.

d. Select a group in the Available groups list in the Signature List Groups area and click >> to move it to the Signatures Req’d list. The members of this group are required to enter their logon names and passwords to electronically sign the report when it is generated.

e. To require signatures from additional groups, repeat step d to add them to the Signatures Req’d list.

f. To require a signature from the current user when the report is generated, select the Current User Must Sign check box.

Note If you do not have any groups available or if the groups do not contain the correct members, see the Xcalibur Administrator’s Guide: Configuring Xcalibur Software for Compliance with 21 CFR Part 11 for information on how to create and modify groups.



At this point, the settings should resemble those depicted in Figure 17.

3. Set permissions for producing signed reports from Quan Browser:

a. Expand the Quan Browser entry and expand the Print entry in the permission level pane.

b. Select Print Reports.

c. Select Signature List in the Permission Level area.

d. Select a group in the Available groups list in the Signature List Groups area and click >> to move it to the Signatures Req’d list. The members of this group are required to enter their logon names and passwords to electronically sign the report when it is generated.

Figure 17. Authorization Manager dialog box, showing settings for producing signed reports from Sequence Setup



e. To require signatures from additional groups, repeat step d to add them to the Signatures Req’d list.

f. To require a signature from the current user when the report is generated, select the Current User Must Sign check box.

At this point, the settings should be similar to the settings in Figure 18.

4. Click OK to close the Authorization Manager dialog box and save the settings.

Note If you do not have any groups available or if the groups do not contain the correct members, see the Xcalibur Administrator’s Guide: Configuring Xcalibur Software for Compliance with 21 CFR Part 11 for information on how to create and modify groups.

Figure 18. Authorization Manager dialog box, showing settings for producing signed reports from Quan Browser



Generating Signed Reports Once you have a template containing an Electronic Signatures object, generate the report as described in “Generating Reports when Batch Reprocessing a Sequence” on page 35 or in “Generating a Report From Quan Browser” on page 36. Xcalibur prompts you to enter signature information when the report is generated. Each user whose signature is required should enter their login name and password to sign the report. Figure 19 displays an example signature dialog box.

Figure 19. Example signature dialog box


Chapter 4 Configuring Objects and Sections

This chapter provides information on configuring the various objects and sections in XReport.

When configuring these objects, you are changing or editing only the individual properties of that specific object. When you add another object of the same type to the report, XReport inserts it with the default settings.

This chapter contains the following sections:

• Configuring a Repeating Section

• Configuring a Text Object

• Configuring an Annotation Object

• Configuring a Table Object

• Configuring a Bitmap Object

• Configuring a Chromatogram

• Configuring a Component Calibration Curve

• Configuring a Spectrum

• Configuring Columns


4 Configuring Objects and SectionsConfiguring a Repeating Section

Configuring aRepeating Section

There are two different types of repeating sections in XReport:

Use the Repeating Section Properties dialog box to specify:

• Whether to exclude Internal Standards or Target Compounds from a Quan repeating section.

• The repeat order for peaks and components.

• Any limit on the number of peaks to be reported.

• How the individual peaks or components are split across pages in the final report.

Qual repeating section Displays details relating to a single Qual peak within some data. The section is repeated for all Qual peaks found.

Quan repeating section Displays details relating to a single Quan peak in some data or a component configured in a processing method. The section is repeated for all Quan peaks or components.



To configure a Qual or Quan repeating section

1. Scroll to where you can see the QL or QN icon at the top left edge of the section in the Template pane and right-click it. Choose Properties from the shortcut menu. The Repeating Section Properties dialog box appears (see Figure 20). This dialog box has three pages: Exclude, Ordering, and Page Breaks.

2. On the Exclude page, when configuring a Quan repeating section, exclude specific elements from the process and discard any components that have not been found.

a. From the Exclude Component Type list, define the exclusions for the Quan repeating section by selecting one of the following options:

• None (no exclusions) - the default

• Internal Standards

• Target Compounds

Figure 20. Repeating Section Properties dialog box - Exclude page



b. Select the Show Only Found Components check box to discard any components that have not been found.

When configuring a Qual repeating section, the parameters on this page are unavailable.

3. Display the Ordering page. Use this page to change the default ordering of processed results, such that the order of peaks and components in a repeating section can be tailored to your specific needs (see Figure 21).

4. Specify the order for the Qual repeating section in the Repeating Section Ordering area by selecting one of the following options from the Order By list:

• RT (Retention Time); the default

• Component Name (Quan only)

• Peak Height Intensity

• Peak Area Intensity

• Peak Response Intensity

• Component Concentration (Quan only)

Figure 21. Repeating Section Properties dialog box - Ordering page



5. Define the direction for the ordering in the Ordering Direction area by selecting one of the following options:

• Ascending—to sort the data in ascending order

• Descending—to sort the data in descending order.

6. Define the maximum number of peaks or components to order (up to 999) in the Limit Repeating Records area. To set a maximum number, select the Maximum Number of Peaks or Components To Order On check box and use the active box to enter a value.

7. Display the Page Breaks page. Use this page to define the layout for the individual peaks that appear in the repeating section in the final report (see Figure 22).

8. Choose whether to print each peak on its own page(s) or to avoid page breaks between the individual peaks.

9. Click OK when you have made selections in the Repeating Sections Properties dialog box. Choose File > Save to save any changes.

Figure 22. Repeating Section Properties dialog box - Page Breaks page


4 Configuring Objects and SectionsConfiguring a Text Object

Configuring a TextObject

To configure a text object, right-click it and choose Properties to open the Properties dialog box (see Figure 32). (See Appendix B for a description of each text object, including which section each object is in.)

Use the Text Properties dialog box to configure a text object within the report. There is a different Properties dialog box for the Annotation object, which is discussed in the next section.

Use the Text Properties dialog box to do the following:

• Configuring Text Fields

• Adding Custom Text Fields

• Configuring Text Attributes

• Setting Text Fonts

Figure 23. Text Properties dialog box - Data page



Configuring Text Fields To configure the text object

1. Select the Include Title In Resolved Report check box in the Text Properties dialog box on the Data page to include a custom title for the object.

2. If you selected to include a custom title, enter it into the Title box.

3. Select the items to include in the Available Items list.

4. Click Add to add the fields to include in the text object to the Selected Columns list or double-click a selected field or add all the available fields by clicking Add All.

5. Select the fields in the Selected list that you do not want to include and click Remove.

6. Click an item and click Move Up and Move Down to change the order of the selected columns in the Selected Columns list box.

7. If a field is a data label, you can edit it: To edit a data label, select it in the Selected list, and edit its text in the Data Label box. Headings cannot be edited. However, use User Text items to add custom Headings to the text object. See “Adding Custom Text Fields” on page 52.

8. Click OK.



Adding Custom Text Fields Add a custom text field to the text object to use as a heading or annotation.

To add a custom text field

1. Select <User Text> in the Text Properties dialog box in the Available Items list and click Add (see Figure 24).

2. Select <User Text> in the Selected list.

3. Type the text in the User Box and press ENTER (see Figure 25).

Figure 24. Text Properties dialog box, showing the addition of a custom text field



4. Click OK.

Configuring TextAttributes

To configure text attributes, right-click a text object and choose Properties from the shortcut menu to open the Text Properties dialog box. Display the Attributes page (see Figure 26).

Figure 25. Text Properties dialog box, showing editing of a custom text field

Figure 26. Text Properties dialog box - Attributes page



To configure the attributes

1. Select the number of columns in the Number Of Columns area to display the text.

2. Select the Include data label check box to include data labels in the object in the Horizontal Spacing area.

3. Select the Include spacing between a label and its data check box to add extra space between data labels and data.

4. Select a style for line spacing in the Vertical Spacing area.

5. Click OK.

Setting Text Fonts To set text fonts, right-click a text object and choose Properties from the shortcut menu to open the Text Properties dialog box. Display the Font page (see Figure 27).

Figure 27. Text Properties dialog box - Font page



To set the font for that type of text for each button on the page

1. Click the button to open the Font dialog box (see Figure 28).

2. Make the font selections and click OK.

Figure 28. Font dialog box

Note The Heading Font selection is also used for User Text.


4 Configuring Objects and SectionsConfiguring an Annotation Object

Configuring anAnnotation Object

An Annotation object can be included in any section type.

To configure the Annotation object

1. Right-click the Annotation object and choose Properties from the shortcut menu to open the Annotation Properties dialog box (see Figure 29).

2. Click in the box on the Annotation Properties dialog box on the Data page to get a cursor. Delete the words Enter Your Text Here and enter annotation text.

Figure 29. Annotation Properties dialog box - Data page


4 Configuring Objects and SectionsConfiguring an Annotation Object

3. Select the number of columns to display annotation text in the Attributes page (see Figure 30) in the Number Of Columns area.

4. Select whether you would like the annotation text aligned left, center, or right in the Horizontal Alignment area.

5. Select whether you would like the annotation text line spacing to be single, 1.5 lines, or double in the Vertical Spacing area.

6. Configure the font on the Font page (see Figure 31) by setting the various parameters.

7. Click OK.

Figure 30. Annotation Properties dialog box - Attributes page

Figure 31. Annotation Properties dialog box - Font page


4 Configuring Objects and SectionsConfiguring a Table Object

Configuring a TableObject

To configure a table object, right-click it and choose Properties from the shortcut menu to open the Table Properties wizard (see Figure 32). (See Appendix B for a description of each table, including which sections each table can be used in.)

Use the Table Properties wizard to configure a table object (that is, change its properties) included in the report template. Use the this wizard for the following:

• Choosing Table Columns

• Configuring Custom (User) Columns

• Specifying Table Sort Order

• Setting Table Fonts

• Setting Additional Table Properties

Figure 32. Table Properties wizard - Select Table Fields page



Choosing Table Columns Use the first page of the Table wizard, the Select Table Fields page, to select the columns to include in the table (see Figure 32). The columns available for a table are given in alphabetical order, but can be added to a report template in any order. The columns available for you to select depend on the type of table object you are configuring.

To fill in the Select Table Fields page of the Table wizard

1. Type the title into the Title box and select the Include Title In Resolved Report check box to include a custom title for the table.

2. Select (highlight) the columns to include in the table from the Available Columns list.

3. Click Add to add columns to include in the table to the Selected Columns list or double-click a selected column or add all the available columns by clicking Add All.

4. Enter the column heading text in the Column Header box.

5. Click Move Up and Move Down to arrange the order of the selected columns in the Selected Columns list.

6. Click Next to move on to the next page of the wizard.

Configuring Custom (User)Columns

The Configure User Column Parameters page of the Table Wizard appears only if you chose to include custom User Columns in the table. Use this page to define parameters for each User Column in the table (see Figure 33).

Use the User Columns to define mathematical formulas to perform calculations on table data. Formulas obey the following syntax rules:

• The formula must begin with an equals sign (=).

• Each table column is represented by an alphabetic letter identifier (A, B, C, and so on) that appears beneath the column title in the Table object.

Note All table objects have User Columns available for selection. Use the User Columns to define formulas to perform mathematical calculations on table data and to display the results in the table. See “Configuring Custom (User) Columns” on page 59 for more information on User Columns.



• Enter simple mathematical expressions (A+B, A-B, A*B, and A/B), as well as any of the functions listed in the Functions list of the Edit Formula dialog box. Formulas are computed on a row-by-row basis. That is, if you enter =A+B as a formula in a User Column, the results are computed as follows:

• The value in the first row of column A is added to the value in the first row of column B, and the result appears in the first row of the User Column.

• The value in the second row of column A is added to the value in the second row of column B, and the result appears in the second row of the User Column.

• This is continued until all rows of the table have been completed.

The User Column(s) you have included in the table are displayed in the User Columns list.

To define each User Column

1. Select a User Column in the User Columns list.

2. Type a title for the User Column in the User Column Title area.

Figure 33. Table Properties dialog box - Configure User Column Parameters page



3. Click Edit Formula in the User Column Formula area to open the Edit Formula dialog box (see Figure 34).

Use the Edit Formula dialog box to edit a formula for the User Column. Use this dialog box to configure valid fields and associated functions for the User Column. There is a brief description of each function in the Functions list at the bottom of the dialog box.

4. Click Add Function or type directly into the box to enter the formula in the Formula box.

5. When you click Add Function, a configuration dialog box appears for that function. For example, for the Average function, choose the column to average.

6. Click OK to return to the Configure User Column Parameters page.


Figure 34. Edit Formula dialog box



Specifying Table SortOrder

Use the next page of the Table Wizard, the Set Table Sort Filter page, to define table data is sorted when you generate a report (see Figure 35).

XReport displays the columns selected for the table in a list on the left of the dialog box. Order the table by any of the selected columns. Use up to three columns for ordering the table: the first order takes precedence over the second order, which takes precedence over the third order.

To select the table order

1. Select the column of the variable from the list to order the table first.

2. Click Add to add the selected column to the First Order box or double-click a selected column.

3. Define how to sort the First Order column data in the Current Sorting Configuration area by selecting one of the following options:

• Ascending—data sorted in ascending order

• Descending—data sorted in descending order

4. Repeat steps 1 to 3 to define the second and the third variable used to order table columns as necessary.

5. To move to the Font page, click Next.

Figure 35. Table Properties dialog box - Set Table Sort Filter page



Setting Table Fonts Use the final page of the Table wizard, the Fonts page, to set the appearance of the fonts in the table (see Figure 36).

1. Click each button to open the Font dialog box and define the font for that element (see Figure 37).

2. Make the font selections and click OK.

Figure 36. Table Properties dialog box - Font page

Figure 37. Font dialog box



Setting Additional TableProperties

After completing the Table Wizard, additional Properties dialog boxes appear for the following table objects:

• Library Search Graphics Table

• Library Search Result Table

• Spectrum List Table

• Sample Table (Quan Results)

• Electronic Signature Table Properties

Library Search Graphics TableProperties

To set Library Search Graphics Table properties, right-click the table and choose Properties from the shortcut menu to open the Table Properties wizard. When you complete the wizard and click Finish or Cancel, the Library Search Graphics Table Properties dialog box appears (see Figure 38).

To set the parameters in this dialog box

1. Enter the total number of search results to display in the table in the Max # Of Hits To Display box.

2. Select whether or not to display column labels by using the Display Column Labels checkbox.

Figure 38. Library Search Graphics Table Properties dialog box



3. Select whether or not to show the peak spectrum by selecting the Show Peak Spectrum check box.

4. Click OK. Choose File > Save to save any changes made.

Library Search Results TableProperties

To set Library Search Results Table properties, right-click the table and choose Properties from the shortcut menu to open the Table Properties wizard. After clicking the wizard and clicking Finish or Cancel, the Library Search Results Table Properties dialog box appears (see Figure 39).


1. Enter the total number of search results to display in the table in the Max # Of Hits To Display box.

2. Click OK.

Figure 39. Library Search Graphics Table Properties dialog box



Sample Table Properties To set Sample Table properties, right-click the table and choose Properties from the shortcut menu to open the Table Properties wizard. After clicking the wizard and clicking Finish or Cancel, the Sample Table Properties dialog box appears (see Figure 40).


1. Select whether or not to include standards, QCs, blanks, or unknowns in the Sample table by using the corresponding checkboxes.

2. Click OK.

Figure 40. Sample Table Properties dialog box



Spectrum List Table Properties To set Spectrum List Table properties, right-click the table and choose Properties from the shortcut menu to open the Table Properties wizard. After clicking the wizard and clicking Finish or Cancel, the Spectrum List Table Properties dialog box appears (see Figure 41).

This dialog box has four pages, as follows:

• Options Page

• Plot Type Page

• Enhancement Page

• Display Page

Options Page

To set the parameters in the Options page

1. Select or deselect the Use Processing Method Properties For Plot Type And Enhancement Info checkbox (see Figure 41).

When you select this checkbox, the parameters on the Plot Type and Enhancement pages are unavailable.

2. Select whether or not to use the ISTD peak when repeating on a component by using the corresponding check box. (This option only

Figure 41. Spectrum List Table Properties dialog box - Options page



applies when this object is used in a Quan Repeating Section and when the Use Processing Method Properties For Plot Type And Enhancement Info check box is selected. This option is unavailable when the Spectrum List Table is used in a Qual Repeating Section.)

3. Click OK.

Plot Type Page

For the parameters on the Plot Type page to be available, deselect the Use Processing Method Properties For Plot Type And Enhancement Info checkbox on the Options page.

To set the parameters in the Plot Type page

1. Enter the mass range to display in the Mass/Wavelength Range box. Enter the values separated by a dash: [lowmass]-[highmass]. Enter * to display the entire range (see Figure 42).

2. From the Detector list, choose the type of detector that you are using: MS or PDA.

3. Enter the time range to display in minutes in the Time box. Enter the values separated by a dash: [firsttime]-[secondtime]. Enter * to display the entire range.

4. Select or enter the scan filter to use with the data in the Scan Filter list.

Figure 42. Spectrum List Table Properties dialog box - Plot Type page



5. Enter or search in the Demo File box for the name of the file you would like to use as a demonstration file for the settings in the template.

6. Click OK.

Enhancement Page

To set the parameters in the Enhancement page

1. To add smoothing to the data, select the Enable checkbox in the Smoothing area (see Figure 43).

a. From the Type list, choose the type of smoothing to apply: Boxcar or Gaussian.

b. Enter the number of smoothing points to apply in the Points box, odd numbers between 3 (minimum smoothing) and 15 (maximum smoothing).

Figure 43. Spectrum List Table Properties dialog box - Enhancement page



2. To refine the data, select the Enable checkbox in the Refine area.

a. Enter the number of seconds on either side of the specified point over which the algorithm uses mass chromatograms in the Window box. A reasonable initial value is the peak width in seconds.

b. Enter the cutoff point for peaks in the Noise Threshold box. Type 0 to show all peaks in the spectrum and slowly increase the value until the noise peaks are eliminated. Use this setting to eliminate peaks generated from baseline noise.

3. To turn on a first baseline region that is used for assessing the background, select one or both of the Time Range checkboxes. Type the time range to use into the box.

The Background Subtraction area shows details of background subtraction if it was applied to the spectrum. The background contribution is determined by averaging the scans from one or two baseline regions.

4. Click OK.



Display Page

To set the parameters in the Display page

1. Either select the All Peaks checkbox to display all peaks in the spectrum or enter a value into the Top box to limit the display to the strongest peaks (see Figure 44).

2. Select whether to order the data by mass or by intensity by clicking the appropriate option in the Order By area.

3. Enter the relative abundance range of mass peaks to include in the table in the Normalization area.

4. Click OK.

Figure 44. Spectrum List Table Properties dialog box - Display page



Electronic Signature TableProperties

The Electronic Signature table object has only one configurable property: whether the Created By signature block appears before or after the Signed By signature block.

To configure the Electronic Signature table object

1. Right-click the Electronic Signature table object and choose Properties from the shortcut menu. The Electronic Signature Properties dialog box appears (see Figure 45).

2. Click the Created By First option in the Signature Information Order area to have the Created By signature block displayed before the Signed By signature block, or click the Signed By First option to have the Signed By block displayed before the Created By block.

3. Click OK to close the dialog box.

Figure 45. Electronic Signature Properties dialog box


4 Configuring Objects and SectionsConfiguring a Bitmap Object

Configuring a BitmapObject

To configure the bitmap object

1. Right-click the bitmap object and choose Properties from the shortcut menu to open the Bitmap Properties dialog box (see Figure 46).

2. Enter or search to the name of the image file. Use files of the format .bmp, .dib, .gif, .jpg, or .ico.

3. To set the size of the bitmap image to the size of the original file, click Reset To Original Size.

4. Click OK.

Figure 46. Bitmap Properties dialog box


4 Configuring Objects and SectionsConfiguring a Chromatogram

Configuring aChromatogram

To configure a Chromatogram report object

1. Right-click the object and choose Properties from the shortcut menu to open the Chromatogram Properties dialog box (see Figure 47).

2. Click Configure to open the Chromatogram Properties Wizard.

The Chromatogram Wizard guides you through the process of configuring a Chromatogram report object (that is, changing its properties) contained in the report template.

The XReport Chromatogram Wizard displays different pages and contains different options depending on the type of section containing the Chromatogram and the selections for the Chromatogram Type and Peak Type properties.

Table 1 lists the wizard pages and their order. These wizard pages are also discussed below. See the appropriate topic for information on how to complete each wizard page.

Figure 47. Chromatogram Properties dialog box



When the Chromatogram report object to be configured is contained in a Quan (or Qual) repeating section, the default Chromatogram Type is Quan (or Qual) Result Based with no explicit Peak Type set. The next page of the wizard (Use Container Supplied Quan (or Qual)) asks you to confirm this.

Table 1. Possible Chromatogram Wizard pages, given the section type, in order of appearance

Non-Repeating Section Repeating Section

Page in the XReport Chromatogram Wizard Raw Quan Qual Quan Qual

Use Container Supplied Quan Peak •

Use Container Supplied Qual Peak •

Select Chromatogram Type • • • •a •a

Select Demo File • • • • •

Select the Quan Peak • •b

Select Component •b

Select the Qual Peak • •b

Select Mass Spectrum Quan Traces to Display • •

Configure How the Peak Window Will Look • • • •

Select Plot Details •

Select Enhance Details •

Select Chromatogram Style • • • • •

Select the Peak Labeling • • • • •

Select How the Chromatogram Axis Will Be Configured • • • • •

Configure Normalization for the Chromatogram • • • • •

aThis page is not displayed if you selected Explicitly Specify the Chromatogram’s Behavior on the Use Container Supplied Quan/Qual peak page.bThis page is only displayed if you selected Explicitly Specify the Chromatogram’s Behavior on the Use Container Supplied Quan/Qual peak page.

Note When you click the All Qual Peaks option for a Qual Result Based Chromatogram, the wizard page order is the same as for the Qual Result Based Chromatogram Type without the Select Qual Peak page.



Use Container SuppliedQuan Peak Page

Use the Use Container Supplied Quan Peak page to display the details of the internal standard associated with the implicit Quan peak or ignore the implicit Quan peak and explicitly configure the chromatogram type.

To fill in the Use Container Supplied Quan Peak page of the Chromatogram

1. Select the Use Quan Peak’s Associated Internal Standard check box in the Implicit Quan Peak Options area to display the details of the internal standard associated with the implicit Quan peak (see Figure 48).

2. Select the Explicitly Specify the Chromatogram’s Behaviour check box in the Explicit Chromatogram Type area to ignore the implicit Quan peak supplied by the container and explicitly configure the chromatogram type.


Figure 48. Chromatogram Wizard - Use Container Supplied Quan Peak page



Use Container SuppliedQual Peak Page

Use the Use Container Supplied Qual Peak page to ignore the implicit Quan peak and explicitly configure the chromatogram type.

To fill in the Use Container Supplied Qual Peak page of the Chromatogram

1. Select the Explicitly Specify the Chromatogram’s Behaviour check box in the Explicit Chromatogram Type area to ignore the implicit Quan peak supplied by the container and explicitly configure the chromatogram type (see Figure 49).


Figure 49. Chromatogram Wizard - Use Container Supplied Qual Peak page



Select ChromatogramType Page

Use the Select Chromatogram Type page to set the Chromatogram Type for the Chromatogram report object being configured in the report template.

To fill in the Select Chromatogram Type page of the Chromatogram

1. Define the Chromatogram Type in the Chromatogram Type area (see Figure 50) by selecting one of the following options:

• Raw File Based Chromatogram

• Quan Result Based Chromatogram

• Qual Result Based Chromatogram

2. If you select a Qual Result Based Chromatogram in step 1, select the Show All Qual Peaks In Result File check box to display all Qual peaks in a resolved Xcalibur report. (This is a Peak Type setting.)


Figure 50. Chromatogram Wizard - Select Chromatogram Type page



Select Demo File Page Use the Select Demo File page to associate a demo file (demonstration file; .raw or .rst file) with a Chromatogram report object.

Use a demo file to see how the Chromatogram report object (in the report template and in wizard page previews) appears with its current settings when applied to real Xcalibur data.

The appearance of the Select Demo File page depends on the chromatogram type and the peak type settings chosen in the Chromatogram Type page of the wizard.



Raw File Based Chromatogram When configuring a Chromatogram report object based on a raw file, use the following procedure to select a file.

To fill in the Select Demo File page of the Chromatogram

1. Select the Use Demo File check box to associate a demo file with the Chromatogram report object (see Figure 51).

2. Click Browse in the Demo File area to open the Select Raw Data File dialog box and search for the required demo file (.raw file).

3. Click Open in the Select Raw File dialog box after you have selected the demo file.


Figure 51. Chromatogram Wizard - Select Demo File page: Raw File Based Chromatogram



Quan Result BasedChromatogram

When configuring a Chromatogram report object based on Quan Results, use the following procedure to select a file.


1. Select the Use Demo File check box to associate a demo file with the Chromatogram report object (Figure 52).



4. Specify the peak to demo as follows:

a. Click Browse in the Demo Peak area to open the Select a Peak dialog box.

b. Select a peak in the Select a Peak dialog box from the list located in the result file. Click OK to apply the selection and return to the wizard.


Figure 52. Chromatogram Wizard - Select Demo File page: Quan Result Based Chromatogram



Qual Result BasedChromatogram - Explicit Peak

When configuring a Chromatogram report object based on Qual Results with an explicit Peak Type required, use the following procedure to select a file.


1. Select the Use Demo File check box to associate a demo file with the Chromatogram report object (Figure 53).



4. Specify the peak to demo as follows:

a. Click Browse in the Demo Peak area to open the Select a Peak dialog box.

b. Select a peak in the Select A Peak dialog box from the list located in the result file. Click OK to apply the selection and return to the wizard.


Figure 53. Chromatogram Wizard - Select Demo File page: Qual Result Based Chromatogram - Explicit Peak



Qual Result BasedChromatogram - All Available

Peaks

When configuring a Chromatogram report object that is Qual Result Based with Show All Qual Peaks set (Peak Type setting), use the following procedure to select a file.


1. Select the Use Demo File check box to associate a demo file with the Chromatogram report object (see Figure 51 on page 80).




Select the Quan PeakPage

Use the Quan Peak page to explicitly specify the Quan peak (component) for a Quan Results Based Chromatogram report object.

To fill in the Select the Quan Peak page of the Chromatogram

1. Specify the Quan peak in the Quan Peak area by typing the text name of the component (see Figure 54).

Figure 54. Chromatogram Wizard - Select the Quan Peak page



The Next button is active only after you have selected a component or select the component by browsing for the required processing method file as follows:

a. Click Browse to open the Select Component dialog box and search for the required file (.pmd file).

b. After selecting a processing method file, use the Select Component dialog box to choose a component. Click OK to return to the wizard.

2. Select the Use Quan Peak’s Associated Internal Standard check box of the Quan peak to use the selected the associated Internal Standard of the Quan peak instead of the Quan peak.


Note Select a valid peak for XReport to resolve the report correctly. If the file used to resolve the report does not contain the specified peak, the chromatogram is removed from the resolved report.



Select the Qual Peak Page Use the Select the Qual Peak page to explicitly specify the Qual peak for a Qual Results Based Chromatogram report object.

To fill in the Select the Qual Peak page of the Chromatogram

1. Specify the Qual peak in the Qual Peak to Display area by typing the appropriate retention time into the Retention Time box (see Figure 55).

The Next button is active only after you have selected a component. Set the retention time to any time within the start and end peak boundaries.


Figure 55. Chromatogram Wizard - Select the Qual Peak page

Note Select a valid retention time for XReport to resolve the report correctly. If the file used to resolve the report does not contain the specified retention time, the chromatogram is removed from the resolved report.



Select Mass SpectrumQuan Traces to Display

Page

Use the Select Mass Spectrum Quan Traces to Display page to configure the Quan Traces property for MS data. (This page is only applicable to MS data and is ignored for other detector types.)

When a Chromatogram report object displays a Quan component, there are potentially six traces associated with the component, as follows:

• Quan Mass (QM) Trace - the actual component peak

• Up to five Confirmation Ions

Select any of these possible six traces to be displayed in the Chromatogram or display all available traces of the component.

To fill in the Select Mass Spectrum Quan Traces to Display page

1. Select the Quan trace in the Quan Traces area to be used from the Quan Traces list (see Figure 56).

Note The Ion Ratio Confirmation settings on this page apply only to GC-MS data.

Figure 56. Chromatogram Wizard - Select Mass Spectrum Quan Traces To Display page



2. After selecting All Quan Traces from the list, select the Common Normalization For All Traces check box to normalize all the traces the same way.


Configure How the PeakWindow Will Look Page

Use the Configure How the Peak Window Will Look page to control the display of the baselines (Quan and Qual peaks) and the peak window width (active for: Qual peak; Quan peak only in some cases) when a peak from a result file is set to display in a Chromatogram.

To fill in the Configure How the Peak Window Will Look page

1. Select the Show Baselines check box to display the baselines for a Chromatogram peak (Quan or Qual) (see Figure 57). When this option is left unchecked, XReport does not display the baselines, peak tracing or full peak annotation.

2. Select the Set Custom Window Width check box to manually override the default value of the peak window width (the default is peak width plus 1 min.). Use the Custom Width edit box to enter a value for the window width (min.). The default value for this field is 0.75 min.


Figure 57. Chromatogram Wizard - Configure How the Peak Window Will Look page



Select Plot Details Page Use the Select Plot Details page to configure how the plot is drawn when raw data is being displayed in a Chromatogram report object.

To fill in the Select Plot details page of the Chromatogram

1. Select the type of detector used to generate the raw file from the Detector list in the Plot Type area (see Figure 58). The type of detector determines the available traces.

2. Type in the offset of the start of a chromatogram trace in the Delay box. This box is available only when a non-MS detector type selected, such as UV or PDA.

3. From the Filter list, select the processing that is applied to a subset of the scans in a .raw file by selecting a filter from the list.

This option is available only when MS detectors are selected. The list displays scan filter options stored in the selected demo .raw file. If no demo file is selected, enter a valid filter string.

Figure 58. Chromatogram Wizard - Select Plot Details page



4. From the Trace lists, select the following:

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

b. From the second list, select a logical operator: + or -. Selecting an operator makes the third list active.

c. From third list, select a second chromatogram type to add to, or subtract from, the first trace (for example, Mass Range). The list features valid plot types.

The list of valid Traces depends on the detector used to generate the data as follows:

5. Depending on the type of chromatogram selected, do the following:

a. If you chose MS detector types, specify the mass or mass range for Mass Range or Base Peak Traces in the Mass list as follows:

If you chose Base Peak ± Mass Range or Mass Range ± Mass Range plot combinations in step 4 above, the identification page displays a Mass (m/z) field for each trace type.

b. If you chose other detector types, use this field to specify the wavelength or wavelength range for the chromatogram. If you use a plot combination such as Wavelength Range + Wavelength Range, an additional Wavelength (nm) box appears for you to specify the second wavelength range.

The valid range is dependent upon the configured detector. The format is [Low Mass/Wavelength]-[High Mass/Wavelength]. Separate entries by dash, with no spaces. For example, for the range m/z 123 through 456, type the following: 123-456.

MS valid traces are Mass Range, TIC, and Base Peak

Analog valid traces are Analog 1-4

A/D card valid traces are A/D Card Ch 1-4

PDA valid traces are Wavelength Range, Total Scan, and Spectrum Maximum

UV valid traces are Channel A-D



6. Specify the lower and upper time limits for the plot (in minutes to 1 decimal place) in the Time Range box. Separate entries by a dash, with no spaces.

Type * (the default setting) to display the complete time range for the plot.

7. Select the Fixed Scale check box to enable or disable the Fixed Scale box. Use this box to set the Y-axis maximum to a specific value.

After selecting the Fixed Scale check box, the Normalize To area on the final page of the wizard is active, as is the box where you enter the maximum Y-axis value on the current page.

8. Select the Autofilter check box to repopulate a Chromatogram view with the following:

• A plot showing the chromatogram without any scan filters

• Plots for each scan filter applied to the chromatogram




Select Enhance DetailsPage

Use the Select Enhance Details page to enhance a Chromatogram plot by applying smoothing (see Figure 59).

To fill in the Select Enhance Details page of the Chromatogram

1. Select the Enable Smoothing check box to apply smoothing to the chromatogram.

2. Select the type of smoothing, either Boxcar or Gaussian, from the Type list in the Smoothing Details area.

3. Select the number of smoothing points (odd numbers from 3 to 15) to be used in the Points list.

4. Click Next to go to the next page of the wizard.

Figure 59. Chromatogram Wizard - Select Enhance Details page



Select ChromatogramStyle Page

Use the Select Chromatogram Style page to determine the appearance of the Chromatogram.

To fill in the Select Chromatogram Style page of the Chromatogram

1. Select one of the following options to define the plotting style in the Plotting area (see Figure 60):

• Point to Point—to display point-to-point peak profiles.

• Stick—to display the chromatogram as vertical lines.

2. Select one of the following options to define the plotting arrangement in the Arrangement area:

• Stack (2D)—to stack plots vertically (same X-axis) with no overlap (own Y-axis).

• Overlay (3D)—to overlay plots vertically (same X-axis). Use the 3D arrangement when you selected Multiple Quan Traces on the Select Mass Spectrum Quan Traces page of the wizard.

Figure 60. Chromatogram Wizard - Select Chromatogram Style page



3. When you select an Overlay (3D) arrangement, set the following in the 3D area:

a. Adjust the Elevation slider bar to set the Elevation angle (from 0 to 60 degrees) for the 3D plot style. Either drag the Elevation slider bar or click the Elevation slider left or right arrows until you reach the desired angle.

b. Adjust the Skew slider bar to set the skew angle for the 3D plot style. Either drag the Skew slider or click the Skew slider left or right arrow until you reach the desired angle (from 0 to 45 degrees).

c. Select the Draw Backdrop check box to add a backdrop to 3D plots.




Select the Peak LabelingPage

Use the Select The Peak Labeling page to choose the type and style of peak labels. From this page click the Advanced button to open a dialog box to set advanced labeling options.

Basic Options To fill in the Select the Peak Labeling page of the Chromatogram

1. Select the Retention Time check box in the Label With area to label peaks with the time in minutes, in the chromatogram plot (see Figure 61). RT prefixes the label.

2. Select the Scan Number check box to label peaks with number of mass scan at peak maximum. S# prefixes label.

3. Select the Base Peak check box to label the base peak in the mass spectrum of the chromatogram peak. BP prefixes the label.

4. Select the Signal-to-Noise check box to label peaks with the signal-to-noise ratio at the peak maximum. SN prefixes the label.

5. Select the Flags check box to label peaks with flags providing supplemental information about the peak data. For example, when a peak is saturated, Xcalibur displays an S above the peak.

Figure 61. Chromatogram Wizard - Select the Peak Labeling page



6. Select the Area check box to label peaks with the integrated area of the peaks, prefixed by AA when detected automatically, or MA when detected manually.

7. Select the Height check box to label peaks with the apex height prefixed by AH when detected automatically, or MH when detected manually.

8. Select the Offset check box in the Label Styles area to offset a label from its normal position to avoid conflict with another label. Choose the amount of the offset (in number of characters) in the Size box.

9. Select the Rotated check box to use vertical, rather than horizontal, labels.

10. Select the Boxed check box to place a rectangular outline around each peak label.

11. Select the Label Threshold check box to limit the labeling of peaks to those exceeding the specified percentage of the base peak.

12. Set the Label threshold box to a value between 0 and 100%.


Advanced Options (Quan) Click the Advanced button in the Select the Peak Labeling page to open the Advanced Quan Peak Annotation Options dialog box. When you set Advanced Labeling options, only the Quan peak is labeled.

Fill in the Advanced Quan Peak Annotation Options dialog box as follows:

1. Select the Use Advanced Quan Peak Annotation check box to enable the advanced Quan peak options (see Figure 62).



2. Select the Component Name check box in the Custom Peak Labels area to label the Quan peak with the component name.

3. Select the Component Key check box to label the Quan peak with the component key.

4. Select the Custom Text Label check box to specify a custom label. Type a custom label for the Quan peak into the box.

5. Select the Retention Time check box to label the Quan peak with the retention time. When you toggle this check box, the change is reflected in the Labels page when you return to it.

6. Select the units in the RT Labeling area for the retention time from the Units list.

7. Select the number of decimal places to be displayed in the retention time label from the Decimals list.

8. Click OK to close the Advanced Quan Peak Annotation Options dialog box.

Figure 62. Advanced Quan Peak Annotation Options dialog box



Advanced Options (Qual) Click the Advanced button in the Select the Peak Labeling page to open the Advanced Qual Peak Annotation Options dialog box. When you set Advanced Labeling options, only the Qual peak is labeled.

To fill in the Advanced Qual Peak Annotation Options dialog box

1. Select the Use Advanced Qual Peak Annotation check box to enable the advanced Qual peak options (see Figure 63).

2. Select the Custom Text Label check box in the Custom Peak Labels area to specify a custom label. Type a custom label for the Qual peak into the box.

3. Select the Retention Time check box to label the Qual peak with the retention time. When you toggle this check box, the change is reflected in the Labels page when you return to it.

4. Select the units for the retention time from the Units list.

5. Select the number of decimal places in the RT Labeling area to be displayed in the retention time label from the Decimals list.

6. Click OK to close the Advanced Qual Peak Annotation Options dialog box.

Figure 63. Advanced Qual Peak Annotation Options dialog box



Select How theChromatogram Axes Will

Be Configured Page

Use the Axes page to set chromatogram axes labels and display options.

To fill in the Select How the Chromatogram Axes Will Be Configured page of the Chromatogram

1. Set the Name of the X axis in the X Axis area by typing it into the Name box (see Figure 64).

2. Select the Offset check box to offset the axis label from the chromatogram.

3. Select the Split Time Range check box to split the chromatograms into two or more separate graphs with equal time ranges.

4. Type the number of split time range graphs displayed for each chromatogram in the Divisions box. This box is active only when you select the Split Time Range check box.

5. Click the From Detector option in the Y Axis area in the Label area to use the detector-specific label for the Y-axis (stored in the .raw file) or click the Custom option to use your own label.

Figure 64. Chromatogram Wizard - Select How the Chromatogram Axes Will Be Configured page



6. Choose between the Absolute and Relative options in the Units area to specify the setting for the Y-axis units: absolute or relative.

7. If you have chosen to use a Custom label for the Y-axis, in the Name box, type a Y-axis name.

8. Select the Offset check box to offset the axis label from the chromatogram.




Configure Normalizationfor the Chromatogram

Page

Use the Normalization page to select the normalization (Y-axis scaling) method used for the chromatogram.

To fill in the Configure Normalization for the Chromatogram page

1. Define the normalizing method in the Normalize Method area (see Figure 65) by selecting one of the following options:

• Auto Zero—to optimize the Y-axis automatically for each chromatogram.

• Intensity range (%)—to set the range manually. Type the minimum and maximum intensity required for the Y-axis. The valid range is -200.00 to +200.00%.

2. Define which peak to normalize to in the Normalize To area by selecting one of the following options:

• Largest Peak in Subsection—normalizes each split time range to the largest peak in the division.

• Largest Peak in Selected Time Range—normalizes the spectrum to the largest peak in the displayed time range.

Figure 65. Chromatogram Wizard - Configure Normalization for the Chromatogram page



• Largest Peak in All Times—normalizes the spectrum to the largest peak in the entire chromatogram.

The Normalize To area is active when you select a .raw-based chromatogram, and the Fixed Scale check box is selected on the Plot Type page.

Finishing theChromatogram Wizard

To change selections in the Chromatogram Wizard, click Back to go back through the previous pages. If the page is done, click Finish.


4 Configuring Objects and SectionsConfiguring a Component Calibration Curve

Configuring aComponent

Calibration Curve

To configure a Component Calibration Curve object, right-click it and choose Properties from the shortcut menu to open the Component Calibration Curve Properties dialog box.

Use the Component Calibration Curve Wizard to specify the name of the component that a non-repeating Component Cal Curve report object is plotted for in the report.

To specify the name of the component

1. Click the Browse button to open the Select Processing File dialog box and search for the required Processing Method file (.pmd) (see Figure 66). By default, the wizard searches in the Xcalibur\methods folder.

Figure 66. Component Cal Curve Properties dialog box


4 Configuring Objects and SectionsConfiguring a Component Calibration Curve

2. Select a file and click Open to open the selected file. The Select Component dialog box appears (see Figure 67).

3. Select the required component from the list available for the chosen processing method and click OK. Xcalibur opens the Component Name page with the specified name of the component displayed in the box.

4. Click OK.

Figure 67. Select Component dialog box


4 Configuring Objects and SectionsConfiguring a Spectrum

Configuring aSpectrum

To configure a Spectrum report object, right-click it and choose Properties from the shortcut menu to open the Spectrum Properties dialog box.

The XReport Spectrum Control Properties dialog box consists of 8 pages, as follows:

• Options• Plot Type• Enhance• Style• Labels• Axis• Normalization• Peak

Each page is discussed in the topics below. Make selections on each page to configure the Spectrum report object.

Figure 68. Spectrum Properties dialog box - Options page



Options Page Use the Options page to configure the Spectrum options.

To fill in the Options page of the XReport Spectrum Control Properties dialog box

1. Select the Use Processing Method Properties For Plot Type And Enhance Info check box to use processing method properties for Plot Type and Enhance information (see Figure 68).

When you select this checkbox, the options on the Plot Type and Enhance pages are unavailable.

2. Select the Use ISTD Peak When Repeating On Component check box to use the Internal Standard peak when repeating on a component. This option is only available when the Use Processing Method Properties For Plot Type and Enhance Info check box is selected.



Plot Type Page When raw data is being displayed in a Spectrum report object, use the Plot Type page to configure how the plot is drawn.

If you selected the Use Processing Method Properties For Plot Type And Enhance Info check box on the Options page, this page is blank.

To fill in the Plot Type page of the XReport Spectrum Control Properties dialog box

1. Specify the mass or mass range for MS detector types in the Mass Range box (see Figure 69).

For PDA detector types, use this parameter to specify the wavelength or wavelength range (nm). Type the lower and upper limits for the plot. Separate entries by a dash (no spaces). To use the entire mass/wavelength range, type: *

2. Select the type of detector used to generate the raw file from the Detector list. Valid types are: MS and PDA. The type of detector determines the available Plot types.

3. Select the time of the mass scan in the host chromatogram in the Time box. Enter a new value or range as required.

Figure 69. Spectrum Properties dialog box - Plot Type page



4. From the Scan Filter list, select a filter from the list, or type a new one using the scan filter format.

5. Click Browse in the Demo File box and select the file. This box shows the path and filename of the demo file (raw file) used to generate the selected plot.

Enhance Page Use the Enhance page to apply smoothing or the refine algorithm to the spectrum and set background subtraction time ranges.

If you selected the Use Processing Method Properties For Plot Type And Enhance Info check box on the Options page, this page is blank.

To fill in the Enhance page of the XReport Spectrum Control Properties dialog box

1. Select the Enable check box in the Smoothing area to turn on spectrum smoothing (see Figure 70).

2. From the Type list, specify the type of smoothing algorithm to apply to the spectrum: Boxcar or Gaussian.

Figure 70. Spectrum Properties dialog box - Enhance page



3. Type the number of points for spectrum smoothing in the Points list. This must be an odd number in the range 3 [minimum smoothing] to 15 [maximum smoothing].

4. Use the Enable check box in the Refine area to turn Refine spectrum enhancement on or off.

5. Type the number of seconds on either side of the specified point over which the algorithm uses mass chromatograms in the Window box. A reasonable initial value is the peak width in seconds.

6. Type 0 (this shows all peaks in the spectrum) in the Noise Threshold box and increase the value until noise peaks are eliminated. Use this parameter to eliminate peaks generated from baseline noise.

7. Select the Time Range 1 check box in the Background Subtraction area to enable a first baseline region used for assessing the background. Type the time range in the box.

The Background Subtraction area shows details of background subtraction when this value has been applied to the spectrum. The background contribution is determined by averaging the scans from one or two baseline regions.

8. Select the Time Range 2 check box to enable a second baseline region used for assessing the background. Type the time range in the box.



Style Page Use the Style page to set parameters that determine the appearance of the spectrum (see Figure 71).

Fill in the Style page of the XReport Spectrum Control Properties dialog box as follows: in the Plotting area, define the plotting style by selecting one of the following options:

• Automatic—to choose the graphic style based upon the data acquisition method used for the active spectrum.

• Point to point—to display a point-to-point peak profile.

• Stick—to display spectral mass peaks as vertical lines.

• Shade—to display the spectrum as a shaded representation of intensity in each amu band for the active spectrum.

Figure 71. Spectrum Properties dialog box - Style page



Labels Page Use the Labels page to choose the type and style of peak labels.

To fill in the Labels page of the XReport Spectrum Control Properties dialog box

1. Select the Mass check box in the Label With area to label spectrum peaks with m/z values (see Figure 72).

2. Select the Flags check box to label spectrum peaks with flags. Flags provide supplemental information about the peak data. For example, when a peak is saturated, Xcalibur displays an S above the peak.

3. Enter a value in the Relative To combo box to specify that other spectrum peaks are labeled relative to that value.

4. Specify the number of decimal places in the Decimals box to be used in the labels.

5. Select the Offset check box in the Label Styles area to offset a label from its normal position to avoid conflict with another label. Choose the amount of the offset (in number of characters) in the Size box.

Figure 72. Spectrum Properties dialog box - Labels page



6. Select the Rotated check box to use vertical, rather than horizontal, labels.

7. Select the Boxed check box to place a rectangular outline around each peak label (but not flags).

8. Limit the labeling of peaks to those exceeding the specified percentage of the base peak in the Label Threshold box.

Axis Page Use the Axis page to set spectrum axis labels and display options.

To fill in the Axis page of the XReport Spectrum Control Properties dialog box

1. Type the X-axis name into the Name box in the X Axis are (see Figure 73).

2. Select the Offset check box to offset the axis label from the spectrum.

3. Select the Split Mass Range check box to split the spectra into two or more separate graphs with equal ranges. Enter the number of split range graphs displayed for each spectrum in the Divisions box.

Figure 73. Spectrum Properties dialog box - Axis page



4. Select one of the following options in the Y Axis area in the Label area:

• From Detector—to use the detector-specific label for the Y-axis (stored in the .raw file)

• Custom—to use your own label.

5. Click the Absolute or the Relative option in the Units area to specify the setting for the Y-axis units: absolute or relative.

6. Enter a Y-axis name in the Name box.

7. Select the Offset check box to offset the axis label from the spectrum.



Normalization Page Use the Normalization page to select normalization options for spectrum plots.

To fill in the Normalization page of the XReport Spectrum Control Properties dialog box

1. Select one of the following options to define the normalization method in the Normalize Method area (see Figure 74).

• Auto zero—to automatically optimize the Y-axis

• Intensity Range (%)—to set the Y-axis range. Use the box to enter the minimum and maximum intensity. The valid range is -200.00 to +200.00%.

2. Define the peak that the spectrum is normalized to in the Normalize To area by selecting one of the following options:

• Largest peak in subsection—to normalize each split mass range to the largest peak in the division.

• Largest peak in mass range—to normalize the spectrum to the largest peak in the displayed mass range.

Figure 74. Spectrum Properties dialog box - Normalization page



• Largest peak in scan—to normalize the spectrum to the largest peak in the entire spectrum.

3. Define how multiple scans are normalized in the Normalize multiple scans area by selecting one of the following options:

• Individually—to normalize each mass plot individually.

• All the same—to normalize all mass plots equally.



Peak Page Use the Peak page to explicitly specify the peak to display in the Spectrum report object.

To fill in the Peak page of the XReport Spectrum Control Properties dialog box

1. Select the Enable Explicit Peak Type check box to enable the controls that allow you to specify the type of peak to appear in the Spectrum (see Figure 75).

2. Click the Quan Peak option in the Peak Type area to specify a Quan peak, or click the Qual Peak option to specify a Qual peak. Use this area to explicitly specify the type of peak to appear in the Spectrum.

3. Type a name for the component for a Quan peak in the Peak Identification area. For a Qual peak, type the retention time (any time between the start time and end time of the peak can be entered) or click Browse to open the Select a Peak dialog box. Select (highlight) a peak and click OK to close the dialog box.

Figure 75. Spectrum Properties dialog box - Peak page


4 Configuring Objects and SectionsConfiguring Columns

Configuring Columns To configure a column object, right-click it and choose Properties from the shortcut menu to open the Column Properties dialog box.

After you have configured a column object, drag objects into the columns.

To configure a column object

1. Select the number of columns to use in the Number Of Columns area (see Figure 76).

2. If the column object is in a Non-Repeating section, configure the Repeat Type. The Repeat Type options are not available in Quan Repeating or Qual Repeating sections. In the Repeat Type area, select whether you would like to use Sample Repeat or Summary Repeat by clicking the appropriate option. See “Sample Repeat Option” on page 117 and “Summary Repeat Option” on page 118 for an example of using the two repeats.

3. If you selected Summary Repeat, select whether you would like to repeat from left to right or from top to bottom by clicking the appropriate option.

4. To have each sample begin on a new row, select the New Sample New Row check box.

Figure 76. Column Properties dialog box



Sample Repeat Option Use the Sample Repeat option to present information relating to a raw file of a single sample and the results created when processing it. Use this repeat type as a layout tool to indicate where objects are placed on the page of the resolved report.

For example, if you place a 2-column object in a Non-Repeating section, add a Quan-based chromatogram to the left column and combine or resolve the template using data of 1 sample with 4 components, the report appears as in Figure 77.

For example, place a 2-column object in a Non-Repeating section, add a chromatogram and a text object to the left column, and a spectrum to the right column. Combine (resolve) the template using data of 1 sample with 4 components. All objects in the column are repeated for a single sample, and the report appears as in Figure 78.

Note The Sample Repeat and Summary Repeat options are applicable only in Non-Repeating report sections. These options are not available in other types of report sections.

Figure 77. 2-column object behavior in a Non-Repeating section, with a chromatogram object

Chrom Chrom 1 Chrom 2

Chrom 3 Chrom 4

Resolve

Sample 1



Summary Repeat Option Use the Summary Repeat option to present information relating to all of the samples in an Xcalibur sequence and the results created when processing them.

For example, if you place a 2-column object in a Non-Repeating section, add a chromatogram (in either column), and combine (resolve) the template using data of 2 samples with 4 components each, the report appears as in Figure 79.

Figure 78. 2-column object behavior in a Non-Repeating section, with chromatogram and spectrum objects

Resolve

Sample 1

SpecChrom

Text

Spec 1Chrom 1

Text

Spec 2Chrom 2

Text

Spec 3Chrom 3

Text

Spec 4Chrom 4

Text

Note The Sample Repeat and Summary Repeat options are applicable only in Non-Repeating report sections. These options are not available in other types of report sections.

Figure 79. 2-column object behavior in a Non-Repeating section, with a chromatogram, Left to Right option

Chrom Chrom 2Chrom 1

Chrom 3 Chrom 4

Chrom 1

Chrom 3

Chrom 2

Chrom 4

Resolve

Sample 1

Sample 2

Left to

Right



If you choose instead the Top To Bottom option, the report appears as in Figure 80.

If you place an object in the right column and leave the left column empty, the software combines the data as if the object is placed in the left column, as illustrated above.

If you place an object in each column, the Top To Bottom and Left To Right options are ignored. The report appears as in Figure 81.

Figure 80. 2-column object behavior in a Non-Repeating section, with a chromatogram, Top to Bottom option

Figure 81. 2-column object behavior in a Non-Repeating section, with chromatogram and spectrum objects

Chrom Chrom 3Chrom 1

Chrom 2 Chrom 4

Chrom 1

Chrom 2

Chrom 3

Chrom 4

Resolve

Sample 1

Sample 2

Top to

Bottom

Spec 1

Spec 2

Spec 3

Spec 4

Chrom 1

Chrom 2

Chrom 3

Chrom 4

Chrom 1

Chrom 2

Chrom 3

Chrom 4

Resolve

Sample 1

Spec 1

Spec 2

Spec 3

Spec 4

Sample 2

SpecChrom

Text

Text


Appendix A Example XReport Template Files

Xcalibur ships with several example XReport templates ready-built for you to use. This appendix provides details of these report templates found at the following location:

Xcalibur\templates

These report templates serve as useful examples of the different types of report template you might want to create.

Table 2. Example XReport template files

Report Template File Name Data Source File(s)

Description / Use

CalibrationFile.xrt .raw, .xcal For generating Sample Reports with calibration data.

CompCalReport.xrt

CompCalReport_Avalon.xrt

CompCalReport_Genesis.xrt

CompCalReport_ICIS.xrt

.rst, .raw,

.pmd, .sldFor generating Summary Reports showing processing method details, calibration curve and sample table (Quan results). Can be used from Xcalibur’s Batch Processing and Quan Browser.

CustLibrSearRept.xrt

LibrarySearchReport.xrt

.rst, .raw For generating Qual Sample Reports that display Qual peaks and library search details. Should be used from Xcalibur’s Batch Processing.

IonRatioConfirmation.xrt .rst, .raw,.pmd

For generating a Quan Sample Report containing non-graphical ion ratio confirmation results.

IonRatioConfirmationGraphical.xrt

IonRatioConfirmationGraphicalSimple.xrt

IonRatioConfirmationGraphicalStacked.xrt

.rst, .raw,

.pmdFor generating Quan Sample Reports containing graphical ion ratio confirmation results. These report templates take advantage of the explicit confirmation ion settings available when using the XReport Chromatogram Wizard.

PeakIntegration.xrt .rst, .raw,.pmd

For generating a Quan Sample Report containing peak integration data generated using Genesis.

ProcessingMethod.xrt

ProcessingMethod_Avalon.xrt

ProcessingMethod_Genesis.xrt

ProcessingMethod_ICIS.xrt

.pmd For generating processing method Sample Reports. Use from Xcalibur’s Processing Method Setup.

QualPeakReport.xrt .rst, .raw For generating a simple Qual Sample Report.Should be used from Xcalibur’s Batch Processing.


A

QuanPeakResults_ESTD.xrt

QuanPeakResults_ISTD.xrt

QuanResults.xrt

QuanSimple.xrt

.rst, .raw,

.pmdFor generating Quan Sample Reports. Can be used from Xcalibur’s Batch Processing or Quan Browser.

QuantifySampleReport.xrt .sld, .pmd,.rst, .raw

For generating a Quan Summary Report containing chromatograms and a Quan summary table.

SequenceReport.xrt .sld For generating a Summary Report showing the sequence being processed. Use from Xcalibur’s Batch Reprocessing

SpectrumCandidates.xrt .rst, .raw For generating a Quan Summary Report (only applicable to GC/MS). Use from Xcalibur’s Batch Reprocessing or Quan Browser.

Table 2. Example XReport template files, continued


Appendix B Report Objects

The following tables list the report objects you can place onto a report template: text objects, table objects, graphic objects, and formatting objects. The tables briefly describe an object and indicate in which sections the object is available.

This appendix lists the following objects:

• Text objects in Table 3

• Table objects in Table 4

• Graphic objects in Table 5

• Formatting objects in Table B-4


B

Table 3. Text Objects

Text Object Data Source File

Description Section Placement

Annotation none Displays static text. Use this object for adding headings or comments.

Any

Component Ident/Detect/Cal Settings

.pmd Shows the peak detection, calibration, and integration parameters for a single component.

Quan Repeating

Component ISTD Settings Summary

.pmd Displays a summary of the configuration details for each component’s ISTD configuration in the Quantitation section of a processing method

Quan Repeating

Component Settings Summary

.pmd Displays a short list of peak detection and integration parameters for a specified component.

Quan Repeating

Component Sys Suit/Flags Settings

.pmd Displays Calibration, Quantitation, and Detection flags along with system suitability parameters, which allow automatic chromatographic checks that assign a pass/fail qualification to a target peak.

Quan Repeating

Instrument Method .raw Displays general instrument method parameters. This text object does not have any editable properties.

Non-Repeating

Processing Method -General

.pmd Displays general processing method parameters. General parameters include date created, date modified, baseline definition, chromatography type (LC / GC).

Non-Repeating

Processing Method - Qual

.pmd Displays Qual processing method parameters. Qual parameters include the following:

• Identification

• Spectrum Enhancement

• Detection Options

• Advanced Detection Options

• Library Search Constraints

• Library Search Options

Non-Repeating

Quan ISTD Peak Summary

.rst, .pmd Displays summary parameters for a Quan component’s associated ISTD peak. For example:

ISTD NameBase LineActual RTSignal To NoiseResponse Expected RT

Quan Repeating

Quan Peak Summary .rst, .pmd Displays Component Peak summary parameters, for example:

Actual RT% DiffCalculated AmountArea RatioResponse Area ISTDBase Line Specified AmountSignal To Noise

Quan Repeating, header/ footer

Report Info none Displays general information about the report itself. Header/ footer


B

Sample Header .raw,

.sld

Displays general information about a sample, for example:

Sample Name OperatorSample Type Run TimeAcquisition Date

Non- Repeating, header/ footer

Table 3. Text Objects, continued

Text Object Data Source File



B

Table 4. Table Objects

Table Object Data Source File


Avalon Qual Events Table

.pmd Displays details of the Avalon peak detection algorithm events configured in the Qual section of a processing method.

Non-Repeating

Avalon Quan Events Table

.pmd Displays details of the Avalon peak detection algorithm events configured for a component in the Quan section of a processing method.

Quan Repeating

Calibration File Table .xcal,.sld,.raw

Displays component names, response factors, and %RSD of standards.

Non-Repeating

Component Cal Level Table

.pmd Shows the calibration levels, amounts, and acceptance test values defined for a specific component.

Quan Repeating, or Non-Repeating

Component QC Level Table

.pmd Shows the QC levels, amounts, and percent test values defined for a specific component.

Quan Repeating

Component Spectrum Table

.pmd Displays m/z and intensity data for up to fifty spectrum peaks. Xcalibur uses this data to identify components when the Spectrum Peak Identification Method is specified in the processing method.

Note. This object is used only for GC chromatography.

Quan Repeating

Dilution Factor Table .rst Displays the names of calibration levels and dilution factors for components other than internal standards.

Non-Repeating

Electronic Signature none Displays up to five electronic signatures in table format. This object is not editable in XReport.

Any

Ion Ratio Confirmation Results Table

.rst Displays the following data about each qualifier ion, based on search criteria specified in the processing method:

Mass

Coelution test pass/fail

Ion Ratio Test Target %

Ion Ratio Test Window %

Quan Repeating

IRC Settings Table .pmd Displays up to five qualifier ions within tolerance limits to confirm the detection of a target analyte. The ions are specified in the processing method.

Quan Repeating

IRC Summary Table .rst Displays all of the information for the confirmation ion for each component. Most useful when the Name column is the first column.

Non-Repeating

Lib. Search Graph Table

.rst, .raw Displays the graphical results from a library search on a Qual peak (for example, Hit Spectrum, Delta, and Compound Structure).

Qual Repeating

Lib. Search Results Table

.rst, .raw Displays the results of a Library Search on a Qual peak (for example, Name, Probability, RSI, SI, CAS#, Area).

Qual Repeating


B

Proc. Method Programs Table

.pmd Displays a list of programs to be run by Xcalibur after the sample has been analyzed and the data has been processed. Xcalibur runs the programs in the order listed.

Non-Repeating

Proc. Method Sample Reports Table

.pmd Displays Sample Report information for each sample in a sequence, including Template name and the Report file name. Specify Sample Type in the processing method.

Non-Repeating

Proc. Method Summary Reports Table

.pmd Displays Summary Reports to be issued after processing the samples in a bracketed or non-bracketed sequence.

Non-Repeating

Qual Peak Table .rst Displays information specific to chromatogram peaks detected by qualitative analysis for a single sample.

Non-Repeating

Qual Summary Table .sld, .rst Displays information specific to chromatogram peaks detected by qualitative analysis for all samples in a sequence.

Non-Repeating

Quan Peak Table .rst, .pmd Displays information specific to component peaks detected by quantitative analysis for a single sample.

Non-Repeating

Quan Summary Table .sld, .rst,.pmd

Displays information specific to component peaks detected by quantitative analysis for all samples in a sequence.

Non-Repeating

Sample Table (Quan Results)

.sld Displays system suitability and flag processing results for each component in a sample, and repeats this information for every sample in a sequence.

Quan Repeating

Sequence Table .sld Displays the contents of the sequence file. Non-Repeating

Spectrum Candidate Results Table

.rst Displays the results of spectrum candidate processing for GC/MS data on a per component basis. Parameters include the following:

Forward fitStart RTReverse fitEnd RTMatchAreaFound RTHeight

Non-Repeating

Spectrum List Table .rst, .raw Displays the text equivalent of the Spectrum graphic object. The Spectrum List Table contains a header, then lists values for the m/z, intensity, and relative intensity.

Qual or Quan Repeating

Table 4. Table Objects, continued

Table Object Data Source File



B

Table 5. Graphic Objects

Graphic Object Data Source File


Bitmap .bmp,.dib, .gif,.jpg, or.ico

Displays a graphical image, for example, a company logo.

Any

Chromatogram .raw, .rst Displays a graphical trace that can show either raw data or processed data for any acquisition device supported by Xcalibur (MS, Analog, A/D Card, PDA, UV).

Qual or Quan Repeating, and Non-Repeating sections

Component Cal Curve .rst.pmd

Shows the calibration curve used to quantify a specified component. The curve is specified in the processing method as response versus amount of standard.

Quan Repeating - repeats on component peak

Non-Repeating - uses the specified component.

Spectrum .raw, .rst Displays a graphical spectrum that can show either raw data or processed data for any acquisition device supported by Xcalibur (MS, PDA).

Qual or Quan Repeating, and Non-Repeating sections

Table 6. Formatting Objects

Graphic Object Data Source File


Columns none Use to manipulate the layout and repeating properties of graphic and text objects.

Any

Page Break none Use to insert a manual page break in the report. Qual or Quan Repeating, and Non-Repeating sections


Appendix C Sample Report

This appendix contains a sample Xcalibur report that is generated when you use the PeakIntegration.xrt report template (located in the Xcalibur\templates folder) to generate a Quan sample report containing certain peak integration data. The data file used is steroids02.rst (located in the Xcalibur\examples\data folder) from the shipped steroid data.


C

Peak Integration Report

There is no signature data to report.

Page 1 of 4

Data File: steroids02 Original Data Path: C:\pitcon\trial2 Current Data Path: C:\Xcalibur\example

s\data

Sample Type: Std Bracket Start Sample ID: Sample02 Sample Name:

Operator: jackc Acquisition Date: 02/28/96 11:20:31 AMRun Time(min): 3.79

Comments: Vial: 1 Scans: 336

Low Mass(m/z): 100.00 High Mass(m/z): 375.00 Sample Weight: 0.00

ISTD Amount: 0.000 Calibration Level: 3 Dilution Factor: 1.00

Instrument Method: C:\pitcon\trial2\steroidMSMSis

Original Processing Method: C:\pitcon\trial2\steroidmsmsIS

Current Processing Method: C:\Xcalibur\examples\methods\steroid


C



Page 2 of 4

methyltestosteronehydrocortisone

Expected

Retention

Time (min): 0.6

Retention

Time Window

(sec): 30.00000

View Width

(min): 1.00000

Retention

Time

Reference: No

Genesis

Minimum Peak

Height (S/N): 3.00

Genesis

Smoothing

Points: 7

Detector Type: MS

Valley

Detection

Enabled: No

Genesis

Constrain Peak

Width Enabled: No

RT: 1.49 - 2.49 SM: 7G

1.5 2.0

Time (min)

0

10

20

30

40

50

60

70

80

90

100

ec

na

dn

ub

A e

v ital

eR

1.99 NL: 9.60E4

m/z= 266.6-267.6+284.7-285.7 F: + c Full ms2 303.30 [ 100.00-310.00] MS Genesis steroids02

RT: 0.18 - 1.18 SM: 7G

0.5 1.0

Time (min)

0

10

20

30

40

50

60

70

80

90

100

ec

na

dn

ub

A e

vital

eR

RT: 0.68 NL: 5.01E5


Expected

Retention

Time (min): 2.0

Retention

Time Window

(sec): 30.00000

View Width

(min): 1.00000

Retention

Time

Reference: Yes

Genesis

Minimum Peak

Height (S/N): 3.00

Genesis

Smoothing

Points: 7

Detector Type: MS

Valley

Detection

Enabled: No

Genesis

Constrain Peak

Width Enabled: No

Component Name: hydrocortisone Actual RT(min): 0.67783 Calculated Amount: 4.95592

Response: 1892942.72621 Base Line: BB Signal To Noise: 707.56

%Diff: -0.88 Area Ratio: 2.763 Area(cts-sec): 1892942.72621

Specified Amount: 5.00000


C



Page 3 of 4

methyltestosteronedeoxycorticosterone

Expected

Retention

Time (min): 1.4

Retention

Time Window

(sec): 30.00000

View Width

(min): 1.00000

Retention

Time

Reference: No

Genesis

Minimum Peak

Height (S/N): 3.00

Genesis

Smoothing

Points: 7

Detector Type: MS

Valley

Detection

Enabled: No

Genesis

Constrain Peak

Width Enabled: No

RT: 1.49 - 2.49 SM: 7G

1.5 2.0

Time (min)

0

10

20

30

40

50

60

70

80

90

100

ec

na

dn

ub

A e

v ital

eR

1.99 NL: 9.60E4


RT: 0.90 - 1.90 SM: 7G

1.0 1.2 1.4 1.6 1.8

Time (min)

0

10

20

30

40

50

60

70

80

90

100

ec

na

dn

ub

A e

vital

eR

RT: 1.40

1.701.21

Expected

Retention

Time (min): 2.0

Retention

Time Window

(sec): 30.00000

View Width

(min): 1.00000

Retention

Time

Reference: Yes

Genesis

Minimum Peak

Height (S/N): 3.00

Genesis

Smoothing

Points: 7

Detector Type: MS

Valley

Detection

Enabled: No

Genesis

Constrain Peak

Width Enabled: No

Component Name: deoxycorticosterone Actual RT(min): 1.39533 Calculated Amount: 5.10841


%Diff: 2.17 Area Ratio: 1.519 Area(cts-sec): 1040530.60245



C



Page 4 of 4

methyltestosteroneprogesterone

Expected

Retention

Time (min): 3.2

Retention

Time Window

(sec): 30.00000

View Width

(min): 1.00000

Retention

Time

Reference: No

Genesis

Minimum Peak

Height (S/N): 3.00

Genesis

Smoothing

Points: 7

Detector Type: MS

Valley

Detection

Enabled: No

Genesis

Constrain Peak

Width Enabled: No

RT: 1.49 - 2.49 SM: 7G

1.5 2.0

Time (min)

0

10

20

30

40

50

60

70

80

90

100

ec

na

dn

ub

A e

v ital

eR

1.99 NL: 9.60E4


RT: 2.67 - 3.67 SM: 7G

2.8 3.0 3.2 3.4 3.6

Time (min)

0

10

20

30

40

50

60

70

80

90

100

ec

na

dn

ub

A e

vital

eR

RT: 3.17

2.89

Expected

Retention

Time (min): 2.0

Retention

Time Window

(sec): 30.00000

View Width

(min): 1.00000

Retention

Time

Reference: Yes

Genesis

Minimum Peak

Height (S/N): 3.00

Genesis

Smoothing

Points: 7

Detector Type: MS

Valley

Detection

Enabled: No

Genesis

Constrain Peak

Width Enabled: No

Component Name: progesterone Actual RT(min): 3.16867 Calculated Amount: 4.94898


%Diff: -1.02 Area Ratio: 4.373 Area(cts-sec): 2995893.97127



Index
Numerics2-column objects
in a Non-Repeating section, with chromatogram and spectrum (Figure) 118

in a Non-Repeating section, with chromatogram and spectrum objects (Figure) 119

in Non-Repeating section with chromatogram (Figure) 117Left to Right option (Figure) 118Top to Bottom option (Figure) 119

AAdding

custom text fields 52objects 20sections 18

Advanced Qual Peak Annotation Options dialog box (Figure) 97Advanced Quan Peak Annotation Options dialog box (Figure) 96Aligning objects 21Annotation Properties dialog box (Figure) 56

Attributes page (Figure) 57Font Page (Figure) 57

BBatch Reprocess dialog box (Figure) 35Batch Reprocessing, generating reports while 35Bitmap objects, configuring 73

CCentering objects 21Choosing data sources 30Choosing table columns 59Chromatogram Properties dialog box (Figure) 74Chromatogram Wizard 5

Configure How the Peak Window Will Look page 87Configure How the Peak Window Will Look page (Figure) 87Configure Normalization for the Chromatogram Page 100Configure Normalization for the Chromatogram page

(Figure) 100pages (Table) 75Select Chromatogram Style page 92

Select Chromatogram Style page (Figure) 92Select Chromatogram Type page 78Select Chromatogram Type page (Figure) 78Select Demo File page 79

Qual Result Based Chromatogram - Explicit Peak (Figure) 82Quan Result Based Chromatogram (Figure) 81Raw File Based Chromatogram (Figure) 80

Select Enhance Details page 91Select Enhance Details page (Figure) 91Select How the Chromatogram Axes Will Be Configured page

98Select How the Chromatogram Axes Will Be Configured page

(Figure) 98Select Mass Spectrum Quan Traces to Display page 86Select Mass Spectrum Quan Traces To Display page (Figure)

86Select Plot Details page 88Select Plot Details page (Figure) 88Select the Peak Labeling page 94Select the Peak Labeling page (Figure) 94Select the Qual Peak Page 85Select the Qual Peak page (Figure) 85Select the Quan Peak page 83Select the Quan Peak page (Figure) 83Use Container Supplied Qual Peak page 77Use Container Supplied Qual Peak page (Figure) 77Use Container Supplied Quan Peak page 76Use Container Supplied Quan Peak page (Figure) 76

Chromatograms, configuring 74Column Properties dialog box (Figure) 23, 116Columns

configuring 116, 116repeating behavior 117resizing in a table 21summary repeating 117, 118using 23

Component Calibration Curve Configuration wizard 6Component calibration curve, configuring 102Configuring

annotation objects 56bitmap objects 73chromatograms 74columns 116component calibration curves 102repeating sections 19spectra 104table objects 58


Index: D

text attributes 53text objects 50XReport Objects 4

Creatingreports from Xcalibur 32reports within XReport 30templates 9

Custom columns, configuring 59Custom text fields

adding 52editing 53

DData Source Browser 6Data source files 15Data Sources dialog box (Figure) 30Default data set 27Deleting

objects 20sections 18

EEdit Formula dialog box (Figure) 61Electronic signatures, creating a report with 39Exiting XReport 10

FFont dialog box (Figure) 55, 63Fonts

settings 24, 54table 63

Footer sections 12Formatting objects 15

GGenerating reports 9

when running a sample or sequence 33Graphic objects 15Grid, report template 22

HHeader sections 12

LLibrary Search Graphics Table Properties dialog box (Figure) 64, 65Library search results table properties 65Locking a template 27

NNon-repeating sections 12

OObjects 12

adding 20aligning 21annotation 56bitmap

configuring 73centering 21configuring 24deleting 20formatting 15graphic 15graphic (Table) 128repositioning 20resizing 20table 14, 58table (Table) 126text 13

configuring 50text (Table) 124

Objects pane 4Overview of XReport 2

PPage breaks 23Page layout 25Page Setup dialog box (Figure) 25Preferences dialog box (Figure) 22Preview window (Figure) 26, 31Previewing a template 26Processing Setup

setting report options in 33

QQuan Browser

generating a report from 36


Index: R

Quan Browser window - Reports dialog box (Figure) 37

RRe-ordering sections 18Repeating objects in columns 117Repeating Section Configuration dialog box 5Repeating Section Properties dialog box

Exclude page (Figure) 47figure 19Ordering page (Figure) 48Page Breaks page (Figure) 49

Repeating sections 12Report options, in Processing Setup 33Report template grid 22Report Template Outline pane 4Reports 15

creating from Xcalibur 32creating within XReport 30generating 9Generating from Quan Browser 36generating from Sequence Setup 32Generating when Batch Reprocessing a sequence 35Generating when running a sample or sequence 33

Repositioning objects 20Resizing objects 20Resizing sections 18Resolved documents 15Run Sequence dialog box (Figure) 34

SSample Reports 32Sample table properties 66Sample Table Properties dialog box (Figure) 66Save As dialog box (Figure) 28Saving a template 26Sections 11

adding 18deleting 18footer 12header 12non-repeating 12re-ordering 18repeating 12

configuring 19, 46resizing 18

Sections pane 3Select Component dialog box (Figure) 103Select Report Samples dialog box (Figure) 38

Sequence Setup, generating a report from 32Setting table fonts 63Setting table properties 64Signatures, electronic 39Specifying table sort order 62Spectra, configuring 104Spectrum List Table Properties dialog box

Display page (Figure) 71Enhancement page (Figure) 69Options page (Figure) 67Plot Type page (Figure) 68

Spectrum Properties dialog boxAxis page (Figure) 111Enhance page (Figure) 107Labels page (Figure) 110Normalization page (Figure) 113Options page (Figure) 104Peak page (Figure) 115Plot Type page (Figure) 106Style page (Figure) 109, 109

Starting XReport 7Summary Reports 32

TTable columns, choosing 59Table Configuration wizard 5Table objects 14Table properties

library search graphics 64library search results 65sample table 66spectrum list 67

Table Properties dialog boxConfigure User Column Parameters page (Figure) 60Set Table Sort Filter page (Figure) 62

Table Properties wizard - Select Table Fields page (Figure) 58Table properties, setting 64Table sort order, specifying 62Template pane 4Templates 11

choosing data sources 30creating 9, 17example files (Table) 121locking 27overview 11pre-built 6previewing 26saving 26

Text attributes, configuring 53Text fields


Index: U

adding custom 52configuring 51

Text objects 13configuring 50

Text Properties dialog boxadding custom text fields (Figure) 52Data page (Figure) 50Font page (Figure) 54

UUser Columns

configuring 59User Columns (Note) 59

XXcalibur documentation (Note) 11XReport

overview 2XReport window 3

figure 3new template (Figure) 8Objects pane 4Report Template Outline pane 4Sections pane 3Template pane 4


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