xcalibur custom reports with merlin

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EDITOR, TECHNICAL PUBLICATIONSTHERMO ELECTRON SAN JOSE355 RIVER OAKS PARKWAYSAN JOSE, CA 95134-1991UNITED STATES OF AMERICA

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Contents________________________________________________________________________

Contents

Read This First ..............................................................................................................................v

Changes to the Manual and Online Help ............................................................................................... vi

Abbreviations ........................................................................................................................................ vii

Typographical Conventions ................................................................................................................... xiData Input ............................................................................................................................. xiBoxed Information............................................................................................................... xiiTopic Headings................................................................................................................... xiii

Reply Cards .......................................................................................................................................... xiv

Introduction to Merlin .............................................................................................................. 1-1

1.1 Overview of Merlin................................................................................................................... 1-2What is Merlin? .................................................................................................................. 1-2Key Features of Merlin....................................................................................................... 1-2Upgrading From a Previous Version .................................................................................. 1-5System / Software Requirements........................................................................................ 1-5Installation .......................................................................................................................... 1-5

1.2 Using Merlin ............................................................................................................................. 1-6Starting Merlin.................................................................................................................... 1-6Creating and Generating Reports with Merlin ................................................................... 1-8Exiting Merlin .................................................................................................................... 1-9

1.3 Overview of Report Templates ............................................................................................... 1-10Report Template ............................................................................................................... 1-10Sections............................................................................................................................. 1-10Report Objects .................................................................................................................. 1-13Data Source Files.............................................................................................................. 1-17Report (Resolved Document) ........................................................................................... 1-17

Creating a Report Template Using the Merlin Wizards ....................................................... 2-1

2.1 The Merlin Report Structure Wizard ........................................................................................ 2-2Step 1 - Selecting the Type of Report................................................................................. 2-2Step 2 - Selecting and Ordering Sections ........................................................................... 2-4Step 3 - Selecting and Ordering Report Objects ................................................................ 2-5Step 4 - Confirming the Report Template Structure........................................................... 2-6

________________ Finnigan Xcalibur: Getting Productive with Merlin ___________________ i

Contents________________________________________________________________________

2.2 The Merlin Repeating Section Wizard ..................................................................................... 2-7Qual Repeating Section...................................................................................................... 2-7Quan Repeating Section.................................................................................................... 2-11

2.3 The Merlin Table Wizard........................................................................................................ 2-15Notification of Table Location......................................................................................... 2-15Choosing Table Columns ................................................................................................. 2-16Configuring Custom (User) Columns .............................................................................. 2-17Specifying Table Sort Order ............................................................................................ 2-19

2.4 The Merlin Chromatogram Wizard ........................................................................................ 2-21Notification of Chromatogram Location.......................................................................... 2-21Use Container Supplied Quan Peak Page ........................................................................ 2-24Use Container Supplied Qual Peak Page ......................................................................... 2-25Select Chromatogram Type Page..................................................................................... 2-26Select Demo File Page ..................................................................................................... 2-27Select the Quan Peak Page............................................................................................... 2-31Select Qual Peak Page...................................................................................................... 2-32Select Mass Spectrum Quan Traces to Display Page....................................................... 2-33Configure How the Peak Window Will Look Page ......................................................... 2-34Select Plot Details Page ................................................................................................... 2-35Select Enhance Details Page ............................................................................................ 2-37Select Chromatogram Style Page..................................................................................... 2-38Select the Peak Labeling Page ......................................................................................... 2-39Select How the Chromatogram Axes Will Be Configured Page ..................................... 2-42Configure Normalization for the Chromatogram Page.................................................... 2-44Finishing the Chromatogram Wizard............................................................................... 2-45

2.5 The Merlin Component Calibration Curve Wizard ................................................................ 2-46Notification of Component Calibration Curve Location ................................................. 2-46Specifying Component Name .......................................................................................... 2-48

2.6 After Using the Wizards… ..................................................................................................... 2-50Saving a Report Template ................................................................................................ 2-52Editing a Report Template with the Merlin Toolbar ........................................................ 2-52Editing a Report Template with Microsoft Word............................................................. 2-53Generating a Report ......................................................................................................... 2-53

Using the Merlin Toolbar ......................................................................................................... 3-1

3.1 Introduction to the Merlin Toolbar ........................................................................................... 3-2

ii ____________________Finnigan Xcalibur: Getting Productive with Merlin_________________

Contents________________________________________________________________________

3.2 Adding Sections and Report Objects to a Template ................................................................. 3-4Adding a Repeating Section ............................................................................................... 3-4Adding a Text Object.......................................................................................................... 3-6Adding a Table Object........................................................................................................ 3-6Adding a Graphic Object.................................................................................................... 3-7

3.3 Configuring Repeating Sections and Report Objects ............................................................. 3-17Configuring a Repeating Section...................................................................................... 3-18Configuring a Table Object .............................................................................................. 3-20Configuring a Chromatogram........................................................................................... 3-22Configuring a Component Calibration Curve Report Object........................................... 3-24Configuring a Spectrum ................................................................................................... 3-26

3.4 Maintaining Report Template Tables ...................................................................................... 3-28

3.5 Resizing a Graphic Object ...................................................................................................... 3-29

3.6 Merlin Operations Menu......................................................................................................... 3-30New Merlin Wizard .......................................................................................................... 3-30Generate Report................................................................................................................ 3-30Show Required Data Sources ........................................................................................... 3-30Clean Report Template ..................................................................................................... 3-31

Generating a Report ................................................................................................................. 4-1

4.1 Generating a Report from a Report Template ........................................................................... 4-2Merlin Data Source Browser (.xcal file) ............................................................................ 4-3Merlin Data Source Browser (.raw file) ............................................................................. 4-4Merlin Data Source Browser (.rst file) ............................................................................... 4-4Merlin Data Source Browser (.pmd file) ............................................................................ 4-5Merlin Data Source Browser (.sld file) .............................................................................. 4-6Merlin Data Source Browser (.sld file) .............................................................................. 4-6Merlin Data Source Browser (.sld file and .xcal file)......................................................... 4-8Tutorial: Generating a Report from a Report Template.................................................... 4-10

4.2 Generating a Report from Xcalibur ........................................................................................ 4-11

Example Merlin Report Template Files ................................................................................. A-1

Report Objects ..........................................................................................................................B-1

Tutorial Report ......................................................................................................................... C-1

________________ Finnigan Xcalibur: Getting Productive with Merlin __________________ iii

Read This First

Welcome to Merlin, the custom reports application of Xcalibur®! Merlin is part of Xcalibur, the Finnigan™ mass spectrometry data system.

This Xcalibur Getting Productive manual includes the following chapters:

Chapter 1: Introducing Merlin provides an introduction to Merlin, with an overview of the software and some of the basic terminology involved.

Chapter 2: Creating a Report Template Using the Merlin Wizards explains how to create your own Merlin report template with the aid of Merlin’s various wizards. Details are given on using the Report Structure Wizard, the Repeating Section Wizard, the Table Wizard, the Chromatogram Wizard and the Component Calibration Curve Wizard.

Chapter 3: Using the Merlin Toolbar provides information on using the Merlin toolbar to create and edit a report template. Most of the tasks that can be accomplished in Merlin can be completed manually using the Merlin toolbar. Details of these tasks are provided in this chapter.

Chapter 4: Generating a Report describes how to generate an Xcalibur report. Reports can be generated directly from a report template (by using the Merlin toolbar in Microsoft® Word) or from Xcalibur. Both methods of report generation are covered in this chapter. A Tutorial is also provided here.

Appendix A: Example Merlin Report Templates contains details of the example Merlin report templates that ship with Xcalibur. These customized report templates are ready-built for you to use. You can use them with your own Xcalibur data to generate Xcalibur reports.

Appendix B: Report Objects contains a tabulated listing of all the Merlin report objects available for you to include in a report template. The tables provide a description of each report object and also give information on how each report object functions when placed inside or outside a repeating section.

Appendix C: Tutorial Report contains a copy of the Xcalibur report that is generated when you have completed the tutorial in Chapter 4.

__________________ Finnigan Xcalibur: Getting Productive with Merlin ________________ v

Read This FirstChanges to the Manual and Online Help

Changes to the Manual and Online HelpTo suggest changes to this manual or the online Help, please send your comments to:

Editor, Technical PublicationsThermo Electron San Jose355 River Oaks ParkwaySan Jose, CA 95134-1991U.S.A.

You are encouraged to report errors or omissions in the text or index. Thank you.

vi ___________________Finnigan Xcalibur: Getting Productive with Merlin_________________

Read This First_____________________________________________________________ Abbreviations

AbbreviationsThe following abbreviations are used in this and other manuals and in the online Help.

A ampere

ac alternating current

ADC analog-to-digital converter

AP acquisition processor

APCI atmospheric pressure chemical ionization

API atmospheric pressure ionization

ASCII American Standard Code for Information Interchange

b bit

B byte (8 b)

baud rate data transmission speed in events per second

°C degrees Celsius

CD compact disc

CD-ROM compact disc read-only memory

cfm cubic feet per minute

CI chemical ionization

CIP carriage and insurance paid to

cm centimeter

cm3 cubic centimeter

CPU central processing unit (of a computer)

CRC cyclic redundancy check

CRM consecutive reaction monitoring

<Ctrl> control key on the terminal keyboard

d depth

Da dalton

DAC digital-to-analog converter

dc direct current

DDS direct digital synthesizer

DEP direct exposure probe

DS data system

DSP digital signal processor

__________________ Finnigan Xcalibur: Getting Productive with Merlin _______________ vii

Read This FirstAbbreviations

EI electron ionization

EMBL European Molecular Biology Laboratory

<Enter> enter key on the terminal keyboard

ESD electrostatic discharge

ESI electrospray ionization

eV electron volt

f femto (10-15)

°F degrees Fahrenheit

.fasta file extension of a SEQUEST search database file

FOB free on board

ft foot

FTP file transfer protocol

g gram

G giga (109)

GC gas chromatograph; gas chromatography

GC/MS gas chromatograph / mass spectrometer

GND electrical ground

GPIB general-purpose interface bus

GUI graphical user interface

h hour

h height

HPLC high-performance liquid chromatograph

HV high voltage

Hz hertz (cycles per second)

ICIS Interactive Chemical Information System

ICL Instrument Control Language

ID inside diameter

IEC International Electrotechnical Commission

IEEE Institute of Electrical and Electronics Engineers

in. inch

I/O input/output

k kilo (103, 1000)

K kilo (210, 1024)

KEGG Kyoto Encyclopedia of Genes and Genomes

kg kilogram

viii __________________Finnigan Xcalibur: Getting Productive with Merlin_________________

Read This First_____________________________________________________________ Abbreviations

l length

L liter

LAN local area network

lb pound

LC liquid chromatograph; liquid chromatography

LC/MS liquid chromatograph / mass spectrometer

LED light-emitting diode

µ micro (10-6)

m meter

m milli (10-3)

M mega (106)

M+ molecular ion

MB Megabyte (1048576 bytes)

MH+ protonated molecular ion

min minute

mL milliliter

mm millimeter

MS mass spectrometer; mass spectrometry

MS MSn power: where n = 1

MS/MS MSn power: where n = 2

MSn MSn power: where n = 1 through 10

m/z mass-to-charge ratio

n nano (10-9)

NCBI National Center for Biotechnology Information (USA)

NIST National Institute of Standards and Technology (USA)

OD outside diameter

Ω ohm

p pico (10-12)

Pa pascal

PCB printed circuit board

PID proportional / integral / differential

P/N part number

P/P peak-to-peak voltage

__________________ Finnigan Xcalibur: Getting Productive with Merlin _______________ ix

Read This FirstAbbreviations

ppm parts per million

psig pounds per square inch, gauge

RAM random access memory

RF radio frequency

RMS root mean square

ROM read-only memory

RS-232 industry standard for serial communications

s second

SIM selected ion monitoring

solids probe direct insertion probe

SRM selected reaction monitoring

SSQ single stage quadrupole

TCP/IP transmission control protocol / Internet protocol

TIC total ion current

Torr torr

TSQ triple stage quadrupole

u atomic mass unit

URL uniform resource locator

V volt

V ac volts alternating current

V dc volts direct current

vol volume

w width

W watt

WWW World Wide Web

Note. Exponents are written as superscripts. In the corresponding online Help, exponents are sometimes written with a caret (^) or with e notation because of design constraints in the online Help. For example:

MSn (in this manual) MS^n (in the online Help)

105 (in this manual) 10^5 (in the online Help)

x____________________Finnigan Xcalibur: Getting Productive with Merlin_________________

Read This First___________________________________________________Typographical Conventions

Typographical ConventionsTypographical conventions have been established for Thermo Electron San Jose manuals for the following:

• Data input

• Boxed information

• Topic headings

Data Input

Throughout this manual, the following conventions indicate data input and output via the computer:

• Messages displayed on the screen are represented by capitalizing the initial letter of each word and by italicizing each word.

• Input that you enter by keyboard is represented in bold face letters. (Titles of topics, chapters, and manuals also appear in bold face letters.)

• For brevity, expressions such as “choose File > Directories” are used rather than “pull down the File menu and choose Directories.”

• Any command enclosed in angle brackets < > represents a single keystroke. For example, “press <F1>” means press the key labeled F1.

• Any command that requires pressing two or more keys simultaneously is shown with a plus sign connecting the keys. For example, “press <Shift> + <F1>” means press and hold the <Shift> key and then press the <F1> key.

• Any button that you click on the screen is represented in bold face letters and a different font. For example, “click on Close”.

__________________ Finnigan Xcalibur: Getting Productive with Merlin _______________ xi

Read This FirstTypographical Conventions

Boxed Information

Information that is important, but not part of the main flow of text, is displayed in a box such as the one below.

Boxed information can be of the following types:

• Note – information that can affect the quality of your data. In addition, notes often contain information that you might need if you are having trouble.

• Tip – helpful information that can make a task easier.

• Important – critical information that can affect the quality of your data.

• Caution – information necessary to protect your instrument from damage.

• CAUTION – hazards to human beings. Each CAUTION is accompanied by a CAUTION symbol. Each hardware manual has a blue CAUTION sheet that lists the CAUTION symbols and their meanings.

• DANGER – laser-related hazards to human beings. It includes information specific to the class of laser involved. Each DANGER is accompanied by the international laser radiation symbol.

Note. Boxes such as this are used to display information.

xii___________________Finnigan Xcalibur: Getting Productive with Merlin_________________

Read This First___________________________________________________Typographical Conventions

Topic Headings

The following headings are used to show the organization of topics within a chapter:

Chapter 1Chapter Name

1.2 Second Level Topics

Third Level Topics

Fourth Level Topics

Fifth Level Topics

__________________ Finnigan Xcalibur: Getting Productive with Merlin ______________ xiii

Read This FirstReply Cards

Reply CardsThermo Electron San Jose manuals contain one or two reply cards. All manuals contain a Customer Registration / Reader Survey card and some contain a Change of Location card. These cards are located at the front of each manual.

The Customer Registration / Reader Survey card has two functions. First, when you return the card, you are placed on the Thermo Electron San Jose mailing list. As a member of this list, you receive application reports and technical reports in your area of interest, and you are notified of events of interest, such as user meetings. Second, it allows you to tell us what you like and do not like about the manual.

The Change of Location card allows us to track the whereabouts of the instrument. Fill out and return the card if you move the instrument to another site within your company or if you sell the instrument. Occasionally, we need to notify owners of our products about safety or other issues.

xiv __________________Finnigan Xcalibur: Getting Productive with Merlin_________________

Chapter 1Introduction to Merlin

Merlin is part of Xcalibur®, the Finnigan™ mass spectrometry data system.

This manual provides you with the information needed to get productive with Merlin, the built-in tool of Xcalibur for designing and generating customized reports.

This chapter contains the following sections:

• Overview of Merlin

• Using Merlin

• Overview of Report Templates

Note. Merlin uses Microsoft Word XP. This manual assumes that you have a reasonable understanding of Microsoft Word. Refer to Microsoft Word documentation and its online Help as required.

________________ Finnigan Xcalibur: Getting Productive with Merlin ________________ 1-1

Introduction to MerlinOverview of Merlin

1.1 Overview of MerlinThis section provides an overview of the fundamental features of Merlin.

This section includes the following topics:

• What is Merlin?

• Key Features of Merlin

• Upgrading From a Previous Version

• System / Software Requirements

• Installation

What is Merlin?

Merlin is the name given to the custom reports application of Xcalibur. It is a combination of Microsoft Word XP, a customized Microsoft Word template (Merlin.dot), and the Xcalibur data system.

Merlin allows you to create customized reports containing all the results and important information you produce with Xcalibur. You can 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, because Merlin uses Microsoft Word, it enables you to format a report to your style, print the report, and save the report in text (.txt file), document (.doc file), rich text (.rtf file) or web page (.htm or .html file) formats. This allows you to e-mail your reports or display them on the Internet.

Key Features of Merlin

This section lists the key features of Merlin:

Merlin.dot

Merlin.dot is the customized Microsoft Word template that Merlin uses in Xcalibur 1.3 and 1.4 (this file replaces the old BaseGRD.dot used in versions of Xcalibur before 1.2). Merlin.dot is installed in the Xcalibur\system\programs folder during the installation of Xcalibur.

1-2 _________________Finnigan Xcalibur: Getting Productive with Merlin_________________

Introduction to Merlin_________________________________________________________ Overview of Merlin

Merlin Report Structure Wizard

The Merlin Report Structure Wizard is activated automatically when you start Merlin. This wizard guides you step-by-step through the creation of an Xcalibur report template. You can use the wizard to do the following:

• Select the type of report for which you want to create a report template

• Choose how the report template is to be divided into sections

• Organize the content of each section in turn by adding report objects

The Merlin toolbar

The Merlin toolbar becomes active in Microsoft Word after you complete or cancel the Merlin Report Structure Wizard. See Figure 1-1.

Most of the tasks that can be accomplished in Merlin can be completed using the Merlin toolbar. You can use the Merlin toolbar to do the following:

• Change and maintain the properties of any repeating sections, table objects or graphic objects contained in a report template

• Start a new Merlin Report Structure Wizard

• Generate a report using the Merlin Data Source Browser

• Access the Merlin Data Source Identifier

• Clean a report template

• Add new sections and report objects to a report template

• Access the Merlin Table Manager in order to maintain tables

Merlin Repeating Section Wizard

The Repeating Section Wizard guides you through the process of configuring a repeating section inserted in your report template. This wizard allows you 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/or components are repeated

• Any limit on number of peaks to be reported

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

Figure 1-1. Merlin Toolbar


Introduction to MerlinOverview of Merlin

Merlin Table Wizard

The Merlin Table Wizard leads you through the process of configuring a table object included in your report template. This wizard allows you to do the following:

• Specify the columns to be included in the table

• Define and customize your own table columns

• Specify how you want the table to be ordered

Merlin Chromatogram Wizard

The Merlin Chromatogram Wizard guides you through the process of configuring a Chromatogram report object inserted in your report template. The wizard allows you 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

Merlin Component Calibration Curve Wizard

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

Merlin Table Manager

You can list and modify any tables contained in a report template using the Merlin Table Manager. This allows you to select individual table objects in the report template to delete them or reconfigure them using the Merlin Table Wizard.

Merlin Data Source Identifier

The Merlin Data Source Identifier lists the required data sources needed to generate an Xcalibur report from the active report template. This allows you to see at a glance the Xcalibur data source files you will need to have before generating a report.

Merlin Data Source Browser

The Merlin Data Source Browser allows you to select Xcalibur data files, which can then be used to generate Xcalibur reports from within Microsoft Word.


Introduction to Merlin_________________________________________________________ Overview of Merlin

Shipped Merlin Report Templates

A Merlin report template is Microsoft Word document (.doc file) with Merlin objects embedded within it. You do not have to create your own Merlin report templates. Merlin comes complete with customized report templates, ready-built for you to use. Full details of these report templates are given in Appendix A.

Upgrading From a Previous Version

Previous versions of Merlin (that is, pre-Xcalibur 1.2) used the BaseGRD.dot Microsoft Word template file. This template is still provided with Xcalibur 1.4 for backwards compatibility. Hence, all reports based on the BaseGRD.dot Microsoft Word template will still print correctly with Xcalibur 1.4, (provided that you have not modified the processing methods to include new Xcalibur 1.4 features). All newly created Merlin report templates will use the Merlin.dot Microsoft Word template (new for Xcalibur 1.2).

System / Software Requirements

In order to use Merlin, ensure that your system has the following software installed:

• Xcalibur 1.4

• Microsoft Office XP, including Microsoft Word XP.

Installation

Merlin is automatically installed for you when you install Xcalibur. Refer to the installation information that comes with your Xcalibur data system CD for details on installing Xcalibur.


Introduction to MerlinUsing Merlin

1.2 Using MerlinThis section describes how to use Merlin and contains the following topics:

• Starting Merlin

• Creating and Generating Reports with Merlin

• Exiting Merlin

Starting Merlin

Start Merlin as follows:

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

You can also start Merlin by opening an existing Merlin template and clicking on New Merlin Wizard from the Merlin toolbar.

Microsoft Word opens and creates a new document with the Merlin.dot template attached to it. The Merlin Report Structure Wizard is activated. See Figure 1-2.

Note. If your security settings in Microsoft Word are set to High, the macros in Merlin are automatically disabled and Merlin will not function.

Change your security settings to Medium or Low by choosing Tools > Macro > Security and selecting either the Medium or the Low option button. If your security settings are set to Medium, each time you open Merlin you will get a warning message asking you to enable or disable macros. Click on Enable Macros to use Merlin.


Introduction to Merlin______________________________________________________________ Using Merlin

Figure 1-2. Microsoft Word XP showing the Merlin Report Structure Wizard front page


Introduction to MerlinUsing Merlin

Creating and Generating Reports with Merlin

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

• Creating a Report Template

• Generating a Report Using a Report Template

These stages are outlined in the following topics.

Creating a Report Template

You can use Merlin to create a customized report template. A report template is a Microsoft Word document (.doc file) that defines how the final Xcalibur report will look and defines the specific information you want it to contain. A report template is created by the following generalized steps:

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

A New Microsoft Word document opens already attached to the Merlin.dot template, and the Merlin Report Structure Wizard appears.

2. Use Merlin to add sections and report objects to the report template.

You do this with the Merlin Report Structure Wizard, which guides you through the various steps and options involved. You can also use the Merlin toolbar to add report objects and sections to a report template.

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

Again, this is done with the Merlin wizards. You can also use the Merlin toolbar to configure sections and report objects.

4. Use the features available in Microsoft Word to format your report template.

5. Save the report template.

More detailed information on how to create a report template is given in Chapter 2 and Chapter 3 of this manual.

Note. Xcalibur ships with several Merlin report templates (.doc file with Merlin 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.

Note. Avoid confusing Microsoft Word templates (.dot files) and report templates (which are Microsoft Word documents, .doc files).


Introduction to Merlin______________________________________________________________ Using Merlin

Generating a Report Using a Report Template

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

There are two ways in which you can generate a report:

• From a report template open in Microsoft Word XP—you can browse for the required data source files and resolve the data to generate a report.

• From Xcalibur— you can associate the data you produce in Xcalibur with a report template (for example, you can do this in Quan Browser), and then resolve the data to generate a report.

Exiting Merlin

Ensure that you save your Merlin report template or Xcalibur report before you exit Microsoft Word.

To exit Merlin, complete or cancel any active wizards and then exit Microsoft Word in the normal way: Choose File > Exit.

Note. More detailed information on how to generate a report from within Xcalibur is given in Chapter 4.


Introduction to MerlinOverview of Report Templates

1.3 Overview of Report TemplatesIn this topic, the basic terminology that is used throughout the software and this manual is defined for new users of Merlin and Xcalibur. This section defines the following key terms, some of which have already been introduced:

• Report template

• Sections

• Report objects (Refer to Appendix B for full details.)

• Data source file (.pmd, .raw, .rst, .sld, .xcal)

• Report (or resolved document)

Report Template

A Merlin report template is a Microsoft Word document (.doc file based on the Merlin.dot Microsoft Word template) that defines the content, layout and style of an Xcalibur report. You can include sections, report objects and standard Microsoft Word features (for example, static text or graphics) in a report template. An Xcalibur report is generated when a report template is resolved (combined) with Xcalibur data (data source files).

Xcalibur ships with several example report templates ready for you to use. These are located in your Xcalibur\Templates folder. Open some of the example report templates in Microsoft Word to view their content and see how they look. Details of these report templates are given in Appendix A.

Sections

You can divide your report template into sections, into which you can add report objects and standard Microsoft Word features (for example, static text or graphics). Sections can be added into a report template using the Merlin wizards or the Merlin toolbar.

There are two basic types of section used in Merlin:

• Repeating section

• Non-repeating section

A report object that is placed in a repeating section can behave differently from the same report object that is placed in a non-repeating section when the report template is resolved with Xcalibur data. Refer to Appendix B: Report Objects for information on how a report object functions when it is placed inside or outside a repeating section.

Note. Refer to your other Xcalibur manuals and/or the Xcalibur online Help for additional information relating to Xcalibur.

1-10 ________________Finnigan Xcalibur: Getting Productive with Merlin_________________

Introduction to Merlin________________________________________________ Overview of Report Templates

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. A repeating section is also an ActiveX™ control and you can change the properties of a repeating section to customize its behavior.

Two types of repeating section can be used in a Merlin report template:

• Qual repeating section—You use a Qual repeating section to display details relating to a single Qual peak within some data. The section is then repeated for all Qual peaks found.

• Quan repeating section—You 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 then repeated for all Quan peaks or components.

Figure 1-3 shows a report template with both a Qual and a Quan repeating section added.

Figure 1-3. A report template containing Qual and Quan repeating sections

________________ Finnigan Xcalibur: Getting Productive with Merlin _______________ 1-11


Non-Repeating Sections

A non-repeating section is defined as any portion of a report template that is not classed as a repeating section. A non-repeating section usually displays static details associated with either data or methods that apply once and globally within the system. The following specific types of non-repeating section can be used in a Merlin report template:

• Non-repeating Qual section

• Non-repeating Quan section

• Processing method configuration section

• Reports section

• Programs section

Note that the above specific types of non-repeating section can only be accessed using the Merlin Structure Report Wizard.

Non-Repeating Qual Section

A non-repeating Qual section usually displays static Qual details. It shows global parameters, for example: processing method settings, instrument method settings, filename, and so on.

Non-Repeating Quan Section

A non-repeating Quan section usually displays static Quan details. It shows global parameters, for example: processing method settings, instrument method settings, filename, confirmation ion information, and so on.

Processing Method Configuration Section

A Processing method configuration section is a section of a report template that contains processing method configuration details.

Reports Section

A reports section is a section of a report template that contains any processing method report details.

Programs Section

A programs section is a section of a report template that contains any processing method program details.



Report Objects

Report objects (or controls) are customized (for Xcalibur) Microsoft Word field codes or ActiveX controls that can be added to a report template using the Merlin Report Structure Wizard or the Merlin toolbar. When a report template is resolved with Xcalibur data (data source files), the report objects in the report template are replaced with data to generate an Xcalibur report.

Report objects include the following:

• Text objects

• Table objects

• Graphic objects

Refer to Appendix B: Report Objects for a descriptive listing of Merlin objects.

Text Objects

Text objects can be added to a report template. They contain static text labels and associated customized Microsoft Word fields. These are discrete fields that (along with their labels) can be deleted, cut, copied, and pasted anywhere in the report template (for example, in a header). The text object fields are replaced with textual information (static text) when a report template is resolved to generate an Xcalibur report.

The following text objects are available in Merlin:

• Component Ident/Detect/Cal Settings

• Component ISTD Settings Summary

• Component Settings Summary

• Component Sys Suit/Flags Settings

• Processing Method - General

• Processing Method - Qual

• Quan ISTD Peak Summary

• Quan Peak Summary

• Sample Header

Figure 1-4 shows a report template containing a Sample Header text object.



Table Objects

Table objects are customized ActiveX controls that can be included in a report template. Table objects have an intrinsic link to a particular Microsoft Word table and are replaced with tabulated information (populated Microsoft Word table) when a report template is resolved. You can configure or change the properties of a table object to customize its output. The following table objects are available in Merlin:

• Avalon Qual Events Table

• Avalon Quan Events Table

• Calibration File Table

• Component Cal Level Table

• Component Ion Ratio Confirmation Table

• Component QC Level Table

• Component Spectrum Table

Figure 1-4. A report template containing a Sample Header text object



• Dilution Factor Table

• Ion Ratio Confirmation Results Table

• IRC Summary Table

• Lib. Search Graph Table

• Lib. Search Result Table

• Mass Spectrum List Table

• Proc. Method Audit Trail Table

• Proc. Method Programs Table

• Proc. Method Sample Reports Table

• Proc. Method Summary Reports Table

• Qual Peak Table

• Quan Peak Table

• Sample Table (Quan Results)

• Sequence Table

• Spectrum Candidate Results Table

Figure 1-5 shows a report template containing a Quan Peak Table object that has been customized using the Merlin Table Wizard.

Figure 1-5. A report template containing a customized Quan Peak Table object



Graphic Objects

Graphic objects are customized ActiveX controls that can be included in a report template. Graphic objects are replaced with graphical information (an embedded Microsoft Word graphic) when a report template is resolved. You can configure or change the properties of a graphic object in order to customize its output. The following graphic objects are available in Merlin:

• Chromatogram

• Component Cal (Calibration) Curve

• Spectrum

Figure 1-6 shows a report template containing a customized Chromatogram graphic object and a Component Cal Curve graphic object. The Chromatogram has been configured to display a demonstration chromatogram using a demo file (demonstration file, Refer to The Merlin Chromatogram Wizard in Chapter 2).

Figure 1-6. A report template containing a customized Chromatogram graphic object and a Component Cal Curve graphic object



Data Source Files

Data source files are those files that contain acquired data from Xcalibur. There are five types of data source files: Processing Method (.pmd), Raw (.raw), Result (.rst), Sequence (.sld), and Calibration (.xcal).

Report (Resolved Document)

An Xcalibur report (or resolved document) is generated using a report template. In an Xcalibur report, the report objects in the report template have been resolved (or replaced) with Xcalibur data. Reports are generated with the prefix ‘~Resolved’. Reports can be saved and presented in standard Microsoft Word document format (.doc file), or in text (.txt file), rich text (.rtf file) or web page (.htm or .html file) format.


Chapter 2Creating a Report Template Using the

Merlin Wizards

This chapter explains how to create your own Xcalibur report template with the aid of the wizards of Merlin. The following wizards are available:

• Merlin Report Structure Wizard

• Merlin Repeating Section Wizard

• Merlin Table Wizard

• Merlin Chromatogram Wizard

• Merlin Component Calibration Curve Wizard

When you start Merlin (refer to Chapter 1), the Merlin Report Structure Wizard is activated. This wizard helps you design the structure of your report template and allows you to choose which sections and report objects to include. Follow the directions and complete each page of the wizard before moving on to the next page.

After you complete the Report Structure Wizard, the Merlin wizards for the individual sections and report objects activate in turn, depending on which sections and report objects you have chosen and the order in which they appear in your report template. You can use the section and report object wizards to configure the sections and report objects included in your report template.

After using the wizards to help you create a report template, you can save the template and use it to generate an Xcalibur report (refer to Chapter 4).

Alternatively, before generating a report, you can to further enhance your report template by making use of the facilities available from the Merlin toolbar (refer to Chapter 3). You can also use of Microsoft Word to add to the style and content of your report template.

Note. You can also activate the section and report object wizards can also be activated from the Merlin toolbar. Refer to Chapter 3 for information on the Merlin toolbar.

Note. The Merlin wizards come complete with on-page Help text. Read the Help text in conjunction with this manual to help you use Merlin and its wizards.


Creating a Report Template Using the Merlin WizardsThe Merlin Report Structure Wizard

2.1 The Merlin Report Structure Wizard

When you start Merlin (refer to Chapter 1), the Merlin Report Structure Wizard is activated. See Figure 2-1. You can use the wizard to lead you step-by-step through the creation of an Xcalibur report template. Alternatively, you can click on Cancel to deactivate the wizard and enable the Merlin toolbar. Refer to Chapter 3 for more information of the Merlin toolbar.

When you use the Merlin Report Structure Wizard, you go through the following steps:

• Selecting the type of report

• Selecting and ordering sections

• Selecting and ordering report objects

• Confirming the report template structure

These steps are described in the topics below.

Step 1 - Selecting the Type of Report

In Step 1, you select the type of report that you want to construct (Figure 2-1).

Table 2-1 lists the types of Xcalibur reports for which you can create a report template.

Table 2-1. Types of Xcalibur Reports

Report Type Description

Sample Reports

A sample report presents information relating to a particular Xcalibur raw file of a sample and the results created when processing it.

Quan reports These use the results generated from the Quan section of a Processing Method. There are many report options, but typical reports can include a calibration curve plot for each component, chromatogram plots showing the integrated peaks used to create that curve and textual quantitative peak information relating to those peaks. This report type does not offer any of the results created using Qual processing.

Qual reports These use the results generated from the Qual section of a Processing Method. These reports are typically used to present a chromatogram plot with detected peaks shown, the spectra associated with the tops of those detected peaks and, if appropriate, the textual results of library searching of those spectra. This report type does not offer any of the results created using Quan processing.

Quan and Qual reports

These can use the results generated from both the Quan and Qual sections of a Processing Method. This sample report type offers the greatest flexibility, since it is possible to combine both quantitative and qualitative, graphical and textual information in one report.


Creating a Report Template Using the Merlin Wizards____________________________________________ The Merlin Report Structure Wizard

The type of report that you choose affects the options available to you in the remaining pages of the wizard.

Complete Step 1 of the wizard as follows:

1. Select the type of report you want to construct.

2. Click on Next to move on to Step 2.

Summary Reports

A summary report presents information relating to all of the samples in an Xcalibur Sequence and the results created when processing them.

Sample Quan reports

These are typically used to list all of the sample file names in a sequence in tabular form, followed for each component by a table of quantitative results generated when the samples have been processed using the Quan section of a Processing Method. Each row of this table corresponds to a sample in the sequence.

Method Reports

A method report presents all of the individual parameters stored in an Xcalibur Method.

Processing reports

These are used to present the values of as many of the parameters as are required that are stored in a Processing Method. They are typically presented to show the essential parameters used for processing and are normally a precursor to the processed results. This is of particular use for GLP (Good Laboratory Practice) related work.

Table 2-1. Types of Xcalibur Reports, continued

Report Type Description

Figure 2-1. Merlin Report Structure Wizard - Step 1



Step 2 - Selecting and Ordering Sections

In Step 2 of the wizard, you select which sections to include in the report template. See Figure 2-2. You can choose to include Quan-based or Qual-based sections and repeating or non-repeating sections in your report template. However, the available sections depend on the type of report you selected in Step 1.

Select and order the sections you want as follows:

1. In the Sections Available list box, select (highlight) the sections that you want.

2. Click on Add to add the sections you want to include in your report template to the Sections Added list box.

Alternatively, you can double-click on a selected section. The current structure of the report template is displayed in the left hand pane of the wizard.

3. Click on Move Up and Move Down to arrange the order of the selected sections in the Sections Added list box.

4. Click on Next to move on to Step 3.



Creating a Report Template Using the Merlin Wizards____________________________________________ The Merlin Report Structure Wizard

Step 3 - Selecting and Ordering Report Objects

In Step 3 of the wizard, you select which report objects you want to include in a specified section of your report template. See Figure 2-3. The wizard automatically repeats Step 3 for each of the sections you chose in Step 2. You can choose to include text objects, table objects, graphic objects and free text. However, the available objects depend on the selections you made in Steps 1 and 2.

Complete Step 3 for each section of your report template as follows:

1. In the Objects Available list box, select the report objects that you want.

2. Click on Add to add the report objects you want to the Objects Added list box. Alternatively, you can double-click on a selected report object.

3. Click on Move Up and Move Down to arrange the order of the selected report objects in the Objects Added box.

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

If, in Step 2, you chose to have more than one section in your report template, the wizard repeats Step 3 for the next section in your report template structure. Select the report objects as described above and click on Next to move on to the final page of the wizard.




Step 4 - Confirming the Report Template Structure

In Step 4 of the wizard, you confirm the structure of your report template. See Figure 2-4.

Check the details to ensure that they are correct. If you want to change the structure, click on Back to go back through the previous Steps. If you are satisfied with the report template structure, click on Finish.

The wizard creates a report template based on your selections. The section and report object wizards of Merlin are then automatically activated as necessary in the order defined by the structure of your report template. Refer to the topics later in this chapter for more information on using each wizard.

When all the wizards have been completed, refer to the topic After Using the Wizards… in this chapter for information on what to do after the wizards are all completed.



Creating a Report Template Using the Merlin Wizards___________________________________________The Merlin Repeating Section Wizard

2.2 The Merlin Repeating Section Wizard

The Merlin Repeating Section Wizard activates automatically on completion of the Report Structure Wizard if you have chosen to include a repeating section in your report template. The wizard will run for each repeating section included in your report template (according to the order defined by the structure of your report template).

The Repeating Section Wizard guides you through the process of configuring a repeating section (that is, changing its properties) contained in your report template.

There are two different types of repeating section in Merlin:

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

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

The Merlin Repeating Section Wizard displays different pages and contains different options depending on the type of repeating section being configured. You can use the Repeating Section Wizard to specify:

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

• The order in which peaks and/or components are repeated.

• Any limit on number of peaks to be reported.

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

The following topics discuss the Repeating Section Wizard for both the Qual and Quan repeating sections.

Qual Repeating Section

This section describes how to use the Merlin Repeating Section Wizard to configure a Qual repeating section.

Note. The Merlin Repeating Section Wizard is also activated if you manually insert a repeating section using the Merlin toolbar. However, the front page of the wizard will be different from the one detailed in this chapter. Refer to Chapter 3 for more information on activating the Repeating Section Wizard from the Merlin toolbar.


Creating a Report Template Using the Merlin WizardsThe Merlin Repeating Section Wizard

Notification of Qual Repeating Section Location

The front page of the Merlin Repeating Section Wizard highlights the Qual repeating section to be configured by the wizard and shows how this repeating section fits into the overall structure of your report template. See Figure 2-5.

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

Selecting How to Order a Qual Repeating Section

This page of the wizard allows you to change the default ordering of processed results such that the order of peaks or components in a repeating section can be tailored to your specific needs. See Figure 2-6.

Figure 2-5. The front page of the Merlin Repeating Section Wizard (Qual repeating section)

Note. If the Merlin Repeating Section Wizard is activated from the Merlin toolbar, rather than via the Merlin Report Structure Wizard, this page of the wizard (shown in Figure 2-5) is not displayed.



Order a Qual repeating section as follows:

1. In the Repeating Section Ordering group box, define how you want the Qual repeating section to be ordered by selecting one of the following options from the Order By list box:

• RT (Retention Time) - the default

• Peak Height Intensity

• Peak Area Intensity

• Peak Response Intensity

2. In the Ordering Direction group box, define the direction for the ordering by selecting one of the following option buttons:

• Ascending—to sort the data in ascending order

• Descending—to sort the data in descending order.

3. In the Limit Repeating Records group box, define the maximum number of peaks or components to order (up to 999). To set a maximum number, select the Maximum Number of Peaks or Components To Order On check box and use the enabled spin box to enter a value.


Figure 2-6. Merlin Repeating Section Wizard - Select How To Order The Repeating Section (Qual)



Configuring Page Layout

The final page of the wizard allows you to define how you want the individual peaks that will appear in the Qual repeating section to be laid out in the final report. See Figure 2-7.

You can choose whether you want each peak to be fully contained on its own page(s) or whether you want no page breaks between the individual peaks.

1. Make your selections on the page. The graphic changes to aid you in your decision.

2. If you want to amend your selections in the Repeating Section Wizard, use the < Back button to go back through the previous pages. If you are happy with your selections, click on Finish.

After completing the Repeating Section Wizard, the other Merlin wizards automatically activate as necessary in the order defined by the structure of your report template. Refer to the appropriate topic in this chapter for more information on each wizard. When all the wizards have been completed, refer to the topic After Using the Wizards… in this chapter for information on what to do next.

Figure 2-7. Merlin Repeating Section Wizard - Configure Peak Reporting Page Layout (Qual)

Note. If you have accessed the Merlin Repeating Section Wizard from the Merlin toolbar, rather than from the Merlin Report Structure Wizard, clicking on Finish returns you to the report template Microsoft Word document. Any amendments to the properties of a repeating section will have been made. Choose File > Save to save the changes to your report template.



Quan Repeating Section

This section describes how to use the Merlin Repeating Section Wizard to configure a Quan repeating section.

Notification of Quan Repeating Section Location

The front page of the Merlin Repeating Section Wizard highlights the Quan repeating section to be configured by the wizard and shows how this repeating section fits into the overall structure of your report template. See Figure 2-8.


Selecting Peaks to Exclude

When processing Quan configurations it is possible to exclude specific elements from the process. It is also possible to discard any components that have not been found. The next page of the wizard allows you to set exclusions for the Quan repeating section. See Figure 2-9.

Figure 2-8. The front page of the Merlin Repeating Section Wizard (Quan repeating section)

Note. If the Merlin Repeating Section Wizard is activated from the Merlin toolbar, rather than from the Merlin Report Structure Wizard, this page of the wizard (displayed in Figure 2-9) is not displayed.



Set exclusions for the Quan repeating section as follows:

1. In the Repeating Section Excludes group box, define the exclusions for the Quan repeating section by selecting one of the following options from the Exclude Component Type list box:

• None (no exclusions) - the default

• Internal Standards

• Target Compounds

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


Selecting How to Order a Quan Repeating Section

This page of the wizard allows you to change the default ordering of processed results such that the order of peaks and/or components in a repeating section can be tailored to your specific needs. See Figure 2-10.

Figure 2-9. Merlin Repeating Section Wizard - Select Any Peak To Exclude (Quan)



Order a Quan repeating section as follows:

1. In the Repeating Section Ordering group box, define how you want the Quan repeating section to be ordered by selecting one of the following options from the Order By list box:

• RT (Retention Time) - the default

• Component Name

• Peak Height Intensity

• Peak Area Intensity

• Peak Response Intensity

• Component Concentration

2. In the Ordering Direction group box, define the direction for the ordering by selecting one of the following option buttons:

• Ascending—to sort the data in ascending order

• Descending—to sort the data in descending order.

3. In the Repeating Records Maximum group box, define the maximum number of peaks or components to order (up to 999). To set a maximum number, select the Limit Number of Reported Peaks or Components To check box and use the enabled spin box to enter a value.


Figure 2-10. Merlin Repeating Section Wizard - Select How To Order The Repeating Section (Quan)



Configuring Page Layout

The final page of the wizard allows you to define how you want the individual peaks that will appear in the Quan repeating section to be laid out in the final report (Figure 2-11)

Choose whether you want each peak to be fully contained on its own page(s) or whether you want no page breaks between the individual peaks as follows:

1. Make your selections on the page. The graphic changes to aid you in your decision.

2. If you want to change your selections in the Repeating Section Wizard, click on Back to go back through the previous pages. If you are satisfied with your selections, click on Finish.

After completing the Repeating Section Wizard, the other Merlin wizards automatically activate as necessary in the order defined by the structure of your report template. Refer to the appropriate topic in this chapter for more information on each wizard. When all the wizards have been completed, refer to the topic After Using the Wizards… in this chapter for information on what to do next.

Figure 2-11. Merlin Repeating Section Wizard - Configure Peak Reporting Page Layout (Quan)

Note. If you have accessed the Merlin Repeating Section Wizard from the Merlin toolbar, rather than from the Merlin Report Structure Wizard, clicking on Finish returns you to the report template Microsoft Word document. Any amendments to the properties of a repeating section will have been made. Choose File > Save to save the changes to your report template.


Creating a Report Template Using the Merlin Wizards_____________________________________________________ The Merlin Table Wizard

2.3 The Merlin Table WizardThe Merlin Table Wizard activates automatically on completion of the Report Structure Wizard if you chose to include a table object in your report template. The wizard will run for each table object included in your report according to the order defined by the report structure wizard.

The Merlin Table Wizard leads you through the process of configuring a table object (that is, changing its properties) included in your report template. You use the Table Wizard for the following:

• Choosing table columns

• Configuring User (custom) Columns

• Specifying table sort order

Notification of Table Location

The front page of the Merlin Table Wizard, the [Table] - Add To Generated Report page, highlights the table object to be configured by the wizard and shows how this object fits into the overall structure of your report template. See Figure 2-12.


Note. The Merlin Table Wizard can also be activated by the Merlin toolbar. Refer to Chapter 3 for a discussion of the Merlin toolbar.

Note. If the Merlin Table Wizard is activated from the Merlin toolbar rather than from the Merlin Report Structure Wizard, this of the wizard (displayed in Figure 2-12) is not displayed.


Creating a Report Template Using the Merlin WizardsThe Merlin Table Wizard

Choosing Table Columns

The second page of the Table Wizard, the [Table] - Select Table Fields page, allows you to select the columns to include in the table. See Figure 2-13. 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.

Figure 2-12. The front page of the Merlin Table Wizard

Figure 2-13. Merlin Table Wizard - Select Table Fields page



Fill in the Select Table Fields page of the Table wizard as follows:

1. In the Available Columns list box, select (highlight) the columns that you want.

2. Click on Add to add the columns you want to include in the table to the Selected Columns list box.

Alternatively, you can double-click on a selected column or you can add all the available columns by clicking on Add All.

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


Configuring Custom (User) Columns

The [Table] - Configure User Column Parameters page of the Table Wizard is displayed only if you chose to include custom User Columns in your table. You use this page to define parameters for each User Column in the table. See Figure 2-14.

Note. All table objects have User Columns available for selection. User Columns take advantage of the Formula functionality of Microsoft Word, which uses the = (Formula) field code and associated functions. User Columns are only recommended for experienced users of Xcalibur and Microsoft Word.

Figure 2-14. Merlin Table Wizard - Configure User Column Parameters page



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

Define each User Column as follows:

1. In the User Columns list box, select a User Column.

2. In the User Column Title group box, type a title for the User Column.

3. In the User Column Formula group box, click on Edit Formula to open the Edit Formula dialog box. See Figure 2-15.

The Edit Formula dialog box allows you to edit a formula for the User Column. Use this dialog box to configure valid Microsoft Word = (Formula) fields and associated functions for the User Column. There is a brief description of each function in the Function list box at the bottom of the dialog box. Refer to your Microsoft Word documentation for full details of the Formula functionality of Microsoft Word.

4. In the Formula text box, enter your formula, either by using Add Function and Insert Column or by typing directly into the text box.

5. Click on OK to return to the Configure User Column Parameters page.

6. In the User Column Type group box, define the type of User Column by selecting one of the following option buttons:

• Numeric—formats the User Column for numeric entries

Figure 2-15. Edit Formula dialog box



• Text—formats the User Column for text entries

• Date—formats the User Column for date entries


Specifying Table Sort Order

The final page of the Table Wizard, the [Table] - Set Table Sort Filter page, allows you to define table data is sorted when you generate a report. See Figure 2-16.

The columns that you selected for the table are displayed in a list box on the left of the dialog box. You can order the table by any of the selected columns. You can 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.

Select the table order as follows:

1. In the list box, select the column of the variable that you want the table ordered by first.

2. Click on Add to add the selected column to the First Order text box. Alternatively, you can double-click on a selected column.

3. In the Current Sorting Configuration group box, define how you want to sort the First Order column data by selecting one of the following option buttons:

• Ascending—data sorted in ascending order

Figure 2-16. Merlin Table Wizard - Set Table Sort Filter page



• 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. If you want to change your selections in the Merlin Table Wizard, click on Back to go back through the previous pages. If you are satisfied with your selections, click on Finish.

After completing the Table Wizard, the other Merlin wizards automatically activate as necessary in the order defined by the structure of your report template. Refer to the appropriate topic in this chapter for more information on each wizard. When all the wizards have been completed, refer to the topic After Using the Wizards… in this chapter for information on what to do next.

Note. If you have accessed the Merlin Table Wizard from the Merlin toolbar, rather than from the Merlin Report Structure Wizard, clicking on Finish returns you to the report template Microsoft Word document. Any amendments to the properties of a table object will have been made. Choose File > Save to save the changes to your report template.


Creating a Report Template Using the Merlin Wizards_____________________________________________ The Merlin Chromatogram Wizard

2.4 The Merlin Chromatogram WizardThe Merlin Chromatogram Wizard activates automatically upon completion of the Report Structure Wizard if you have chosen to include a Chromatogram report object (a graphic object) in your report template.

The wizard runs for each Chromatogram report object included in your report template according to the order defined by the structure of your report template.

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

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

Notification of Chromatogram Location

If the Merlin Chromatogram Wizard has been activated from the Merlin Report Structure Wizard, the front page of the wizard (Chromatogram Generated From Report Structure Wizard) highlights the Chromatogram report object to be configured and shows how it fits into the overall structure of your report template. See Figure 2-17.


Note. The Merlin Chromatogram Wizard can also be activated from the Merlin toolbar. Refer to Chapter 3 for a discussion of the Merlin toolbar.


Creating a Report Template Using the Merlin WizardsThe Merlin Chromatogram Wizard

The remaining wizard pages and their order is given in Table 2-2. These wizard pages are also discussed below. Refer to the appropriate topic for information on how to complete each wizard page.

Figure 2-17. The front page of the Merlin Chromatogram Wizard

Note. If the Merlin Chromatogram Wizard is activated from the Merlin toolbar, rather than from the Merlin Report Structure Wizard, this page of the wizard (displayed in Figure 2-17) is not displayed.



* If you use the container-supplied peak, then the Select Chromatogram Type page is not displayed.

If 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 2-2. Possible Chromatogram Wizard pages, given the section type, in order of appearance

Non-Repeating Section Repeating Section

Page in the Merlin Chromatogram Wizard Raw Quan Qual Quan Qual

Use Container Supplied Quan Peak •

Use Container Supplied Qual Peak •

Select Chromatogram Type • • • •∗ •∗

Select Demo File • • • • •

Select the Quan Peak •

Select the Qual Peak •

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 • • • • •

Note. If you select 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 Supplied Quan Peak Page

The Use Container Supplied Quan Peak page allows you 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. See Figure 2-18.

Fill in the Use Container Supplied Quan Peak page of the Chromatogram wizard as follows:

1. In the Implicit Quan Peak Options group box, select the Use Quan Peak’s Associated Internal Standard check box to display the details of the internal standard associated with the implicit Quan peak.

2. In the Explicit Chromatogram Type group box, select the Explicitly Specify the Chromatogram’s Behaviour check box to ignore the implicit Quan peak supplied by the container and explicitly configure the chromatogram type.


Figure 2-18. Chromatogram Wizard - Use Container Supplied Quan Peak page



Use Container Supplied Qual Peak Page

The Use Container Supplied Qual Peak page allows you to ignore the implicit Quan peak and explicitly configure the chromatogram type. See Figure 2-19.

Fill in the Use Container Supplied Qual Peak page of the Chromatogram wizard as follows:

1. In the Explicit Chromatogram Type group box, select the Explicitly Specify the Chromatogram’s Behaviour check box to ignore the implicit Quan peak supplied by the container and explicitly configure the chromatogram type.


Figure 2-19. Chromatogram Wizard - Use Container Supplied Qual Peak page



Select Chromatogram Type Page

The Select Chromatogram Type page allows you to set the Chromatogram Type for the Chromatogram report object being configured in your report template. See Figure 2-20.

Fill in the Select Chromatogram Type page of the Chromatogram wizard as follows:

1. In the Chromatogram Type group box, define the Chromatogram Type by selecting one of the following option buttons:

• 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 2-20. Chromatogram Wizard - Select Chromatogram Type page



Select Demo File Page

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

A demo file allows you to see how the Chromatogram report object (in the report template and in wizard page previews) will display 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

If the Chromatogram report object being configured is based on a raw file, the Select Demo File page is as shown in Figure 2-21.

Fill in the Select Demo File page of the Chromatogram wizard as follows:

1. Select the Use Demo File check box if you want to associate a demo file with the Chromatogram report object.

2. In the Demo File group box, click on the Browse (…) button to open the Select Raw Data File dialog box and Browse for the required demo file (.raw file).

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

Figure 2-21. Chromatogram Wizard - Select Demo File page: Raw File Based Chromatogram




Quan Result Based Chromatogram

If the Chromatogram report object being configured is based on Quan Results, the Select Demo File page is as shown in Figure 2-22.





4. Specify the peak to demo as follows:

a. In the Demo Peak group box, click on the Browse (…) button to open the Select a Peak dialog box.

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


Figure 2-22. Chromatogram Wizard - Select Demo File page: Quan Result Based Chromatogram



Qual Result Based Chromatogram - Explicit Peak

If the Chromatogram report object being configured is based on Qual Results with an explicit Peak Type required, the Select Demo File page is as shown in Figure 2-23.





4. Specify the peak to demo as follows:

a. In the Demo Peak group box, click on the Browse (…) button to open the Select a Peak dialog box.

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


Figure 2-23. Chromatogram Wizard - Select Demo File page: Qual Result Based Chromatogram - Explicit Peak



Qual Result Based Chromatogram - All Available Peaks

If the Chromatogram report object being configured is Qual Result Based with Show All Qual Peaks set (Peak Type setting), the Select Demo File page displays the same as that shown in Figure 2-21 on page 2-27.








Select the Quan Peak Page

The Quan Peak page allows you to explicitly specify the Quan peak (component) for a Quan Results Based Chromatogram report object. See Figure 2-24.

Fill in the Select the Quan Peak page of the Chromatogram wizard as follows:

1. In the Quan Peak group box, specify the Quan peak by typing the text name of the component. The Next button is enabled only after you have selected a component. Alternatively, you can select the component by browsing for the required processing method file as follows:

a. Click on the Browse (…) button to open the Select Component dialog box and browse for the required file (.pmd file). See Figure 2-25.

b. When you have selected a processing method file, use the Select Component dialog box to choose a component. Click on OK to return to the wizard.

Figure 2-24. Chromatogram Wizard - Select the Quan Peak page

Figure 2-25. Select Component dialog box



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


Select Qual Peak Page

The Select Qual Peak page allows you to explicitly specify the Qual peak for a Qual Results Based Chromatogram report object. See Figure 2-26.

Fill in the Select Qual Peak page of the Chromatogram wizard as follows:

1. In the Qual Peak to Display group box, specify the Qual peak by typing the appropriate retention time into the Retention Time edit box. The Next button is enabled only after you have selected a component. The retention time can be any time within the start and end peak boundaries.


Note. You must select a valid peak for Merlin 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.

Figure 2-26. Chromatogram Wizard - Select Qual Peak page

Note. You must select a valid retention time for Merlin 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 Spectrum Quan Traces to Display Page

The Select Mass Spectrum Quan Traces to Display page allows you to configure the Quan Traces property for MS data. See Figure 2-27. (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

You can select any of these possible six traces to be displayed in the Chromatogram. Alternatively, all of the available traces of the component can be displayed.

Fill in the Select Mass Spectrum Quan Traces to Display page of the Chromatogram wizard as follows:

1. In the Quan Traces group box, select the Quan trace to be used from the Quan Traces list box.

2. If you select All Quan Traces from the list box, select the Common Normalization for all Traces check box to normalize all the traces the same way.


Figure 2-27. Chromatogram Wizard - Select Mass Spectrum Quan Traces To Display page



Configure How the Peak Window Will Look Page

The Configure How the Peak Window Will Look page allows you to control the display of the baselines (Quan and Qual peaks) and the peak window width (enabled for: Qual peak; Quan peak only in some cases) when a peak from a result file is set to display in a Chromatogram. See Figure 2-28.

Fill in the Configure How the Peak Window Will Look page of the Chromatogram wizard as follows:

1. Select the Show Baselines check box to display the baselines for a Chromatogram peak (Quan or Qual). If this option is left unchecked, the baselines are not displayed (peak tracing and full peak annotation are also not displayed).

2. If enabled, 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 2-28. Chromatogram Wizard - Configure How the Peak Window Will Look page



Select Plot Details Page

The Select Plot Details page allows you to configure how the plot is drawn when raw data is being displayed in a Chromatogram report object. See Figure 2-29.

Fill in the Select Plot details page of the Chromatogram wizard as follows:

1. In the Plot Type group box, select the type of detector used to generate the raw file from the Detector list box. The type of detector determines the available traces.

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

3. From the Filter list box, 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, you must enter a valid filter string.

4. From the Trace list boxes, select the following:

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

b. From the second list box, select a logical operator: + or -. Your selection of an operator then enables the third list box.

Figure 2-29. Chromatogram Wizard - Select Plot Details page



c. From third list box, 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 will depend on the detector used to generate the data as follows:

• 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

5. In the Mass list box, specify the mass or mass range for Mass Range or Base Peak Traces for MS detector types 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.

• If you use 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) text box is displayed 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.

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

The default setting is: *, which is used to display the complete time range for the plot.

7. Select the Fixed Scale check box to enable or disable the Fixed Scale text box. This text box allows you to set the Y-axis maximum to a specific value.

If you select the Fixed Scale check box, the Normalize To group box on the final page of the wizard is enabled, as is the text box enabling you to 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 Details Page

The Select Enhance Details page allows you to enhance a Chromatogram plot by applying smoothing. See Figure 2-30.

Fill in the Select Enhance Details page of the Chromatogram wizard as follows:

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

2. In the Smoothing Details group box, select the type of smoothing, either Boxcar or Gaussian, from the Type list box.

3. Select the number of smoothing points to be used in the Points list box.


Figure 2-30. Chromatogram Wizard - Select Enhance Details page



Select Chromatogram Style Page

The Select Chromatogram Style page allows you to determine the appearance of the Chromatogram. See Figure 2-31.

Fill in the Select Chromatogram Style page of the Chromatogram wizard as follows:

1. In the Plotting group box, define the plotting style by selecting one of the following option buttons:

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

• Stick—to display the chromatogram as vertical lines.

2. In the Arrangement group box, define the plotting arrangement by selecting one of the following option buttons:

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

• Overlay (3D)—to overlay plots vertically (same X-axis) with an optional horizontal skew (Y-axis time offset). When selected, the 3D display options are enabled (see below). You use the 3D arrangement if you selected Multiple Quan Traces on the Select Mass Spectrum Quan Traces page of the wizard.

3. If you select an Overlay (3D) arrangement, set the following in the 3D group box:

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 or click

Figure 2-31. Chromatogram Wizard - Select Chromatogram Style page



on the Elevation slider left or right arrow 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 on 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 Labeling Page

The Select The Peak Labeling page allows you to choose the type and style of peak labels. See Figure 2-32. From this page you can open a dialog box that allows you to set advanced labeling options by clicking on the Advanced button.

Basic Options

Fill in the Select the Peak Labeling page of the Chromatogram wizard as follows:

1. In the Label With group box, select the Retention Time check box to label peaks with the time in minutes, in the chromatogram plot. 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.

Figure 2-32. Chromatogram Wizard - Select the Peak Labeling page



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, if a peak is saturated, Xcalibur displays an S above the peak.

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

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

8. In the Label Styles group box, select the Offset check box 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 text 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 text box to a value between 0 and 100%.


Advanced Options (Quan)

Click on the Advanced button in the Select the Peak Labeling page to open the Advanced Quan Peak Annotation Options dialog box. See Figure 2-33. 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.

2. In the Custom Peak Labels group box, select the Component Name check box 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 your custom label for the Quan peak into the text box.

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



6. In the RT Labeling group box, select the units for the retention time from the Units list box.

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

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

Advanced Options (Qual)

Click on the Advanced button in the Select the Peak Labeling page to open the Advanced Qual Peak Annotation Options dialog box. See Figure 2-34. When you set Advanced Labeling options, only the Qual peak is labeled.

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

1. Select the Use Advanced Qual Peak Annotation check box to enable the advanced Qual peak options.

2. In the Custom Peak Labels group box, select the Custom Text Label check box to specify a custom label. Type your custom label for the Qual peak into the text box.

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

4. In the RT Labeling group box, select the units for the retention time from the Units list box.

Figure 2-33. Advanced Quan Peak Annotation Options dialog box



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

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

Select How the Chromatogram Axes Will Be Configured Page

The Axes page allows you to set chromatogram axes labels and display options. See Figure 2-35.

Fill in the Select How the Chromatogram Axes Will Be Configured page of the Chromatogram wizard as follows:

1. In the X Axis group box, set the Name of the X axis by typing it into the Name text box.

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. In the Divisions text box, type the number of split time range graphs displayed for each chromatogram. This text box is enabled only if you select the Split Time Range check box.

Figure 2-34. Advanced Qual Peak Annotation Options dialog box



5. In the Y Axis group box, in the Label group box, select the From Detector option button to use the detector-specific label for the Y-axis (stored in the .raw file).

Alternatively, select the Custom option button to use your own label.

6. In the Units group box, choose between the Absolute and Relative option buttons 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 text box, type a Y-axis name.

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


Figure 2-35. Chromatogram Wizard - Select How the Chromatogram Axes Will Be Configured page



Configure Normalization for the Chromatogram Page

The Normalization page allows you to select the normalization (Y-axis scaling) method used for the chromatogram. See Figure 2-36.

Fill in the Configure Normalization for the Chromatogram page of the Chromatogram wizard as follows:

1. In the Normalize Method group box, define the normalizing method by selecting one of the following option buttons:

• 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. In the Normalize To group box, define which peak to normalize to by selecting one of the following option buttons:

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

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

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

Figure 2-36. Chromatogram Wizard - Configure Normalization for the Chromatogram page



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

Finishing the Chromatogram Wizard

If you want to change your selections in the Chromatogram Wizard, click on Back to go back through the previous pages. If you are happy with your selections, click on Finish.

After completing the Chromatogram Wizard, the other Merlin wizards automatically activate as necessary in the order defined by the structure of your report template. Refer to the appropriate topic in this chapter for more information on each wizard. When all the wizards have been completed, refer to the topic After Using the Wizards… in this chapter for information on what to do next.

Note. If you have accessed the Merlin Chromatogram Wizard from the Merlin toolbar, rather than from the Merlin Report Structure Wizard, clicking on Finish returns you to the report template Microsoft Word document. Any amendments to the properties of a Chromatogram report object will have been made. Choose File > Save to save the changes to your report template.


Creating a Report Template Using the Merlin WizardsThe Merlin Component Calibration Curve Wizard

2.5 The Merlin Component Calibration Curve Wizard

The Merlin Component Calibration (Cal) Curve Wizard activates automatically on completion of the Report Structure Wizard if you have chosen to include a Component Cal Curve report object (a graphic object) in a non-repeating section of your report template.

The wizard runs for each Component Cal Curve report object included in your report template (according to the order defined by the structure of your report template).

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

Notification of Component Calibration Curve Location

The front page of the Component Calibration Curve Wizard highlights the Component Cal Curve report object to be configured by the wizard and shows how it fits into the overall structure of your report template. See Figure 2-37.


Note. The Merlin Component Calibration Curve Wizard can also be activated from the Merlin toolbar. Refer to Chapter 3 for a discussion of the Merlin toolbar.

Note. If the Merlin Calibration Curve Wizard is activated from the Merlin toolbar, rather than from the Merlin Report Structure Wizard, this page of the wizard (displayed in Figure 2-37) is not displayed.


Creating a Report Template Using the Merlin Wizards__________________________________The Merlin Component Calibration Curve Wizard

Figure 2-37. The front page of the Merlin Component Calibration Curve Wizard


Creating a Report Template Using the Merlin WizardsThe Merlin Component Calibration Curve Wizard

Specifying Component Name

When placing a Component Cal Curve report object outside a Quan repeating section, you must explicitly specify the name of the component that the curve will be plotted for. The second (and final) page of the wizard allows you to do this. See Figure 2-38.

Specify the name of the component that the curve will be plotted for as follows:

1. Click on the Browse button to open the Select Processing File dialog box that allows you to browse for the required Processing Method file (.pmd). By default, the wizard searches in your Xcalibur\methods folder.

2. Select a file, then click on Open to open the selected file. The Select Component dialog box displays. See Figure 2-39.

Figure 2-38. Component Calibration Curve Wizard - Component Name page

Figure 2-39. Select Component dialog box


Creating a Report Template Using the Merlin Wizards__________________________________The Merlin Component Calibration Curve Wizard

3. Select the required component from the list available for the chosen processing method and click on OK. The wizard returns you back to the Component Name page with the specified name of the component on display in the text box.

4. If you are satisfied with your selection, click on Finish to complete the wizard.

After completing the Component Calibration Curve Wizard, the other Merlin wizards automatically activate as necessary in the order defined by the structure of your report template. Refer to the appropriate topic in this chapter for more information on each wizard. When all the wizards have been completed, refer to the topic After Using the Wizards… in this chapter for information on what to do next.

Note. If you have accessed the Merlin Component Calibration Curve Wizard from the Merlin toolbar, rather than from the Merlin Report Structure Wizard, clicking on Finish returns you to the report template Microsoft Word document. Any amendments to the properties of a Component Cal Curve report object will have been made. Choose File > Save to save the changes to your report template.


Creating a Report Template Using the Merlin WizardsAfter Using the Wizards…

2.6 After Using the Wizards…After you finish the Merlin Report Structure Wizard and the individual section and report object wizards, save your report template. You then refine your report template by using the following:

• Merlin toolbar to edit your report template.

• Microsoft Word to edit your report template.

Figure 2-40 shows part of the PeakIntegration2.doc report template (located in your Xcalibur\templates folder), created using the Merlin Report Structure Wizard and edited using the Merlin toolbar and Microsoft Word. This particular report template serves as a good example of the type of customized report template that you are able to create.

This section contains the following topics:

• Saving a Report Template

• Editing a Report Template with the Merlin Toolbar

• Editing a Report Template with Microsoft Word

• Generating a Report


Creating a Report Template Using the Merlin Wizards____________________________________________________After Using the Wizards…

Figure 2-40. A customized Xcalibur report template (PeakIntegration2.doc)


Creating a Report Template Using the Merlin WizardsAfter Using the Wizards…

Saving a Report Template

Save your report template as follows:

1. Choose File > Save As to open the Save As dialog box.

2. Give your report template an appropriate name and save it as a Microsoft Word .doc file in a suitable location. You can save your customized report templates in a new folder, or in the Xcalibur\templates folder along with the report templates that ship with Xcalibur.

You must save your unresolved template as a .doc file. You can change the output to a different file format after you resolve the report.

Editing a Report Template with the Merlin Toolbar

After you finish the Merlin Report Structure Wizard and the individual Merlin wizards, the Merlin toolbar becomes active. You can use the Merlin toolbar to make changes to your report template. Among the things that you can do with the toolbar are the following:

• Create a new Merlin template.

• Insert more report objects and sections.

• Change and maintain the properties of any repeating sections, table objects or graphic objects (that is, ActiveX controls) contained in a report template. In particular, consider manually configuring any Spectrum report objects included in your report template.

• Maintain any tables included in the report template using the Merlin Table Manager.

• Resize graphic objects contained in the report template.

Refer to Chapter 3 for information on completing the above tasks using the Merlin toolbar.


Creating a Report Template Using the Merlin Wizards____________________________________________________After Using the Wizards…

Editing a Report Template with Microsoft Word

Merlin report templates are Microsoft Word documents (.doc file). Therefore, you can use Microsoft Word to change the layout, style and presentation of your report template. You can customize your report template by the following:

• Inserting static text

Use Microsoft Word to add static text to your report template. If you have inserted any text labels in your report template using the Merlin Report Structure Wizard, edit these as required using Microsoft Word. Unedited text labels display in the report template as: < “Insert your text here” >

• Adding headers and footers

Choose View > Header and Footer to display the Header and Footer toolbar. Use the toolbar to create headers and footers for your report template. You can insert static text, Microsoft Word field codes (for example, the date and time) and/or Microsoft Word AutoText entries in your headers and footers.

• Using Microsoft Word tables to display information

You can use Microsoft Word tables to change the layout of Merlin graphic or text report objects contained in your report template. For example, you can design your report template so that report objects display side-by-side in the columns of a Microsoft Word table.

• Altering the pagination

You can change the layout of your report template by manually adding page or column breaks. Choose Insert > Break to insert breaks in your report template.

Generating a Report

When you have completed and saved your report template, you are ready to generate an Xcalibur report. An Xcalibur report is generated when Xcalibur data is resolved with a report template. Refer to Chapter 4 for full details of how to use your completed report template to generate an Xcalibur report.

Note. You can insert Merlin text objects in the headers and footers of a report template. You can also insert a Merlin Chromatogram report object in a header.

Note. More detailed information on the use of Microsoft Word is beyond the scope of this manual. Refer to the documentation and online Help that accompanies Microsoft Word for detailed information on its use.


Chapter 3Using the Merlin Toolbar

This chapter provides information on using the Merlin toolbar. Most of the tasks that can be accomplished in Merlin can be completed using the Merlin toolbar.

This chapter contains the following sections:

• Introduction to the Merlin Toolbar

• Adding sections and report objects to a template

• Configuring repeating sections and report objects

• Maintaining Report Template Tables

• Resizing graphic objects

• Merlin Operations menu

You can create a report template from scratch with the aid of the Merlin toolbar. However, as you have seen in Chapter 2, you can do this more easily with the Merlin Report Structure Wizard, which guides you through the process step-by-step. For new users to Merlin, the Merlin toolbar is best used as a report template editing tool, and as a means of generating Xcalibur reports.


Using the Merlin ToolbarIntroduction to the Merlin Toolbar

3.1 Introduction to the Merlin ToolbarThe Merlin toolbar becomes active in Microsoft Word after you complete or cancel the Merlin Report Structure Wizard. See Figure 3-1. The toolbar also becomes active when you open any report template (Microsoft Word document) attached to the Merlin.dot Microsoft Word template.

A brief overview of the Merlin toolbar buttons is given in Table 3-1.

Figure 3-1. The Merlin toolbar

Note. If the Merlin toolbar is not displayed in Microsoft Word, choose View > Toolbars > Merlin to display the toolbar.

Table 3-1. Merlin toolbar buttons and functions

Button Function

Properties The Properties button is a standard Microsoft Word button that can also be found on the Control Toolbox toolbar. When in design mode (click on the Design Mode button), you can use this button to configure or change the properties of any repeating sections, table objects or graphic objects (that is, ActiveX controls) contained in your report template. Refer to your Microsoft Word documentation for full details of the functionality of the Properties button.

Design Mode / Exit Design Mode

The Design Mode / Exit Design Mode button is a standard Microsoft Word button that can also be found on the Control Toolbox toolbar. You can use this button to enter or exit the design mode. In design mode, you can do the following:

Configure or change the properties of any selected repeating sections, table objects or graphic objects (that is, ActiveX controls) contained in your report template.

Resize any selected graphic objects in the report template using your mouse.

Refer to your Microsoft Word documentation for full details of the functionality of the Design Mode / Exit Design Mode button.

Merlin Operations

The Merlin Operations button is a drop-down menu button. You can use this button to do the following:

• Create a new Merlin template

• Generate an Xcalibur report using the Merlin Data Source Browser.

• Show required data sources needed to generate a report from the active report template using the Merlin Data Source Identifier.

• Clean a report template.

Add Repeating Section

You can use the Add Repeating Section button to add a new repeating section to your report template.

Text Objects The Text Objects button is a drop-down menu button. You can use this button to add a new text object from the drop-down menu to your report template.


Using the Merlin Toolbar______________________________________________ Introduction to the Merlin Toolbar

Table Objects

The Table Objects button is a drop-down menu button. You can use this button to add a new table object from the drop-down menu to your report template.

You can also use the Table Objects button to maintain the tables (table objects) contained in a report template with the aid of the Merlin Table Manager. This allows you to select individual table objects in the report template in order to modify or delete them using the Merlin Table Wizard.

Graphic Objects

The Graphic Objects button is a drop-down menu button. You can use this button to add a new graphic object from the drop-down menu to your report template.

Table 3-1. Merlin toolbar buttons and functions, continued

Button Function


Using the Merlin ToolbarAdding Sections and Report Objects to a Template

3.2 Adding Sections and Report Objects to a Template

This section describes how to use the Merlin toolbar to add new sections and report objects to a report template. You can use the toolbar to add the following:

• Repeating sections

• Text objects

• Table objects

• Graphic objects

New sections and report objects are added to your report template at the position of the insertion point (cursor location).

Table objects and graphic objects cannot be added to an invalid section. If you try to add a text object to an invalid section, Merlin asks you to confirm the addition. See Figure 3-2. Click on Yes or No as appropriate.

Adding a Repeating Section

To add a repeating section to your report template, click on the Add Repeating Section button. To help you configure the repeating section, Merlin automatically activates the Merlin Repeating Section Wizard with the Select Type of Peak to Repeat On page. See Figure 3-3. You use this page to define the repeating section type: Quan or Qual.

Figure 3-2. Confirming addition of a report object to an inappropriate section of a report template


Using the Merlin Toolbar________________________________ Adding Sections and Report Objects to a Template

Complete this page of the wizard as follows:

1. In the Repeat On group box, define the type of repeating section by selecting one of the following option buttons:

• Quan Components and Peak—for a Quan repeating section

• Qual Peaks—for a Qual repeating section

2. If you select the Quan Components and Peak option button, you can exclude specific elements from the process and to discard any components that have not been found:

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

• None (no exclusions) - the default

• Internal Standards

• Target Compounds

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


The remaining wizard pages follow exactly the same format as described in the relevant (Quan or Qual) of The Merlin Repeating Section Wizard. Refer to this topic in Chapter 2 for information on completing the remaining wizard pages.

Figure 3-3. Merlin Repeating Section Wizard - Select Type of Peak to Repeat On



Adding a Text Object

To add a text object to your report template, click on the Text Objects button and select the required text object from the drop-down menu. You can choose from the following text objects (refer to Appendix B for a description of each object, including which section each object must be in):

• Component Ident/Detect/Cal Settings

• Component ISTD Settings Summary

• Component Settings Summary

• Component Sys Suit/Flags Settings

• Processing Method - General

• Processing Method - Qual

• Quan ISTD Peak Summary

• Quan Peak Summary

• Sample Header

Adding a Table Object

To add a table object to your report template, click on the Table Objects button and select the required table object from the drop-down menu. You can choose from the following table objects (refer to Appendix B for a description of each object, including which section each object must be in):

• Avalon Qual Events Table

• Avalon Quan Events Table

• Calibration File Table

• Component Cal Level Table

• Component Ion Ratio Confirmation Table

• Component QC Level Table

• Component Spectrum Table

• Dilution Factor Table

• Ion Ratio Confirmation Results Table

• IRC Summary Table

• Lib. Search Graphics Table



• Proc. Method Audit Trail Table



• Proc. Method Programs Table

• Proc. Method Sample Reports Table

• Proc. Method Summary Reports Table

• Qual Peak Table

• Quan Peak Table


• Sequence Table

• Spectrum Candidate Results Table

To help you configure the table object, Merlin automatically activates the Merlin Table Wizard with the Select Table Fields page. Full details of how to complete this page and the remaining pages of the wizard can be found in The Merlin Table Wizard (Chapter 2).

Adding a Graphic Object

To add a graphic object to your report template, click on the Graphic Objects button and select the required graphic object from the drop-down menu. You can choose from the following graphic objects (refer to Appendix B for a description of each object, including which section each object must be in):

• Chromatogram

• Component Cal (Calibration) Curve

• Spectrum

Adding a Chromatogram Report Object

To add a Chromatogram report object to your report template, choose Graphic Objects > Chromatogram. To help you configure the Chromatogram report object, Merlin automatically activates the Merlin Chromatogram Wizard. Refer to The Merlin Chromatogram Wizard topic in Chapter 2 for information on using this wizard.

Adding a Component Calibration Curve Report Object

To add a Component Calibration Curve report object to your report template, choose Graphic Objects > Component Cal Curve. If the Component Calibration Curve report object is inserted in a non-repeating section, Merlin automatically activates the Merlin Component Calibration Curve Wizard. Refer to The Merlin Component Calibration Curve Wizard topic in Chapter 2 for information on using this wizard.



Adding a Spectrum Report Object

To add a Spectrum report object to your report template, choose Graphic Objects > Spectrum. To help you configure the Spectrum report object, Merlin automatically activates the Merlin Spectrum Control Properties dialog box. See Figure 3-4.

The Merlin 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 your selections on each page to configure the Spectrum report object.

Figure 3-4. Merlin Spectrum Control Properties dialog box



Options

The Options page allows you to configure the Spectrum options. See Figure 3-4. Fill in the Options page of the Merlin Spectrum Control Properties dialog box as follows:

1. Select the Use Processing Method Properties check box to use processing method properties for Plot Type and Enhance information.

2. Select the Use ISTD Peak When check box to use the Internal Standard peak when repeating on a component.

Plot Type

When raw data is being displayed in a Spectrum report object, you can use the Plot Type page to configure how the plot is drawn. See Figure 3-5.

Fill in the Plot Type page of the Merlin Spectrum Control Properties dialog box as follows:

1. In the Mass text box, specify the mass or mass range for MS detector types. For PDA detector types, you can 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: *

Figure 3-5. Merlin Spectrum Control Properties dialog box - Plot Type page



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

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

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

5. In the Demo File text box, click on the browse button, and identify the file in the normal manner. This shows the path and filename of the demo file (raw file) used to generate the selected plot.

Enhance

The Enhance page allows you to apply smoothing or the refine algorithm to the spectrum. You can also set background subtraction time ranges. See Figure 3-6.

Fill in the Enhance page of the Merlin Spectrum Control Properties dialog box as follows:

1. In the Smoothing group box, select the Enable check box to enable spectrum smoothing.

Figure 3-6. Merlin Spectrum Control Properties dialog box - Enhance page



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

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

4. In the Refine group box, select the Enable check box to enable or disable Refine spectrum enhancement.

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

6. In the Noise Threshold text box, type 0 (this will show all peaks in the spectrum) and increase the value until noise peaks are eliminated. Use this parameter to eliminate peaks generated from baseline noise.

7. In the Background Subtraction group box, select the Time Range 1 check box to enable a first baseline region used for assessing the background. Type the time range in the text box.

The Background Subtraction group box shows details of background subtraction if this 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 text box.

Style

The Style page allows you to set parameters that determine the appearance of the spectrum. See Figure 3-7.

Fill in the Style page of the Merlin Spectrum Control Properties dialog box as follows:

1. In the Plotting group box, define the plotting style by selecting one of the following option buttons:

• 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.

2. In the Arrangement group box, define the plot arrangement by selecting one of the following option buttons:

• Stack (2D)—to stack plots vertically with no overlap for the active map.



• Overlay (3D)—to overlay plots vertically with an optional horizontal skew (time offset) for the active map.

Labels

The Labels page allows you to choose the type and style of peak labels. See Figure 3-8.

Fill in the Labels page of the Merlin Spectrum Control Properties dialog box as follows:

1. In the Label With group box, select the Mass check box to label spectrum peaks with m/z values. Use the Decimals text box to specify the number of decimal places to be used in the label.

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

3. In the Label group box, select the Offset check box 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 text box.

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

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

Figure 3-7. Merlin Spectrum Control Properties dialog box - Style page



6. In the Label Threshold text box, limit the labeling of peaks to those exceeding the specified percentage of the base peak.

Axis

The Axis page allows you to set spectrum axis labels and display options. See Figure 3-9.

Fill in the Axis page of the Merlin Spectrum Control Properties dialog box as follows:

1. In the X Axis group box, type the X-axis name into the Name text box.

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 text box.

4. In the Y Axis group box, in the Label group box, select one of the following option buttons:

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

• Custom—to use your own label.

5. In the Units group box, select the Absolute or the Relative option button to specify the setting for the Y-axis units: absolute or relative.

Figure 3-8. Merlin Spectrum Control Properties dialog box - Labels page



6. In the Name text box, enter a Y-axis name if you have a custom label for the Y-axis, use this text box to.

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

8. In the Z Axis group box, type the Z-axis name into the Name text box.

Normalization

The Normalization page allows you to select normalization options for spectrum plots. See Figure 3-10.

Fill in the Normalization page of the Merlin Spectrum Control Properties dialog box as follows:

1. In the Normalize Method group box, define the normalization method by selecting one of the following option buttons:

• Auto zero—to automatically optimize the Y-axis

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

2. In the Normalize To group box, define the peak that the spectrum is normalized to by selecting one of the following option buttons:

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

Figure 3-9. Merlin Spectrum Control Properties dialog box - Axis page



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

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

3. In the Normalize multiple scans group box, define how multiple scans are normalized by selecting one of the following option buttons:

• Individually—to normalize each mass plot individually.

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

Peak

The Peak page allows you to explicitly specify the peak to display in the Spectrum report object. See Figure 3-11.

Fill in the Peak page of the Merlin Spectrum Control Properties dialog box as follows:

1. Select the Enable Explicit Peak check box to enable the controls that allow you to specify the type of peak to appear in the Spectrum.

2. In the Peak Type group box, select the Quan Peak option button to specify a Quan peak, or select the Qual Peak option button to specify a Qual peak. Use this group box to explicitly specify the type of peak to appear in the Spectrum.

Figure 3-10. Merlin Spectrum Control Properties dialog box - Normalization page



3. In the Peak Identification group box, type a name for the component for a Quan peak. For a Qual peak, type the retention time (any time between the start time and end time of the peak can be entered). Alternatively, click on the browse button to open the Select a Peak dialog box. Select (highlight) a peak and click on OK to close the dialog box.

Figure 3-11. Merlin Spectrum Control Properties dialog box - Peak page


Using the Merlin Toolbar_______________________________ Configuring Repeating Sections and Report Objects

3.3 Configuring Repeating Sections and Report Objects

In Microsoft Word, a Property is defined as a named attribute of a control or object that you set to define one of the characteristics of the object or an aspect of its behavior.

As discussed previously, Merlin automatically prompts you to configure each repeating section, table object or graphic object (ActiveX controls) added to a report template. When configuring these controls, you are changing or editing the individual properties of that control.

There might be times when you want to reconfigure or change and maintain the properties of a repeating section, table object or graphic object contained in a report template. You can use the Merlin toolbar to do this as described in the following topics:

• Configuring a repeating section

• Configuring a table object

• Configuring a chromatogram

• Configuring a component calibration curve report object

• Configuring a spectrum


Using the Merlin ToolbarConfiguring Repeating Sections and Report Objects

Configuring a Repeating Section

You can configure a repeating section contained in a report template as follows:

1. Click on the Design Mode button in the Merlin toolbar to activate the design mode. The Control Toolbox toolbar appears and the Properties button on the Merlin toolbar is enabled.

2. Click on the gray repeating section control in the report template to select it. (A control is selected when the black handlebars on each side and at each corner become visible.)

3. Click on the Properties button in the Merlin toolbar. The Properties list displays, showing the current settings for the repeating section. See Figure 3-12.

4. Select (highlight) the (Custom) field in the Properties list. Then click on the Browse button (…) for the (Custom) field. The repeating section Property Pages dialog box displays containing three tabbed pages: Exclude, Ordering, and Page Breaks. See Figure 3-13.

Figure 3-12. Properties list for a repeating section

Note. You can select and edit the individual property fields displayed on the Properties list. However, this is only recommended for advanced users of Xcalibur and Merlin. The (Custom) field provides access to a more user-friendly representation of the property fields in the Properties list.



5. Use the pages of the Property Pages dialog box to configure the repeating section. The three pages (Exclude, Ordering, and Page Breaks) are equivalent to the pages of The Merlin Repeating Section Wizard as described in Chapter 2. Refer to this topic in Chapter 2 for information on completing these pages.

6. Click on OK when you have made your selections in the Property Pages dialog box. Close the Properties list and return to your report template. It is a good idea to save any changes made by choosing File > Save.

Figure 3-13. Property Pages dialog box for a repeating section



Configuring a Table Object

You can maintain a table object contained in a report object by using the Merlin Table Manager. The Merlin Table Manager is discussed in the topic Maintaining Report Template Tables later in this chapter.

You can also access the Properties list for a table object to configure its properties. However, this is only necessary in the case of the following table objects:

• Lib. Search Graphics Table




Configure the above table objects as follows:


2. Click on the gray table object control in the report template to select it. (A control is selected when the black handlebars on each side and at each corner become visible.)

3. Click on the Properties button in the Merlin toolbar. The Properties list displays, showing the current settings for the table object. See Figure 3-14.

Note. All other Merlin table objects do not have any significant properties available for editing. The Height and Width property fields found in the Properties list for all table objects control the size of the gray table object control in the report template.



1. Select (highlight) the (Custom) field in the Properties list. Then click on the Browse button (…) for the (Custom) field. The more user-friendly table object Property Pages dialog box displays (Figure 3-13). The appearance of this page is dependant on the table object being configured.

2. Make your selections on the table object Property Pages dialog box to configure the table object.

3. Click on OK when you have made your selections on the table object Property Pages dialog box. Close the Properties list and return to your report template. It is a good idea to save any changes made by choosing File > Save.

Figure 3-14. Properties list for a Mass Spectrum List Table

Note. You can select and edit the individual property fields displayed on the Properties list. However, this is only recommended for advanced users of Xcalibur and Merlin. The (Custom) field provides access to a more user-friendly representation of the property fields in the Properties list.



Configuring a Chromatogram

The simplest method of configuring a Chromatogram report object contained in a report template is as follows:

1. Ensure that the design mode is switched off. If you are in design mode, click on the Exit Design Mode button on the Merlin toolbar.

2. Using your mouse, right-click anywhere on a gray Chromatogram report object and choose Reconfigure from the shortcut menu. Merlin automatically activates the Merlin Chromatogram Wizard. Refer to The Merlin Chromatogram Wizard topic in Chapter 2 for information on using this wizard.

Alternatively, You can also configure a Chromatogram report object as follows:


2. Click on the gray Chromatogram report object in the report template to select it. (A control is selected when the black handlebars on each side and at each corner become visible.)

3. Click on the Properties button in the Merlin toolbar. The Properties list displays, showing only a few of current settings for the Chromatogram report object. See Figure 3-15. The majority of settings for the Chromatogram can only be accessed from the (Custom) field.

4. Select (highlight) the (Custom) field in the Properties list. Then click on the Browse button (…) for the (Custom) field. The Chromatogram report

Figure 3-15. Properties list for a Chromatogram report object

Note. The property fields displaying in the Chromatogram Properties list are not of great significance. The Height and Width property fields simply control the size of the gray Chromatogram report object in the report template. The (Custom) field provides access to a more user-friendly and comprehensive representation of the properties for a Chromatogram report object.



object Property Pages dialog box displays with the current configuration details. See Figure 3-16.

5. Click on the Configure button. Merlin automatically activates the Merlin Chromatogram Wizard. Refer to The Merlin Chromatogram Wizard topic in Chapter 2 for information on using this wizard.

6. After completing the Merlin Chromatogram Wizard, click on OK on the Chromatogram report object Property Pages dialog box. Close the Properties list and return to your report template. It is a good idea to save any changes made by choosing File > Save.

Figure 3-16. Property Pages dialog box for a Chromatogram report object



Configuring a Component Calibration Curve Report Object

You can configure a Component Calibration Curve report object that is contained in a report template as follows:


2. Click on the gray Component Cal Curve report object in the report template to select it. (A control is selected when the black handlebars on each side and at each corner become visible.)

3. Click on the Properties button in the Merlin toolbar. The Properties list displays, showing the current settings for the Component Cal Curve. See Figure 3-17.

4. Select (highlight) the (Custom) field in the Properties list. Then click on the Browse button (…) for the (Custom) field. The Component Cal Curve Property Pages dialog box displays containing a single tabbed page: Component. See Figure 3-18.

Figure 3-17. Properties list for a Component Cal Curve report object

Note. You can select and edit the individual property fields displayed on the Properties list. However, this is only recommended for advanced users of Xcalibur and Merlin. The (Custom) field provides access to a more user-friendly and simpler property field editor for a Component Cal Curve report object.



5. Use the Component page of the Property Pages dialog box to specify the name of the component that the Component Cal Curve will be plotted for. The Component page is equivalent to the Component Name page of The Merlin Component Calibration Curve Wizard as described in Chapter 2. Refer to this topic in Chapter 2 for information on completing this page.

6. Click on OK when you have specified a component name in the Property Pages dialog box. Close the Properties list and return to your report template. It is a good idea to save any changes made by choosing File > Save.

Figure 3-18. Property Pages dialog box for a Component Cal Curve report object



Configuring a Spectrum

You can configure a Spectrum report object contained in a report template as follows:


2. Click on the gray Spectrum report object in the report template to select it. (A control is selected when the black handlebars on each side and at each corner become visible.)

3. Click on the Properties button in the Merlin toolbar. The Properties list displays, showing the current settings for the Spectrum report object. See Figure 3-19.

Figure 3-19. Properties list for a Spectrum report object

Note. You can select and edit the individual property fields displayed on the Properties list. However, this is only recommended for advanced users of Xcalibur and Merlin. The (Custom) field provides access to a more user-friendly representation of the properties for a Spectrum report object.



4. Select (highlight) the (Custom) field in the Properties list. Then click on the Browse button (…) for the (Custom) field. The Spectrum report object Property Pages dialog box displays with eight pages containing the current Spectrum configuration details. See Figure 3-20.

5. Configure the Spectrum report object by completing the eight tabbed pages. Refer to the topic Adding a Spectrum Report Object earlier in this chapter (page 3-8) for details of how to complete each page.

6. After completing the eight pages, click on OK on the Spectrum report object Property Pages dialog box. Close the Properties list and return to your report template. It is a good idea to save any changes made by choosing File > Save.

Figure 3-20. Property Pages dialog box for a Spectrum report object


Using the Merlin ToolbarMaintaining Report Template Tables

3.4 Maintaining Report Template Tables

You can maintain any table objects contained in a report template using the Merlin Table Manager, which is accessed from the Merlin toolbar. The Merlin Table Manager allows you to do the following:

• List all the table objects contained in the active report template

• Configure any table objects contained in the active report template

• Delete any table objects contained in the active report template

Use the Merlin Table Manager as follows:

1. From the Merlin toolbar, choose Table Objects > Maintain Template Tables to access the Merlin Table Manager. The Maintain Template Tables dialog box appears with a list of all the table objects contained in the active report template. See Figure 3-21.

2. Select (highlight) the table object to be maintained. The selected table is also highlighted in the report template.

3. To delete the selected table object, click on Delete. You are required to confirm the deletion of the table object. Click on Yes or No as appropriate.

4. To configure the selected table object, click on Reconfigure. Merlin automatically activates the Merlin Table Wizard with the Select Table Fields page to help you configure the table object. Full details of how to complete this page and the remaining pages of the wizard can be found in The Merlin Table Wizard (Chapter 2).

5. Click on Close to close the Merlin Table Manager and return to the report template. It is a good idea to save any changes made by choosing File > Save.

Figure 3-21. The Merlin Table Manager - Maintain Template Tables


Using the Merlin Toolbar___________________________________________________ Resizing a Graphic Object

3.5 Resizing a Graphic ObjectUse the following procedure to resize any graphic object contained in a report template:

1. Click on the Design Mode button in the Merlin toolbar to activate the design mode.

2. Click on the gray graphic object in the report template to select it. (A control is selected when the black handlebars on each side and at each corner become visible.)

3. Click and drag on any of the handlebars. Resize the graphic object as required.

4. It is a good idea to save any changes made by choosing File > Save.


Using the Merlin ToolbarMerlin Operations Menu

3.6 Merlin Operations MenuYou can use the Merlin Operations button to access the following commands on a drop-down menu:

• New Merlin Wizard

• Generate Report

• Show Required Data Sources

• Clean Document

These commands are discussed in the topics below.

New Merlin Wizard

Choose Merlin Operations > New Merlin Wizard to open the Merlin Report Structure Wizard. Refer to Chapter 2 for more information on using the Merlin Report Structure Wizard. If Merlin.dot is not installed in the default Xcalibur\system\programs folder, an error message appears. Copy the Merlin.dot file into the correct folder.

Generate Report

Choose Merlin Operations > Generate Report to generate a report with the aid of the Merlin Data Source Browser. Refer to Chapter 4 for more information on generating an Xcalibur report.

Show Required Data Sources

Choose Merlin Operations > Show Required Data Sources to access the Merlin Data Source Identifier. See Figure 3-22. You can use this feature of Merlin to see which data source files are required to generate a report using the active report template.

Figure 3-22. The Merlin Data Source Identifier


Using the Merlin Toolbar_____________________________________________________ Merlin Operations Menu

Clean Report Template

Choose Merlin Operations > Clean Template to delete the contents of the active report template. When you use this command, the Delete Document Contents warning dialog box displays asking you to confirm that you want to delete the contents of the document. Click on Yes or No as appropriate.

Note. You must use this command to effectively clean a report template. Do not use Microsoft Word to manually delete the content of a report template.


Chapter 4Generating a Report

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

• From a Merlin report template open in Microsoft Word—you can use the Merlin Data Source Browser to automatically browse for the required data source files and resolve the data to generate a report. A single report is generated by this method.

• From Xcalibur—you can associate the data you produced in Xcalibur with a report template, then resolve the data to generate a report. It is possible to generate multiple reports from Xcalibur.

Both methods of report generation are covered in this chapter. A tutorial is also provided, which leads you through the steps involved in generating an Xcalibur report from a report template open in Microsoft Word.


Generating a ReportGenerating a Report from a Report Template

4.1 Generating a Report from a Report Template

This topic describes how to generate a report from a Merlin report template open in Microsoft Word. It also contains a tutorial that uses a specific example to illustrate the steps involved. The tutorial uses a Merlin report template and data that ship as part of Xcalibur.

The process of generating a report from a Merlin report template involves using the Merlin Data Source Browser (accessed from the Merlin toolbar) to browse for the required data source file(s) and resolve the data to generate a report. The data source file(s) required to generate a report depends on the content (sections and report objects) of the report template.

You can use the Data Source Identifier for Merlin (accessed from the Merlin toolbar) to establish exactly which data source files are required to generate a report from a report template. Refer to the topic Merlin Operations in Chapter 2 of this manual for more information on using the Merlin Data Source Identifier.

The procedure for generating a report from a report template using the Merlin Data Source Browser is as follows:

1. Open the Merlin report template in Microsoft Word. Ensure that the Merlin toolbar is displaying.

2. From the Merlin toolbar choose Merlin Operations > Generate Report to access the Merlin Data Source Browser. The individual pages in the Merlin Data Source Browser are discussed in the next topics.

3. Use the Data Source Browser (Merlin Data Sources dialog box) to browse for the required data source file(s).

4. Click on OK in the Merlin Data Sources dialog box when the required data source file(s) has been selected. Microsoft Word automatically resolves the data with the active report template and generates a report. The report is generated as a new Microsoft Word document with a ‘~Resolved’ prefix and you are prompted to save the report. You can save the report with any name.

Note. A single report is created each time you generate a report from a report template.

Note. If the Merlin toolbar is not displayed in Microsoft Word, choose View > Toolbars > Merlin to display the toolbar.


Generating a Report_____________________________________Generating a Report from a Report Template

5. Save the report in a suitable location by choosing File > Save As to open the Save As dialog box. You can save the report as a text (.txt file), document (.doc file), rich text (.rtf file), or web page (.htm or .html file) format. You can to use Microsoft Word to edit or reformat the report, print out the report, or e-mail your report.

The following data source files might be required to generate a report from a report template:

• Calibration file (.xcal file)

• Raw data file (.raw file)

• Result file (.rst file)

• Processing Method file (.pmd file)

• Sequence (.sld file)

The Merlin Data Source Browser automatically prompts you for the required file(s). The appearance of the Data Source Browser is dependent on the data source file(s) required. The following topics describe the appearance of the Data Source Browser for all possible combinations of required data source file(s).

Merlin Data Source Browser (.xcal file)

When a Calibration file (.xcal file) is required to generate a report from the active report template, the Merlin Data Source Browser prompts you for this file with the Merlin Data Sources dialog box shown in Figure 4-1.

Fill in the Merlin Data Sources - Select Xcalibur Data File to Generate Report dialog box as follows:

1. In the Calibration File group box, click on the Browse (…) button to browse for the required Calibration file. The Select Calibration File dialog box appears.

Note. A report is generated as a new Microsoft Word document. The report is based on the Normal.dot template of Microsoft Word.

Figure 4-1. Merlin Data Sources dialog box: Select Calibration file



2. Use the Select Calibration File dialog box to browse for the Calibration file. When you have found the required file, click on Open. You are returned to the Merlin Data Sources dialog box. The full path of the selected file is shown in the Calibration File box.

3. Click on OK to generate the report.

Merlin Data Source Browser (.raw file)

When a Raw file (.raw file) is required to generate a report from the active report template, the Merlin Data Source Browser prompts you for this file with the Merlin Data Sources dialog box shown in Figure 4-2.


1. In the Raw File group box, click on the Browse (…) button to browse for the required Raw file. The Select Raw Data File dialog box appears.

2. Use the Select Raw File dialog box to browse for the Raw file. When you have found the required file, click on Open. You are returned to the Merlin Data Sources dialog box. The full path of the selected file is shown in the Raw File box.


Merlin Data Source Browser (.rst file)

When a Results file (.rst file) (or any combination of the following files: .raw/.rst/.pmd) is required to generate a report from the active report template, the Merlin Data Source Browser prompts you for this file with the Merlin Data Sources dialog box shown in Figure 4-3.

Figure 4-2. Merlin Data Sources dialog box: Select Raw file




1. In the Results File group box, click on the Browse (…) button to browse for the required Results file. The Select Results File dialog box appears.

2. Use the Select Results File dialog box to browse for the Results file. When you have found the required file, click on Open. You are returned to the Merlin Data Sources dialog box. The full path of the selected file is shown in the Results File box.


Merlin Data Source Browser (.pmd file)

When a Processing Method file (.pmd file) is required to generate a report from the active report template, the Merlin Data Source Browser prompts you for this file with the Merlin Data Sources dialog box shown in Figure 4-4.


Figure 4-3. Merlin Data Sources dialog box: Select Results file

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, you will receive an error message. Ensure the .raw file is in the correct folder.

Figure 4-4. Merlin Data Sources dialog box: Select Processing Method file



1. In the Processing Method group box, click on the Browse (…) button to browse for the required .pmd file. The Select Processing File dialog box appears.

2. Use the Select Processing File dialog box to browse for the Processing Method file. When you have found the required file, click on Open. You are returned to the Merlin Data Sources dialog box. The full path of the selected file is shown in the Processing Method box.


Merlin Data Source Browser (.sld file)

When a Sequence file (.sld file) is required to generate a report from the active report template, the Merlin Data Source Browser prompts you for this file with the Merlin Data Sources dialog box shown in Figure 4-5.


1. In the Sequence File group box, click on the Browse (…) button to browse for the required Sequence file. The Select Sequence dialog box appears.

2. Use the Select Sequence dialog box to browse for the Sequence file. When you have found the required file, click on Open. You are returned to the Merlin Data Sources dialog box. The full path of the selected file is shown in the Sequence File box.


Merlin Data Source Browser (.sld file)

When a Sequence file (.sld file) and specific sample information is required to generate a report from the active report template, the Merlin Data Source Browser prompts you with the Merlin Data Sources dialog box shown in Figure 4-6.

Figure 4-5. Merlin Data Sources dialog box: Select Sequence file



Fill in the Merlin Data Sources - Select Sequence and Sample to Generate Report dialog box as follows:

1. Click on the Sequence File Browse (…) button to browse for the required Sequence file. The Select Sequence dialog box appears.

2. Use the Select Sequence dialog box to browse for the Sequence file. When you have found the required file, click on Open. You are returned to the Merlin Data Sources dialog box. The full path of the selected file is shown in the Sequence File box.

3. In the Sequence Row Details group box, click on the Row Browse (…) button to browse for the required sample details. The Select A Sample From The Sequence File dialog box appears (Figure 4-7).

4. Use the Select A Sample From The Sequence File dialog box to select (highlight) the required sample from the sequence. Click on OK when you have chosen the required sample. You are returned to the Merlin Data Sources dialog box. The selected sample details are displayed in the Sequence Row Details group box.


Figure 4-6. Merlin Data Sources dialog box: Select Sequence and Sample



Merlin Data Source Browser (.sld file and .xcal file)

When a Sequence file (.sld file), specific sample information and a Calibration file (.xcal file) are required to generate a report from the active report template, the Merlin Data Source Browser prompts you with the Merlin Data Sources dialog box shown in Figure 4-8.

1. Click on the Sequence File Browse (…) button to browse for the required Sequence file. The Select Sequence dialog box appears.

2. Use the Select Sequence dialog box to browse for the Sequence file. When you have found the required file, click on Open. You are returned

Figure 4-7. Select A Sample From The Sequence File dialog box

Figure 4-8. Merlin Data Sources dialog box: Select Sequence and Sample



to the Merlin Data Sources dialog box. The full path of the selected file is shown in the Sequence File box.

3. In the Sequence Row Details group box, click on the Row Browse (…) button to browse for the required sample details. The Select A Sample From The Sequence File dialog box appears (Figure 4-7).

4. Use the Select A Sample From The Sequence File dialog box to select (highlight) the required sample from the sequence. Click on OK when you have chosen the required sample. You are returned to the Merlin Data Sources dialog box. The selected sample details are displayed in the Sequence Row Details group box.

5. To use an external Calibration file, select the Use External Calibration File check box.

6. Click on the Browse (…) button to browse for the required Calibration file. The Select Calibration File dialog box appears.

7. Use the Select Calibration File dialog box to browse for the Calibration file. When you have found the required file, click on Open. You are returned to the Merlin Data Sources dialog box. The full path of the selected file is shown in the Calibration File text box.




Tutorial: Generating a Report from a Report Template

This tutorial takes you through generating a report from one of the custom report templates that ship with Xcalibur. The tutorial uses a report template to generate a Quan sample report containing certain peak integration data.

1. Open Microsoft Word by choosing Start > Programs > Microsoft Microsoft Word. Alternatively, you can double-click on the Microsoft Word icon on your desktop.

2. Open the PeakIntegration2.doc report template in Microsoft Word by choosing File > Open and selecting PeakIntegration2.doc from the Open dialog box. You can find this report template in your Xcalibur\templates folder.

3. From the Merlin toolbar choose Merlin Operations > Generate Report. The Merlin Data Source Browser prompts you for a Results file with the Merlin Data Sources dialog box (Figure 4-9).

4. Click on the Browse (…) button to open the Select Results File dialog box.

5. Use the Select Results File dialog box to browse for the steroids02.rst file located in your Xcalibur\examples\data folder. When you have selected this file, click on Open. You are returned to the Merlin Data Sources dialog box. The full path of the selected file is shown in the Results File box.

6. Click on OK to generate the report. Microsoft Word automatically resolves the selected steroid data with the PeakIntegration2.doc report template to generate the peak integration report. The report is displayed in a separate Microsoft Word window.

7. Save the report as a .doc file by choosing File > Save As.

8. Print the report from Microsoft Word.

Figure 4-9. Merlin Data Sources dialog box: Results file

Note. Appendix C contains a copy of the report generated by following the steps in the above tutorial.


Generating a Report_____________________________________________ Generating a Report from Xcalibur

4.2 Generating a Report from Xcalibur

Reports are generated from Xcalibur by associating the data that you produced in Xcalibur with a report template. Xcalibur then resolves the data with the specified report template to generate a report. It is possible to generate multiple reports from Xcalibur.

Reports can be readily generated from several different areas of Xcalibur. This topic highlights these areas. Refer to your other Xcalibur Getting Productive manuals and the Xcalibur online Help for detailed information on generating a report from a specific area of Xcalibur.

You can generate a report from the following areas of Xcalibur:

• Sequence Setup—Running a Sample, Running a Sequence, and Batch Reprocessing

• Quan Browser—Reports dialog box

• Processing Setup—Reports view

Note. Ensure that you do not have a report template open in Microsoft Word when using it to generate a report from Xcalibur.

Note. Refer to your other Xcalibur Getting Productive manuals and the Xcalibur online Help for detailed information on generating a report from a specific area of Xcalibur.


Appendix AExample Merlin Report Template Files

Xcalibur ships with several example Merlin report templates ready-built for you to use. This appendix provides details of these report templates. You can find them 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. Try opening some of the example report templates in Microsoft Word to view their content and see how they look. You may like to use some of these report templates to generate your own Xcalibur reports.

________________ Finnigan Xcalibur: Getting Productive with Merlin ________________ A-1

Example Merlin Report Template Files

Table A-1. Example Merlin report template files

Report Template File Name Data Source File(s)

Description / Use

CalibrationFile2.doc .raw, .xcal For reporting calibration data

CompCalReport2.doc

CompCalReport2_Avalon.doc

CompCalReport2_Genesis.doc

CompCalReport2_ICIS.doc

.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.

CustLibrSearRept2.doc

LibrarySearchReport2.doc

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

IonRatioConfirmation2.doc .rst, .raw, .pmd

For generating a Quan sample report containing non-graphical ion ratio confirmation results.

IonRatioConfirmationGraphical.doc

IonRatioConfirmationGraphicalSimple.doc

IonRatioConfirmationGraphicalStacked.doc

.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 Merlin Chromatogram Wizard (see Chapter 2).

PeakIntegration2.doc .rst, .raw, .pmd

For generating a Quan sample report containing peak integration data.

ProcessingMethod2.doc

ProcessingMethod2_Avalon.doc

ProcessingMethod2_Genesis.doc

ProcessingMethod2_ICIS.doc

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

QualPeakReport2.doc .rst, .raw For generating a simple Qual sample report.Should be used from Xcalibur’s Batch Processing.

QuanPeakResults.doc

QuanResults.doc

QuanSimple.doc

.rst, .raw,

.pmdFor generating Quan sample reports. May be used from Xcalibur’s Batch Processing or Quan Browser.

SequenceReport2.doc .sld For generating a summary report showing the sequence being processed. Use from Xcalibur’s Batch Processing

SpectrumCandidates2.doc .rst, .raw For generating a Quan sample report (only applicable to GC/MS). Use from Xcalibur’s Batch Processing or Quan Browser.

A-2 _________________Finnigan Xcalibur: Getting Productive with Merlin_________________

Appendix BReport Objects

The following tables list the report objects you can place onto your report template: text objects, table objects, and graphic objects. The tables briefly describe an object and indicate the preferred placement of the object inside or outside a repeating section. The placement of objects in your report template determines how your custom Xcalibur report will look when it is generated.

This chapter lists the following objects:

• Text objects in Table B-1

• Table objects in Table B-2

• Graphic objects in Table B-3

________________ Finnigan Xcalibur: Getting Productive with Merlin ________________ B-1

Report Objects

Table B-1. Text Objects

Text Object Data Source File

Description Repeating Section Placement

Component Ident/Detect/Cal Settings

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

Inside (Quan) - Repeats on Component Peak

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


Component Settings Summary

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


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.


Processing Method -General

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

Does not repeat.

Processing Method - Qual

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

Identification

Detection Options

Advanced Detection Options

Spectrum Enhancement

Library Search options

Library Search Constraints

Does not repeat.

Quan ISTD Peak Summary

.rst,

.pmdDisplays summary parameters for a Quan component’s associated ISTD peak. For example:

ISTD Name

Actual RT

Response

Base Line

Signal To Noise

Expected RT


B-2 _________________Finnigan Xcalibur: Getting Productive with Merlin_________________

Report Objects________________________________________________________________________

Quan Peak Summary

.rst,

.pmdDisplays Component Peak summary parameters, for example:

Actual RT

Calculated Amount

Response

Base Line

Signal To Noise

% Diff

Area Ratio

Area ISTD

Specified Amount


Sample Header .raw Displays general information about a sample, for example:

Sample Name

Sample Type

Acquisition Date

Operator

Run Time

Does not repeat.

Table B-1. Text Objects, continued

Text Object Data Source File



Report Objects

Table B-2. 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.

Does not repeat.

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.


Calibration File Table

.xcal,

.sld,

.raw

Displays calibration levels, raw file names, and acquisition dates of standards.

Does not repeat.

Component Cal Level Table

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


Component Ion Ratio Confirmation 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.


Component QC Level Table

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


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.


Dilution Factor Table

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

Does not repeat.

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 %



Report Objects________________________________________________________________________

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.

Does not repeat.

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).

Inside (Qual) - Repeats on Qual Peak

Lib. Search Result Table

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

Inside (Qual) - Repeats on Qual Peak

Mass Spectrum List Table

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

Inside (Qual or Quan) - Repeats on Component Peak or Qual Peak

Proc. Method Audit Trail Table

.pmd Displays audit trail information about the Processing Method.

Does not repeat.

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.

Does not repeat.

Proc. Method Sample Reports Table

.pmd Displays Sample Report information for each sample in a sequence, including Template name and the Report file name. You specify Sample Type in the Processing Method.

Does not repeat.

Proc. Method Summary Reports Table

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

Does not repeat.

Qual Peak Table .rst Displays information specific to chromatogram peaks detected by qualitative analysis.

Does not repeat.

Quan Peak Table .rst, .pmd

Displays information specific to component peaks detected by quantitative analysis.

Does not repeat.

Table B-2. Table Objects, continued




Report Objects

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.


Sequence Table .sld Displays the contents of the sequence file.

Does not repeat.

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 fit

Reverse fit

Match

Found RT

Start RT

End RT

Area

Height

Does not repeat.

Table B-2. Table Objects, continued




Report Objects________________________________________________________________________

Table B-3. Graphic Objects

Graphic Object Data Source File


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).

Can be placed in any Merlin section type depending on its configuration.

Component Cal Curve

.rst

.pmdShows the calibration curve used to quantify a specified component. The curve is specified in the Processing Method as response versus amount of standard.

Inside (Quan) - Repeats on component peak

Outside - 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).

Can be placed in any Merlin section type depending on its configuration.


Appendix CTutorial Report

This appendix contains a copy of the Xcalibur report that is generated when you have completed the tutorial Generating a Report From a Report Template in Chapter 4 of this manual.

The tutorial uses the PeakIntegration2.doc report template (located in your Xcalibur\Templates folder) to generate a Quan sample report containing certain peak integration data. The data file used is steroids02.rst (located in your Xcalibur\examples\data folder) from the shipped steroid data.

________________ Finnigan Xcalibur: Getting Productive with Merlin ________________ C-1

Peak Integration Reporthydrocortisone

Study

Client

Laboratory

Company

Phone

Sample Name: Sample Type: Start Bracket Sample ID: Sample02Acquisition Date: 02/28/96 11:20:31 Revision: 1.3 Beta 5b Operator: jackcHigh Mass (m/z): 375.00 Low Mass (m/z): 100.00 Scans: 336Run Time (min): 3.79 Inj Vol (uL): 20.00 Vial: 1Cal Level: 3 Samp Wt: 0.00 Samp Vol: 0.00ISTD Amt: 0.000 Dil Factor: 1.00Comments:Inst Method: C:\pitcon\trial2\steroidMSMSisData Path: C:\pitcon\trial2\steroids02.RAWProc Method: C:\pitcon\trial2\steroidmsmsIS

Component: hydrocortisone ISTD: methyltestosteroneERT: 0.64

RTW: 30.00

VW: 1.00

RTR: No

MPH: 3.00

SM: 7

PDAU: Genesis

VD: No

CP: No

ERT: 2.01

RTW: 30.00

VW: 1.00

RTR: Yes

MPH: 3.00

SM: 7

PDAU: Genesis

VD: No

CP: No

RT: 0.18 - 1.18 SM: 7G

0.5 1.0Time (min)

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

RT: 0.68

0.47

RT: 1.49 - 2.49 SM: 7G

1.5 2.0Time (min)

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

RT: 1.99

Component Name Actual RT

Calculated Amount

Response

Base Line

Signal To Noise

% Diff Area Ratio

Area ISTD

Specified Amount

hydrocortisone 0.68 4.956 1892943 BB 707.56 -0.88 0.000 685110

5.000

Page 1 of 3

Peak Integration Reportdeoxycorticosterone

Study

Client

Laboratory

Company

Phone


Component: deoxycorticosterone ISTD: methyltestosteroneERT: 1.40

RTW: 30.00

VW: 1.00

RTR: No

MPH: 3.00

SM: 7

PDAU: Genesis

VD: No

CP: No

ERT: 2.01

RTW: 30.00

VW: 1.00

RTR: Yes

MPH: 3.00

SM: 7

PDAU: Genesis

VD: No

CP: No

RT: 0.90 - 1.90 SM: 7G

1.0 1.5Time (min)

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

RT: 1.40

1.70

RT: 1.49 - 2.49 SM: 7G

1.5 2.0Time (min)

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

RT: 1.99


Calculated Amount

Response

Base Line

Signal To Noise

% Diff Area Ratio

Area ISTD

Specified Amount

deoxycorticosterone

1.40 5.108 1040531 BB 148.23 2.17 0.000 685110 5.000

Page 2 of 3

Peak Integration Reportprogesterone

Study

Client

Laboratory

Company

Phone


Component: progesterone ISTD: methyltestosteroneERT: 3.19

RTW: 30.00

VW: 1.00

RTR: No

MPH: 3.00

SM: 7

PDAU: Genesis

VD: No

CP: No

ERT: 2.01

RTW: 30.00

VW: 1.00

RTR: Yes

MPH: 3.00

SM: 7

PDAU: Genesis

VD: No

CP: No

RT: 2.67 - 3.67 SM: 7G

3.0 3.5Time (min)

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

RT: 3.17

RT: 1.49 - 2.49 SM: 7G

1.5 2.0Time (min)

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

RT: 1.99


Calculated Amount

Response

Base Line

Signal To Noise

% Diff Area Ratio

Area ISTD

Specified Amount

progesterone 3.17 4.949 2995894 BB 344.16 -1.02 0.000 685110

5.000

Page 3 of 3

Index________________________________________________________________________

Index

AActiveX control, 1-11, 1-13Add Repeating Section button, 3-2adding

Chromatogram report object, 3-7Component Calibration Curve report object, 3-7repeating sections, 3-4report objects, 2-5, 3-4sections, 2-4, 3-4Spectrum report object, 3-8table objects, 3-6text objects, 3-6

Autofilter commandChromatogram, 2-36

axesChromatogram, 2-42Spectrum, 3-13

BBaseGRD.dot, 1-5

Ccalibration (.xcal) file, 4-3Chromatogram report object

adding, 3-7configuring, 2-21, 3-22configuring peak window display, 2-34container supplied Quan peak, 2-24, 2-25notification of location, 2-21properties, 3-22Properties list, 3-22Property Pages d.b., 3-22selecting a demo file, 2-27selecting axes details, 2-42selecting chromatogram type, 2-26selecting enhance details, 2-37selecting MS Quan traces, 2-33selecting normalization method, 2-44selecting peak labeling, 2-39selecting plot details, 2-35selecting Quan peak, 2-31selecting style details, 2-38

chromatogram type, 2-26Chromatogram Wizard, 2-21

Chromatogram Generated From page, 2-21Configure How Peak Window Looks page, 2-34Configure Normalization For Chromatogram page,

2-44finishing, 2-45key features, 1-4page order, 2-22Select Chromatogram Style page, 2-38Select Chromatogram Type page, 2-26Select Demo File page, 2-27Select Enhance Details page, 2-37

Select How Chromatogram Axis page, 2-42Select Mass Spectrum Quan Traces page, 2-33Select Peak Labeling page, 2-39Select Plot Details page, 2-35Select The Quan Peak page, 2-31starting, 2-21Use Container Supplied Quan Peak page, 2-24, 2-25

cleaning report templates, 3-31Component Calibration Curve report object

adding, 3-7configuring, 2-46, 3-24notification of location, 2-46properties, 3-24Properties list, 3-24Property Pages d.b., 3-24specifying component name, 2-48

Component Calibration Curve Wizard, 2-46Calibration Curve Generated From page, 2-46Component Name page, 2-48finishing, 2-49key features, 1-4starting, 2-46

component nameComponent Calibration Curve, 2-48

configuringChromatogram report object, 3-22Component Calibration Curve report object, 3-24repeating section, 3-18repeating sections, 2-7report objects, 3-17sections, 3-17Spectrum report object, 3-26table objects, 2-15, 3-20, 3-28

controls, 1-13creating

report templates, 1-8report templates with wizards, 2-1

DData Source Browser, 4-2

key features, 1-4Merlin Data Sources d.b.

calibration (.xcal) file, 4-3processing method (.pmd) file, 4-5raw (.raw) file, 4-4result (.rst) file, 4-4sequence (.sld) file, 4-6sequence (.sld) file and sample details, 4-7sequence (.sld) file, calibration (.xcal) file and

sample details, 4-8Select A Sample d.b., 4-7Select Calibration File d.b., 4-3Select Processing File d.b., 4-5Select Raw Data File d.b., 4-4Select Result File d.b., 4-4Select Sequence d.b., 4-6

data source filetable, B-2

________________ Finnigan Xcalibur: Getting Productive with Merlin ___________________ I

Index________________________________________________________________________

data source files, 4-3calibration (.xcal) file, 4-3definition, 1-17processing method (.pmd) file, 4-5raw (.raw) file, 4-4required, 3-30result (.rst) file, 4-4sequence (.sld) file, 4-6

Data Source Identifier, 3-30, 4-2key features, 1-4

demo fileChromatogram, 2-27Spectrum, 3-10

design mode, 3-2Design Mode button, 3-2detector delay

Chromatogram, 2-35detector type

Chromatogram, 2-35Spectrum, 3-10

Eenhance details

Chromatogram, 2-37example report templates, A-1Exit Design Mode button, 3-2exiting

Merlin, 1-9Word, 1-9

Ffield codes, 1-13

Ggenerating

reports, 1-9, 2-53, 3-30, 4-1from report template, 4-2from report template (tutorial), 4-10from Xcalibur, 4-11

graphic objectsadd button, 3-3Chromatogram, 2-21Component Calibration Curve, 2-46data source files required, B-7definition, 1-16descriptive tables, B-7repeating section placement, B-7resizing, 3-29

Graphic Objects button, 3-3

Iinstallation, 1-5

Llabels

Chromatogram, 2-39Chromatogram axes, 2-42Spectrum, 3-12Spectrum axes, 3-13

Mmaintaining report template tables, 3-28Merlin

definition, 1-2exiting, 1-9installation, 1-5key features, 1-2key terms, 1-10overview, 1-2starting, 1-6system and software requirements, 1-5upgrading from a previous version, 1-5using, 1-8

Merlin Chromatogram Wizard, 1-4Merlin Component Calibration Curve Wizard, 1-4Merlin Data Source Browser, 1-4Merlin Data Source Identifier, 1-4Merlin Operations button, 3-2, 3-30Merlin Repeating Section Wizard, 1-3Merlin Report Structure Wizard, 1-3Merlin Spectrum Control Properties d.b., 3-8Merlin Table Manager, 1-4Merlin Table Wizard, 1-4Merlin toolbar, 1-3Merlin.dot, 1-2method report, 2-3

processing, 2-3MS Quan traces

Chromatogram, 2-33

Nnon-repeating Qual section, 1-12non-repeating Quan section, 1-12non-repeating section

adding, 2-4definition, 1-12processing method configuration, 1-12programs, 1-12Qual, 1-12Quan, 1-12reports, 1-12

normalizationChromatogram, 2-44Spectrum, 3-14

Oobjects

report, 1-13objects, graphic, 1-16objects, table, 1-14

II____________________Finnigan Xcalibur: Getting Productive with Merlin_________________

Index________________________________________________________________________

objects, text, 1-13options

Spectrum, 3-9

Ppeak labels

Chromatogram, 2-39Spectrum, 3-12

peak windowChromatogram, 2-34

plot typeChromatogram, 2-35Spectrum, 3-9

plotsChromatogram, 2-35

processing method (.pmd) file, 4-5processing method configuration section, 1-12processing method report, 2-3programs section, 1-12properties, 3-17

QQual repeating section, 1-11Quan peak

Chromatogram, 2-31Quan repeating section, 1-11

Rraw (.raw) file, 4-4repeating section, 1-11

add button, 3-2adding, 2-4, 3-4configuring, 2-7, 3-18definition, 1-11properties, 3-18Properties list, 3-18Property Pages d.b., 3-18report object placement in

table, B-2selecting type, 3-5

Repeating Section Wizard, 2-7, 3-4Configure Peak Reporting Layout page, Qual, 2-10Configure Peak Reporting Layout page, Quan, 2-14finishing, 2-14key features, 1-3Repeating Section Generated page, Qual, 2-8Repeating Section Generated page, Quan, 2-11Select How To Order page, Qual, 2-8Select How To Order page, Quan, 2-12Select Peak To Exclude page, Quan, 2-11Select Type of Peak to Repeat On page, 3-5starting, 2-7

repeating section, Qualadding, 3-5configuring, 2-7configuring page layout, 2-10definition, 1-11

notification of location, 2-8ordering, 2-8

repeating section, Quanadding, 3-5configuring, 2-11configuring page layout, 2-14definition, 1-11excluding peaks, 2-11notification of location, 2-11ordering, 2-12

report objectsadding, 2-5, 3-4Chromatogram, 2-21Component Calibration Curve, 2-46configuring, 3-17data source files required, B-1definition, 1-13descriptive tables, B-1graphic, 1-13repeating section placement, B-1selecting, 2-5table, 1-13text, 1-13

Report Structure Wizardkey features, 1-3

report templatesadding breaks, 2-53adding headers and footers, 2-53cleaning, 3-31confirming structure, 2-6creating, 1-8creating and editing with toolbar, 3-1creating with wizards, 2-1definition, 1-10generating a report, 2-53generating report from, 4-2generating report from (tutorial), 4-10maintaining tables, 3-28saving, 2-52shipped examples, A-1toolbar editing, 2-52using tables, 2-53Word editing, 2-53

reportsdefinition, 1-17generating, 1-9, 2-53, 3-30, 4-1

from report template, 4-2from report template (tutorial), 4-10from Xcalibur, 4-11

method, 2-3sample, 2-2saving, 1-17, 4-3selecting type, 2-2summary, 2-3type, 2-2type, selecting, 2-2

reports section, 1-12resizing graphic objects, 3-29resolved document, 1-17result (.rst) file, 4-4

________________ Finnigan Xcalibur: Getting Productive with Merlin __________________ III

Index________________________________________________________________________

Ssample report, 2-2

Qual, 2-2Quan, 2-2Quan and Qual, 2-2

savingreport templates, 2-52reports, 1-17, 4-3

scan filtersChromatogram, 2-35

sectionsadding, 3-4configuring, 3-17definition, 1-10non-repeating, 1-12repeating, 1-11selecting, 2-4

sequence (.sld) file, 4-6smoothing

Spectrum, 3-10software requirements, 1-5source file, data

Xcalibur, 1-17Spectrum Control Properties d.b., 3-8

Axis page, 3-13Enhance page, 3-10Labels page, 3-12Normalization page, 3-14Options page, 3-9Peak page, 3-15Plot Type page, 3-9Style page, 3-11

Spectrum report objectadding, 3-8configuring, 3-8, 3-26Merlin Spectrum Control Properties d.b., 3-8properties, 3-26Properties list, 3-26Property Pages d.b., 3-27selecting axis details, 3-13selecting enhance details, 3-10selecting labels, 3-12selecting normalization options, 3-14selecting options, 3-9selecting plot type, 3-9selecting style details, 3-11specifying peak to display, 3-15

startingMerlin, 1-6Word, 1-6

Structure Report Wizard, 2-2Confirm Report page, 2-6creating report templates, 2-1finishing, 2-6Select Objects page, 2-5Select Report page, 2-2Select Sections page, 2-4starting, 2-2

styleChromatogram, 2-38Spectrum, 3-11

summary report, 2-3by sample Quan, 2-3

system requirements, 1-5

TTable Manager, 3-28

key features, 1-4Maintain Template Tables d.b., 3-28

table objectsadd button, 3-3adding, 3-6adding table columns, 2-16configuring, 2-15, 3-20, 3-28configuring user columns, 2-17data source files required, B-4definition, 1-14descriptive tables, B-4maintaining, 3-28notification of location, 2-15ordering columns, 2-19properties, 3-20Properties list, 3-21Property Pages d.b., 3-21repeating section placement, B-4

Table Objects button, 3-3Table Wizard

Add to Generated Report page, 2-15Configure User Column page, 2-17finishing, 2-20key features, 1-4Select Table Fields page, 2-16Set Table Sort Filter page, 2-19starting, 2-15

templates, report, 1-6templates, Word, 1-6terminology, 1-10text objects

add button, 3-2adding, 3-6data source files required, B-2definition, 1-13descriptive tables, B-2field codes, 1-13labels, 1-13repeating section placement, B-2

Text Objects button, 3-2time range

Chromatogram, 2-35toolbar

Add Repeating Section button, 3-2Design Mode button, 3-2editing report template, 2-52Exit Design Mode button, 3-2Graphic Objects button, 3-3key features, 1-3Merlin Operations, 3-2, 3-30overview, 3-2Properties button, 3-2Table Objects button, 3-3Text Objects button, 3-2using, 3-1

IV___________________Finnigan Xcalibur: Getting Productive with Merlin_________________

Index________________________________________________________________________

tutorialcopy of report generated, C-1generating report from report template, 4-10

Wwizards, 1-3Word

adding breaks, 2-53adding headers and footers, 2-53design mode, 3-2editing report template, 2-53

using tables, 2-53Word templates

BaseGRD.dot, 1-5Merlin.dot, 1-2

XXcalibur

data source files, 1-17generating report from, 4-11report

definition, 1-17

________________ Finnigan Xcalibur: Getting Productive with Merlin __________________ V

xcalibur custom reports with merlin

Documents

xcalibur examples data folder

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acquisition device supported

xcaliburs batch processing

pitcon trial2 steroids02

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