Xcalibur Custom Reports With Merlin

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Software Revision: Xcalibur 1.4
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fold
Contents
'JOOJHBO9DBMJCVS ________________________________________________________________________
Contents
Read This First ..............................................................................................................................v

Changes to the Manual and Online Help ............................................................................................... vi
Abbreviations ........................................................................................................................................ vii
Typographical Conventions ................................................................................................................... xi

Data Input ............................................................................................................................. xi
Boxed Information............................................................................................................... xii
Topic Headings................................................................................................................... xiii
Reply Cards .......................................................................................................................................... xiv
Introduction to Merlin .............................................................................................................. 1-1

1.1 Overview of Merlin................................................................................................................... 1-2
What is Merlin? .................................................................................................................. 1-2
Key Features of Merlin....................................................................................................... 1-2
Upgrading From a Previous Version .................................................................................. 1-5
System / Software Requirements........................................................................................ 1-5
Installation .......................................................................................................................... 1-5
1.2 Using Merlin ............................................................................................................................. 1-6

Starting Merlin.................................................................................................................... 1-6
Creating and Generating Reports with Merlin ................................................................... 1-8
Exiting Merlin .................................................................................................................... 1-9
1.3 Overview of Report Templates ............................................................................................... 1-10

Report Template ............................................................................................................... 1-10
Sections............................................................................................................................. 1-10
Report Objects .................................................................................................................. 1-13
Data Source Files.............................................................................................................. 1-17
Report (Resolved Document) ........................................................................................... 1-17
Creating a Report Template Using the Merlin Wizards ....................................................... 2-1

2.1 The Merlin Report Structure Wizard ........................................................................................ 2-2
Step 1 - Selecting the Type of Report................................................................................. 2-2
Step 2 - Selecting and Ordering Sections ........................................................................... 2-4
Step 3 - Selecting and Ordering Report Objects ................................................................ 2-5
Step 4 - Confirming the Report Template Structure........................................................... 2-6
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Contents
________________________________________________________________________ 'JOOJHBO9DBMJCVS
2.2 The Merlin Repeating Section Wizard ..................................................................................... 2-7

Qual Repeating Section...................................................................................................... 2-7
Quan Repeating Section.................................................................................................... 2-11
2.3 The Merlin Table Wizard........................................................................................................ 2-15

Notification of Table Location ......................................................................................... 2-15
Choosing Table Columns ................................................................................................. 2-16
Configuring Custom (User) Columns .............................................................................. 2-17
Specifying Table Sort Order ............................................................................................ 2-19
2.4 The Merlin Chromatogram Wizard ........................................................................................ 2-21

Notification of Chromatogram Location.......................................................................... 2-21
Use Container Supplied Quan Peak Page ........................................................................ 2-24
Use Container Supplied Qual Peak Page ......................................................................... 2-25
Select Chromatogram Type Page ..................................................................................... 2-26
Select Demo File Page ..................................................................................................... 2-27
Select the Quan Peak Page............................................................................................... 2-31
Select Qual Peak Page...................................................................................................... 2-32
Select Mass Spectrum Quan Traces to Display Page....................................................... 2-33
Configure How the Peak Window Will Look Page ......................................................... 2-34
Select Plot Details Page ................................................................................................... 2-35
Select Enhance Details Page ............................................................................................ 2-37
Select Chromatogram Style Page..................................................................................... 2-38
Select the Peak Labeling Page ......................................................................................... 2-39
Select How the Chromatogram Axes Will Be Configured Page ..................................... 2-42
Configure Normalization for the Chromatogram Page.................................................... 2-44
Finishing the Chromatogram Wizard............................................................................... 2-45
2.5 The Merlin Component Calibration Curve Wizard ................................................................ 2-46

Notification of Component Calibration Curve Location ................................................. 2-46
Specifying Component Name .......................................................................................... 2-48
2.6 After Using the Wizards… ..................................................................................................... 2-50

Saving a Report Template ................................................................................................ 2-52
Editing a Report Template with the Merlin Toolbar ........................................................ 2-52
Editing a Report Template with Microsoft Word............................................................. 2-53
Generating a Report ......................................................................................................... 2-53
Using the Merlin Toolbar ......................................................................................................... 3-1

3.1 Introduction to the Merlin Toolbar ........................................................................................... 3-2
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Contents
'JOOJHBO9DBMJCVS ________________________________________________________________________
3.2 Adding Sections and Report Objects to a Template ................................................................. 3-4

Adding a Repeating Section ............................................................................................... 3-4
Adding a Text Object.......................................................................................................... 3-6
Adding a Table Object........................................................................................................ 3-6
Adding a Graphic Object.................................................................................................... 3-7
3.3 Configuring Repeating Sections and Report Objects ............................................................. 3-17

Configuring a Repeating Section...................................................................................... 3-18
Configuring a Table Object .............................................................................................. 3-20
Configuring a Chromatogram........................................................................................... 3-22
Configuring a Component Calibration Curve Report Object........................................... 3-24
Configuring 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......................................................................................................... 3-30

New Merlin Wizard .......................................................................................................... 3-30
Generate Report................................................................................................................ 3-30
Show Required Data Sources ........................................................................................... 3-30
Clean Report Template ..................................................................................................... 3-31
Generating a Report ................................................................................................................. 4-1

4.1 Generating a Report from a Report Template ........................................................................... 4-2
Merlin Data Source Browser (.xcal file) ............................................................................ 4-3
Merlin Data Source Browser (.raw file) ............................................................................. 4-4
Merlin Data Source Browser (.rst file) ............................................................................... 4-4
Merlin Data Source Browser (.pmd file)............................................................................ 4-5
Merlin Data Source Browser (.sld file) .............................................................................. 4-6
Merlin Data Source Browser (.sld file) .............................................................................. 4-6
Merlin Data Source Browser (.sld file and .xcal file)......................................................... 4-8
Tutorial: 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
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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.
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Read This First
Changes to the Manual and Online Help @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Changes to the Manual and Online Help

To suggest changes to this manual or the online Help, please send your
comments to:
Editor, Technical Publications
Thermo Electron San Jose
355 River Oaks Parkway
San Jose, CA 95134-1991
U.S.A.
You are encouraged to report errors or omissions in the text or index.
Thank you.
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Read This First
'JOOJHBO9DBMJCVS _____________________________________________________________ Abbreviations
Abbreviations
The 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
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Abbreviations @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
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
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'JOOJHBO9DBMJCVS _____________________________________________________________ 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
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Abbreviations @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
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)
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Read This First
'JOOJHBO9DBMJCVS ___________________________________________________Typographical Conventions
Typographical Conventions
Typographical 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”.
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Typographical Conventions @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
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.
Note. Boxes such as this are used to display information.
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.
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'JOOJHBO9DBMJCVS ___________________________________________________Typographical Conventions
Topic Headings
The following headings are used to show the organization of topics within a
chapter:
Chapter 1
Chapter Name
1.2 Second Level Topics
Third Level Topics
Fourth Level Topics
Fifth Level Topics
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Read This First
Reply Cards @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Reply Cards
Thermo 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.
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Chapter 1
Introduction 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.
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1.1 Overview of Merlin

This 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 5IFSNP
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'JOOJHBO9DBMJCVS _________________________________________________________ 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.
Figure 1-1. Merlin Toolbar
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
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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.
1-4 5IFSNP
'JOOJHBO9DBMJCVS _________________________________________________________ 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.
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1.2 Using Merlin

This 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.
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'JOOJHBO9DBMJCVS ______________________________________________________________ Using Merlin
Figure 1-2. Microsoft Word XP showing the Merlin Report Structure Wizard front page
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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.
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.
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. Avoid confusing Microsoft Word templates (.dot files) and report
templates (which are Microsoft Word documents, .doc files).
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'JOOJHBO9DBMJCVS ______________________________________________________________ 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.
Note. More detailed information on how to generate a report from within

Xcalibur is given in Chapter 4.
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.
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1.3 Overview of Report Templates

In 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)
Note. Refer to your other Xcalibur manuals and/or the Xcalibur online Help
for additional information relating to Xcalibur.
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.
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'JOOJHBO9DBMJCVS ________________________________________________ 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
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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.

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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.
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Figure 1-4. 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

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• 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
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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

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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.
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Chapter 2
Creating 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.
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.
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. 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.
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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 These can use the results generated from both the Quan and Qual sections of a
Qual reports 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.
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'JOOJHBO9DBMJCVS ____________________________________________ The Merlin Report Structure Wizard
Table 2-1. Types of Xcalibur Reports, continued
Report Type Description

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 These are typically used to list all of the sample file names in a sequence in tabular
Quan reports 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 These are used to present the values of as many of the parameters as are required that
reports 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.
The type of report that you choose affects the options available to you in the
remaining pages of the wizard.
Figure 2-1. Merlin Report Structure Wizard - Step 1
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.
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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.
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'JOOJHBO9DBMJCVS ____________________________________________ 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.
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.
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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.
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'JOOJHBO9DBMJCVS ___________________________________________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.
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.
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.
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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.
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.
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.
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Figure 2-6. Merlin Repeating Section Wizard - Select How To Order

The Repeating Section (Qual)
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.
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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.
Figure 2-7. Merlin Repeating Section Wizard - Configure Peak

Reporting Page Layout (Qual)
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.
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.

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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.
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.
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.
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Figure 2-9. Merlin Repeating Section Wizard - Select Any Peak To

Exclude (Quan)
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.

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Figure 2-10. Merlin Repeating Section Wizard - Select How To Order

The Repeating Section (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.
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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)
Figure 2-11. Merlin Repeating Section Wizard - Configure Peak

Reporting Page Layout (Quan)
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
what to do next.
Note. If you have accessed the Merlin Repeating Section Wizard from the
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.

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'JOOJHBO9DBMJCVS _____________________________________________________ The Merlin Table Wizard
2.3 The Merlin Table Wizard

The 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
Note. The Merlin Table Wizard can also be activated by the Merlin toolbar.
Refer to Chapter 3 for a discussion of the Merlin toolbar.
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. 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.
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Figure 2-12. The front page of the 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 2-13. Merlin Table Wizard - Select Table Fields page

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

page
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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.
Figure 2-15. Edit Formula dialog box
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

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

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'JOOJHBO9DBMJCVS _____________________________________________ The Merlin Chromatogram Wizard
2.4 The Merlin Chromatogram Wizard

The 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.
Note. The Merlin Chromatogram Wizard can also be activated from the
Merlin toolbar. Refer to Chapter 3 for a discussion of the Merlin toolbar.
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.
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The Merlin Chromatogram Wizard @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Figure 2-17. The front page of the Merlin Chromatogram Wizard
Note. If the Merlin Chromatogram Wizard is activated from the Merlin

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.

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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 • • • • •
* If you use the container-supplied peak, then the Select Chromatogram Type
page is not displayed.
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.
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.
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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.
Figure 2-18. Chromatogram Wizard - Use Container Supplied Quan

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

Peak page
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.
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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.
Figure 2-20. Chromatogram Wizard - Select Chromatogram Type page
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
• 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.)
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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.
Figure 2-21. Chromatogram Wizard - Select Demo File page: Raw File
Based Chromatogram
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.
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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.
Figure 2-22. Chromatogram Wizard - Select Demo File page: Quan

Result Based Chromatogram
(.raw file).
the demo file.
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.

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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.
Figure 2-23. Chromatogram Wizard - Select Demo File page: Qual

Result Based Chromatogram - Explicit Peak
(.raw file).
the demo file.
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.
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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.
(.raw file).
the demo file.
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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.
Figure 2-24. Chromatogram Wizard - Select the Quan Peak page
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 2-25. Select Component dialog box
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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.
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.
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.
Figure 2-26. Chromatogram Wizard - Select Qual Peak page
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 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.

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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.
Figure 2-27. Chromatogram Wizard - Select Mass Spectrum Quan

Traces To Display page
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.
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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.
Figure 2-28. Chromatogram Wizard - Configure How the Peak Window

Will Look page
Fill in the Configure How the Peak Window Will Look page of the
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.

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

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Select Enhance Details Page

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

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

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

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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.
Figure 2-33. Advanced Quan Peak Annotation Options dialog 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.
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5. Select the number of decimal places to be displayed in the retention time

label from the Decimals list box.
Figure 2-34. Advanced Qual Peak Annotation Options dialog 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.

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Figure 2-35. Chromatogram Wizard - Select How the Chromatogram

Axes Will Be Configured page
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.
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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.
Figure 2-36. Chromatogram Wizard - Configure Normalization for the

Chromatogram page
Fill in the Configure Normalization for the Chromatogram page of the

1. In the Normalize Method group box, define the normalizing method by
• 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
• 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.
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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
what to do next.
Note. If you have accessed the Merlin Chromatogram Wizard from the
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.
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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.
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.
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. If the Merlin Calibration Curve Wizard is activated from the Merlin

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'JOOJHBO9DBMJCVS __________________________________The Merlin Component Calibration Curve Wizard
Figure 2-37. The front page of the Merlin Component Calibration Curve
Wizard
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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.
Figure 2-38. Component Calibration Curve Wizard - Component Name

page
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 2-39. Select Component dialog box

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'JOOJHBO9DBMJCVS __________________________________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.
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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

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'JOOJHBO9DBMJCVS ____________________________________________________ After Using the Wizards…
Figure 2-40. A customized Xcalibur report template (PeakIntegration2.doc)
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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.

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'JOOJHBO9DBMJCVS ____________________________________________________ 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.
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.
• 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.
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.
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.
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Chapter 3
Using 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.
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3.1 Introduction to the Merlin Toolbar

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

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 The Design Mode / Exit Design Mode button is a standard Microsoft Word button that
Mode / Exit can also be found on the Control Toolbox toolbar. You can use this button to enter or exit
Design the design mode. In design mode, you can do the following:
Mode 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 The Merlin Operations button is a drop-down menu button. You can use this button to do
Operations 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 You can use the Add Repeating Section button to add a new repeating section to your
Repeating report template.
Section
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.
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'JOOJHBO9DBMJCVS ______________________________________________ Introduction to the Merlin Toolbar
Table 3-1. Merlin toolbar buttons and functions, continued
Button Function
Table The Table Objects button is a drop-down menu button. You can use this button to add a
Objects 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 The Graphic Objects button is a drop-down menu button. You can use this button to add
Objects a new graphic object from the drop-down menu to your report template.
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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.
Figure 3-2. Confirming addition of a report object to an inappropriate

section of a report template
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.
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'JOOJHBO9DBMJCVS ________________________________ Adding Sections and Report Objects to a Template
Figure 3-3. Merlin Repeating Section Wizard - Select Type of Peak to

Repeat On
Complete this page of the wizard as follows:

1. In the Repeat On group box, define the type of repeating section by
• 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.
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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
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• 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.
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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.
Figure 3-4. Merlin Spectrum Control Properties dialog box
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.
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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.
Figure 3-5. Merlin Spectrum Control Properties dialog box - Plot Type
page
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: *
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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.
Figure 3-6. Merlin Spectrum Control Properties dialog box - Enhance

page
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.

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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
• 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.
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• Overlay (3D)—to overlay plots vertically with an optional horizontal

skew (time offset) for the active map.
Figure 3-7. Merlin Spectrum Control Properties dialog box - Style

page
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.

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6. In the Label Threshold text box, limit the labeling of peaks to those
exceeding the specified percentage of the base peak.
Figure 3-8. Merlin Spectrum Control Properties dialog box -

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

page
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
1. In the Normalize Method group box, define the normalization method by
• 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.

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• 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.
Figure 3-10. Merlin Spectrum Control Properties dialog box -

Normalization page
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.
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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

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'JOOJHBO9DBMJCVS _______________________________ 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
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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.
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.
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.

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Figure 3-13. Property Pages dialog box for a repeating section
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.
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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
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.
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.)
displays, showing the current settings for the table object. See
Figure 3-14.

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Figure 3-14. Properties list for a Mass Spectrum List Table
user-friendly representation of the property fields in the Properties list.
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.
5IFSNP
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.)
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.
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.
the Browse button (…) for the (Custom) field. The Chromatogram report

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

object
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.
5IFSNP
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.)
displays, showing the current settings for the Component Cal Curve. See
Figure 3-17.
Figure 3-17. Properties list for a Component Cal Curve report object
user-friendly and simpler property field editor for a Component Cal Curve
report object.
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.

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Figure 3-18. Property Pages dialog box 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.
5IFSNP
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
displays, showing the current settings for the Spectrum report object. See
Figure 3-19.
Figure 3-19. Properties list for a Spectrum report object
user-friendly representation of the properties for a Spectrum report object.

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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.
Figure 3-20. Property Pages dialog box for a Spectrum report object
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.
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Maintaining Report Template Tables @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
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.
Figure 3-21. The Merlin Table Manager - Maintain Template Tables
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.

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'JOOJHBO9DBMJCVS ___________________________________________________ Resizing a Graphic Object
3.5 Resizing a Graphic Object

Use the following procedure to resize any graphic object contained in a report
template:
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
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.
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Merlin Operations Menu @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
3.6 Merlin Operations Menu

You 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

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'JOOJHBO9DBMJCVS _____________________________________________________ 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.
5IFSNP
Chapter 4
Generating 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.
5IFSNP
Generating a Report
Generating a Report from a Report Template @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
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.
Note. A single report is created each time you generate a report from a report
template.
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.
Note. If the Merlin toolbar is not displayed in Microsoft Word, choose

View > Toolbars > Merlin to display the toolbar.
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.
4-2 5IFSNP
Generating a Report
'JOOJHBO9DBMJCVS _____________________________________Generating a Report from a Report Template
Note. A report is generated as a new Microsoft Word document. The report

is based on the Normal.dot template of Microsoft Word.
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.
Figure 4-1. Merlin Data Sources dialog box: Select Calibration file
Fill in the Merlin Data Sources - Select Xcalibur Data File to Generate Report
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.
5IFSNP
Generating a Report
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.
Figure 4-2. Merlin Data Sources dialog box: Select Raw file
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.
4-4 5IFSNP
Generating a Report
Figure 4-3. Merlin Data Sources dialog box: Select Results 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.
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.
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 4-4. Merlin Data Sources dialog box: Select Processing

Method file
5IFSNP
Generating a Report
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.
Figure 4-5. Merlin Data Sources dialog box: Select Sequence file
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.
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.
4-6 5IFSNP
Generating a Report
Figure 4-6. Merlin Data Sources dialog box: Select Sequence and
Sample
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.
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.
5IFSNP
Generating a Report
Figure 4-7. Select A Sample From The Sequence File dialog box
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.
Figure 4-8. Merlin Data Sources dialog box: Select Sequence and
Sample
1. Click on the Sequence File Browse (…) button to browse for the required
Sequence file. The Select Sequence dialog box appears.
4-8 5IFSNP
Generating a Report
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.
5IFSNP
Generating a Report
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).
Figure 4-9. Merlin Data Sources dialog box: Results file
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.
Note. Appendix C contains a copy of the report generated by following the

steps in the above tutorial.

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Generating a Report
'JOOJHBO9DBMJCVS _____________________________________________ 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.
5IFSNP
Appendix A
Example 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.
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&-&$530/$03103"5*0/ ________________ Finnigan Xcalibur: Getting Productive with Merlin ________________ A-1
Example Merlin Report Template Files
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Table A-1. Example Merlin report template files
Report Template File Name Data Description / Use

Source
File(s)
CalibrationFile2.doc .raw, .xcal For reporting calibration data
CompCalReport2.doc .rst, .raw, For generating summary reports showing
CompCalReport2_Avalon.doc .pmd, .sld processing method details, calibration curve and
sample table (Quan results). Can be used from
CompCalReport2_Genesis.doc
Xcalibur’s Batch Processing and Quan Browser.
CompCalReport2_ICIS.doc
CustLibrSearRept2.doc .rst, .raw For generating Qual Sample reports that display
LibrarySearchReport2.doc Qual peaks and library search details. Should be
used from Xcalibur’s Batch Processing.
IonRatioConfirmation2.doc .rst, .raw, For generating a Quan sample report containing
.pmd non-graphical ion ratio confirmation results.
IonRatioConfirmationGraphical .rst, .raw, For generating Quan sample reports containing
.doc .pmd graphical ion ratio confirmation results. These
IonRatioConfirmationGraphical report templates take advantage of the explicit
Simple.doc confirmation ion settings available when using the
Merlin Chromatogram Wizard (see Chapter 2).
IonRatioConfirmationGraphical
Stacked.doc
PeakIntegration2.doc .rst, .raw, For generating a Quan sample report containing
.pmd peak integration data.
ProcessingMethod2.doc .pmd For generating processing method reports. Use
ProcessingMethod2_Avalon.doc from Xcalibur’s Processing Method Setup.
ProcessingMethod2_Genesis.doc
ProcessingMethod2_ICIS.doc
QualPeakReport2.doc .rst, .raw For generating a simple Qual sample report.
Should be used from Xcalibur’s Batch Processing.
QuanPeakResults.doc .rst, .raw, For generating Quan sample reports. May be used
QuanResults.doc .pmd from Xcalibur’s Batch Processing or Quan Browser.
QuanSimple.doc
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_________________5IFSNP

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Appendix B
Report 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
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&-&$530/$03103"5*0/ ________________ Finnigan Xcalibur: Getting Productive with Merlin ________________ B-1
Report Objects
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Table B-1. Text Objects
Text Object Data Description Repeating Section

Source Placement
File
Component .pmd Shows the peak detection, calibration, Inside (Quan) -
Ident/Detect/Cal and integration parameters for a single Repeats on Component
Settings component. Peak
Component ISTD .pmd Displays a summary of the Inside (Quan) -
Settings configuration details for each Repeats on Component
Summary component’s ISTD configuration in the Peak
Quantitation section of a Processing
Method
Component .pmd Displays a short list of peak detection Inside (Quan) -
Settings and integration parameters for a Repeats on Component
Summary specified component. Peak
Component Sys .pmd Displays Calibration, Quantitation, and Inside (Quan) -
Suit/Flags Detection flags along with system Repeats on Component
Settings suitability parameters, which allow Peak
automatic chromatographic checks that
assign a pass/fail qualification to a
target peak.
Processing .pmd Displays general processing method Does not repeat.
Method -General parameters. General parameters
include date created, date modified,
baseline definition, chromatography
type (LC / GC).
Processing .pmd Displays Qual processing method Does not repeat.
Method - Qual parameters. Qual parameters include
the following:
Identification
Detection Options
Advanced Detection Options
Spectrum Enhancement
Library Search options
Library Search Constraints
Quan ISTD Peak .rst, Displays summary parameters for a Inside (Quan) -
Summary .pmd Quan component’s associated ISTD Repeats on Component
peak. For example: Peak
ISTD Name
Actual RT
Response
Base Line
Signal To Noise
Expected RT
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Report Objects
'JOOJHBO9DBMJCVS ________________________________________________________________________
Table B-1. Text Objects, continued
Text Object Data Description Repeating Section

Source Placement
File
Quan Peak .rst, Displays Component Peak summary Inside (Quan) -
Summary .pmd parameters, for example: Repeats on Component
Actual RT Peak
Calculated Amount
Response
Base Line
Signal To Noise
% Diff
Area Ratio
Area ISTD
Specified Amount
Sample Header .raw Displays general information about a Does not repeat.
sample, for example:
Sample Name
Sample Type
Acquisition Date
Operator
Run Time
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Report Objects
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Table B-2. Table Objects
Table Object Data Description Repeating Section

Source Placement
File
Avalon Qual .pmd Displays details of the Avalon peak Does not repeat.
Events Table detection algorithm events configured
in the Qual section of a Processing
Method.
Avalon Quan .pmd Displays details of the Avalon peak Inside (Quan) -
Events Table detection algorithm events configured Repeats on Component
for a component in the Quan section of Peak
a Processing Method.
Calibration File .xcal, Displays calibration levels, raw file Does not repeat.
Table .sld, names, and acquisition dates of
.raw standards.
Component Cal .pmd Shows the calibration levels, amounts, Inside (Quan) -
Level Table and acceptance test values defined for Repeats on Component
a specific component. Peak
Component Ion .pmd Displays up to five qualifier ions within Inside (Quan) -
Ratio tolerance limits to confirm the detection Repeats on Component
Confirmation of a target analyte. The ions are Peak
Table specified in the Processing Method.
Component QC .pmd Shows the QC levels, amounts, and Inside (Quan) -
Level Table percent test values defined for a Repeats on Component
specific component. Peak
Component .pmd Displays m/z and intensity data for up Inside (Quan) -
Spectrum Table to fifty spectrum peaks. Xcalibur uses Repeats on Component
this data to identify components when Peak
the Spectrum Peak Identification
Method is specified in the Processing
Method.
Note. This object is used only for GC
chromatography.
Dilution Factor .rst Displays the names of calibration Does not repeat.
Table levels and dilution factors for
components other than internal
standards.
Ion Ratio .rst Displays the following data about each Inside (Quan) -
Confirmation qualifier ion, based on search criteria Repeats on Component
Results Table specified in the Processing Method: Peak
Mass
Coelution test pass/fail
Ion Ratio Test Target %
Ion Ratio Test Window %
B-4 _________________Finnigan Xcalibur: Getting Productive with Merlin_________________ 5IFSNP

&-&$530/$03103"5*0/
Report Objects
'JOOJHBO9DBMJCVS ________________________________________________________________________
Table B-2. Table Objects, continued

Source Placement
File
IRC Summary .rst Displays all of the information for the Does not repeat.
Table confirmation ion for each component.
Most useful when the Name column is
the first column.
Lib. Search .rst, .raw Displays the graphical results from a Inside (Qual) - Repeats
Graph Table library search on a Qual peak (for on Qual Peak
example, Hit Spectrum, Delta, and
Compound Structure).
Lib. Search .rst, .raw Displays the results of a Library Search Inside (Qual) - Repeats
Result Table on a Qual peak (for example, Name, on Qual Peak
Probability, RSI, SI, CAS#, Area).
Mass Spectrum .rst, .raw Displays the text equivalent of the Inside (Qual or Quan) -
List Table Spectrum graphic object. The Mass Repeats on Component
Spectrum List Table contains a header, Peak or Qual Peak
then lists values for the m/z, intensity,
and relative intensity.
Proc. Method .pmd Displays audit trail information about Does not repeat.
Audit Trail Table the Processing Method.
Proc. Method .pmd Displays a list of programs to be run by Does not repeat.
Programs Table Xcalibur after the sample has been
analyzed and the data has been
processed. Xcalibur runs the programs
in the order listed.
Proc. Method .pmd Displays Sample Report information for Does not repeat.
Sample Reports each sample in a sequence, including
Table Template name and the Report file
name. You specify Sample Type in the
Processing Method.
Proc. Method .pmd Displays Summary Reports to be Does not repeat.
Summary issued after processing the samples in
Reports Table a bracketed or non-bracketed
sequence.
Qual Peak Table .rst Displays information specific to Does not repeat.
chromatogram peaks detected by
qualitative analysis.
Quan Peak Table .rst, Displays information specific to Does not repeat.
.pmd component peaks detected by
quantitative analysis.
5IFSNP
Report Objects
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ 'JOOJHBO9DBMJCVS
Table B-2. Table Objects, continued

Source Placement
File
Sample Table .sld Displays system suitability and flag Inside (Quan) -
(Quan Results) processing results for each component Repeats on Component
in a sample, and repeats this Peak
information for every sample in a
sequence.
Sequence Table .sld Displays the contents of the sequence Does not repeat.
file.
Spectrum .rst Displays the results of spectrum Does not repeat.
Candidate candidate processing for GC/MS data
Results Table on a per component basis. Parameters
include the following:
Forward fit
Reverse fit
Match
Found RT
Start RT
End RT
Area
Height
5IFSNP
B-6 _________________Finnigan Xcalibur: Getting Productive with Merlin_________________ &-&$530/$03103"5*0/
Report Objects
'JOOJHBO9DBMJCVS ________________________________________________________________________
Table B-3. Graphic Objects
Graphic Object Data Description Repeating Section

Source Placement
File
Chromatogram .raw, .rst Displays a graphical trace that can Can be placed in any
show either raw data or processed data Merlin section type
for any acquisition device supported by depending on its
Xcalibur (MS, Analog, A/D Card, PDA, configuration.
UV).
Component Cal .rst Shows the calibration curve used to Inside (Quan) -
Curve .pmd quantify a specified component. The Repeats on component
curve is specified in the Processing peak
Method as response versus amount of
standard.
Outside - uses the
specified component.
Spectrum .raw, .rst Displays a graphical spectrum that can Can be placed in any
show either raw data or processed data Merlin section type
for any acquisition device supported by depending on its
Xcalibur (MS, PDA). configuration.
5IFSNP
Appendix C
Tutorial 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.
5IFSNP
&-&$530/$03103"5*0/ ________________ Finnigan Xcalibur: Getting Productive with Merlin ________________ C-1
Peak Integration Report
hydrocortisone
Sample Name: Sample Type: Start Bracket Sample ID: Sample02
Acquisition Date: 02/28/96 11:20:31 Revision: 1.3 Beta 5b Operator: jackc
High Mass (m/z): 375.00 Low Mass (m/z): 100.00 Scans: 336
Run Time (min): 3.79 Inj Vol (uL): 20.00 Vial: 1
Cal Level: 3 Samp Wt: 0.00 Samp Vol: 0.00
ISTD Amt: 0.000 Dil Factor: 1.00
Comments:
Inst Method: C:\pitcon\trial2\steroidMSMSis
Data Path: C:\pitcon\trial2\steroids02.RAW
Proc Method: C:\pitcon\trial2\steroidmsmsIS
Study
Client
Laboratory
Company
Phone
Component: hydrocortisone ISTD: methyltestosterone

ERT: 0.64 ERT: 2.01 RT: 1.49 - 2.49 SM: 7G
RT: 1.99
100
RTW: 30.00 RT: 0.18 - 1.18 SM: 7G RTW: 30.00
RT: 0.68 90
100
VW: 1.00 VW: 1.00
90 80
RTR: No RTR: Yes
80 70
Relative Abundance
MPH: 3.00 MPH: 3.00

70 60
Relative Abundance
SM: 7 SM: 7 50
60
PDAU: Genesis 50
PDAU: Genesis 40
VD: No 40
VD: No 30
CP: No 30 CP: No 20
20 10
10 0
1.5 2.0
0.47
0 Time (min)
0.5 1.0
Time (min)
Component Name Actua Calculate Respon Base Signal % Diff Area Area Specifie
l RT d Amount se Line To Ratio ISTD d
Noise Amount
hydrocortisone 0.68 4.956 1892943 BB 707.56 -0.88 0.000 68511 5.000
0
Page 1 of 3
deoxycorticosterone
Comments:
Study
Client
Laboratory
Company
Phone
Component: deoxycorticosterone ISTD: methyltestosterone

ERT: 1.40 ERT: 2.01 RT: 1.49 - 2.49 SM: 7G
RT: 1.99
100
RTW: 30.00 RT: 0.90 - 1.90 SM: 7G RTW: 30.00
RT: 1.40 90
100
VW: 1.00 VW: 1.00
90 80
RTR: No RTR: Yes
80 70
Relative Abundance
MPH: 3.00 MPH: 3.00

70 60
Relative Abundance
SM: 7 SM: 7 50
60
PDAU: Genesis 50
PDAU: Genesis 40
VD: No 40
VD: No 30
CP: No 30 CP: No 20
20 10
10 0
1.70 1.5 2.0
0 Time (min)
1.0 1.5
Time (min)
Component Name Actua Calculate Respon Bas Signal % Diff Area Area Specified
l RT d Amount se e To Ratio ISTD Amount
Line Noise
deoxycorticosteron 1.40 5.108 1040531 BB 148.23 2.17 0.000 685110 5.000
e
Page 2 of 3
progesterone
Comments:
Study
Client
Laboratory
Company
Phone
Component: progesterone ISTD: methyltestosterone

ERT: 3.19 ERT: 2.01 RT: 1.49 - 2.49 SM: 7G
RT: 1.99
100
RTW: 30.00 RT: 2.67 - 3.67 SM: 7G RTW: 30.00
RT: 3.17 90
100
VW: 1.00 VW: 1.00
90 80
RTR: No RTR: Yes
80 70
Relative Abundance
MPH: 3.00 MPH: 3.00

70 60
Relative Abundance
SM: 7 SM: 7 50
60
PDAU: Genesis 50
PDAU: Genesis 40
VD: No 40
VD: No 30
CP: No 30 CP: No 20
20 10
10 0
1.5 2.0
0 Time (min)
3.0 3.5
Time (min)
Component Name Actua Calculate Respon Bas Signal % Diff Area Area Specified
l RT d Amount se e To Ratio ISTD Amount
Line Noise
progesterone 3.17 4.949 2995894 BB 344.16 -1.02 0.000 68511 5.000
0
Page 3 of 3
Index
'JOOJHBO9DBMJCVS ________________________________________________________________________
Index
Select How Chromatogram Axis page, 2-42

A Select Mass Spectrum Quan Traces page, 2-33
Select Peak Labeling page, 2-39
ActiveX control, 1-11, 1-13
Select Plot Details page, 2-35
Add Repeating Section button, 3-2
Select The Quan Peak page, 2-31
adding
starting, 2-21
Chromatogram report object, 3-7
Use Container Supplied Quan Peak page, 2-24, 2-25
Component Calibration Curve report object, 3-7
cleaning report templates, 3-31
repeating sections, 3-4
Component Calibration Curve report object
report objects, 2-5, 3-4
adding, 3-7
sections, 2-4, 3-4
configuring, 2-46, 3-24
Spectrum report object, 3-8
notification of location, 2-46
table objects, 3-6
properties, 3-24
text objects, 3-6
Properties list, 3-24
Autofilter command
Property Pages d.b., 3-24
Chromatogram, 2-36
specifying component name, 2-48
axes
Component Calibration Curve Wizard, 2-46
Chromatogram, 2-42
Calibration Curve Generated From page, 2-46
Spectrum, 3-13
Component Name page, 2-48
finishing, 2-49
B key features, 1-4
starting, 2-46
BaseGRD.dot, 1-5 component name
Component Calibration Curve, 2-48
C configuring
Chromatogram report object, 3-22
calibration (.xcal) file, 4-3 Component Calibration Curve report object, 3-24
Chromatogram report object repeating section, 3-18
adding, 3-7 repeating sections, 2-7
configuring, 2-21, 3-22 report objects, 3-17
configuring peak window display, 2-34 sections, 3-17
container supplied Quan peak, 2-24, 2-25 Spectrum report object, 3-26
notification of location, 2-21 table objects, 2-15, 3-20, 3-28
properties, 3-22 controls, 1-13
Properties list, 3-22 creating
Property Pages d.b., 3-22 report templates, 1-8
selecting a demo file, 2-27 report templates with wizards, 2-1
selecting axes details, 2-42
selecting chromatogram type, 2-26 D
selecting enhance details, 2-37
selecting MS Quan traces, 2-33 Data Source Browser, 4-2
selecting normalization method, 2-44 key features, 1-4
selecting peak labeling, 2-39 Merlin Data Sources d.b.
selecting plot details, 2-35 calibration (.xcal) file, 4-3
selecting Quan peak, 2-31 processing method (.pmd) file, 4-5
selecting style details, 2-38 raw (.raw) file, 4-4
chromatogram type, 2-26 result (.rst) file, 4-4
Chromatogram Wizard, 2-21 sequence (.sld) file, 4-6
Chromatogram Generated From page, 2-21 sequence (.sld) file and sample details, 4-7
Configure How Peak Window Looks page, 2-34 sequence (.sld) file, calibration (.xcal) file and
Configure Normalization For Chromatogram page, sample details, 4-8
2-44 Select A Sample d.b., 4-7
finishing, 2-45 Select Calibration File d.b., 4-3
key features, 1-4 Select Processing File d.b., 4-5
page order, 2-22 Select Raw Data File d.b., 4-4
Select Chromatogram Style page, 2-38 Select Result File d.b., 4-4
Select Chromatogram Type page, 2-26 Select Sequence d.b., 4-6
Select Demo File page, 2-27 data source file
Select Enhance Details page, 2-37 table, B-2
5IFSNP
&-&$530/$03103"5*0/ ________________ Finnigan Xcalibur: Getting Productive with Merlin ___________________ I
Index
________________________________________________________________________ 'JOOJHBO9DBMJCVS
data source files, 4-3

calibration (.xcal) file, 4-3
L
definition, 1-17
labels
processing method (.pmd) file, 4-5
Chromatogram, 2-39
raw (.raw) file, 4-4
Chromatogram axes, 2-42
required, 3-30
Spectrum, 3-12
result (.rst) file, 4-4
Spectrum axes, 3-13
sequence (.sld) file, 4-6
Data Source Identifier, 3-30, 4-2
key features, 1-4 M
demo file
Chromatogram, 2-27 maintaining report template tables, 3-28
Spectrum, 3-10 Merlin
design mode, 3-2 definition, 1-2
Design Mode button, 3-2 exiting, 1-9
detector delay installation, 1-5
Chromatogram, 2-35 key features, 1-2
detector type key terms, 1-10
Chromatogram, 2-35 overview, 1-2
Spectrum, 3-10 starting, 1-6
system and software requirements, 1-5
upgrading from a previous version, 1-5
E using, 1-8
Merlin Chromatogram Wizard, 1-4
enhance details
Merlin Component Calibration Curve Wizard, 1-4
Chromatogram, 2-37
Merlin Data Source Browser, 1-4
example report templates, A-1
Merlin Data Source Identifier, 1-4
Exit Design Mode button, 3-2
Merlin Operations button, 3-2, 3-30
exiting
Merlin Repeating Section Wizard, 1-3
Merlin, 1-9
Merlin Report Structure Wizard, 1-3
Word, 1-9
Merlin Spectrum Control Properties d.b., 3-8
Merlin Table Manager, 1-4
F Merlin Table Wizard, 1-4
Merlin toolbar, 1-3
field codes, 1-13 Merlin.dot, 1-2
method report, 2-3
G processing, 2-3
MS Quan traces
generating Chromatogram, 2-33
reports, 1-9, 2-53, 3-30, 4-1
from report template, 4-2 N
from report template (tutorial), 4-10
from Xcalibur, 4-11 non-repeating Qual section, 1-12
graphic objects non-repeating Quan section, 1-12
add button, 3-3 non-repeating section
Chromatogram, 2-21 adding, 2-4
Component Calibration Curve, 2-46 definition, 1-12
data source files required, B-7 processing method configuration, 1-12
definition, 1-16 programs, 1-12
descriptive tables, B-7 Qual, 1-12
repeating section placement, B-7 Quan, 1-12
resizing, 3-29 reports, 1-12
Graphic Objects button, 3-3 normalization
Chromatogram, 2-44
I Spectrum, 3-14
installation, 1-5 O
objects
report, 1-13
objects, graphic, 1-16
objects, table, 1-14
II____________________Finnigan Xcalibur: Getting Productive with Merlin_________________ 5IFSNP

&-&$530/$03103"5*0/
Index
'JOOJHBO9DBMJCVS ________________________________________________________________________
objects, text, 1-13 notification of location, 2-8

options ordering, 2-8
Spectrum, 3-9 repeating section, Quan
adding, 3-5
P configuring, 2-11
configuring page layout, 2-14
peak labels definition, 1-11
Chromatogram, 2-39 excluding peaks, 2-11
Spectrum, 3-12 notification of location, 2-11
peak window ordering, 2-12
Chromatogram, 2-34 report objects
plot type adding, 2-5, 3-4
Chromatogram, 2-35 Chromatogram, 2-21
Spectrum, 3-9 Component Calibration Curve, 2-46
plots configuring, 3-17
Chromatogram, 2-35 data source files required, B-1
processing method (.pmd) file, 4-5 definition, 1-13
processing method configuration section, 1-12 descriptive tables, B-1
processing method report, 2-3 graphic, 1-13
programs section, 1-12 repeating section placement, B-1
properties, 3-17 selecting, 2-5
table, 1-13
text, 1-13
Q Report Structure Wizard
key features, 1-3
Qual repeating section, 1-11 report templates
Quan peak adding breaks, 2-53
Chromatogram, 2-31 adding headers and footers, 2-53
Quan repeating section, 1-11 cleaning, 3-31
confirming structure, 2-6
R creating, 1-8
creating and editing with toolbar, 3-1
raw (.raw) file, 4-4 creating with wizards, 2-1
repeating section, 1-11 definition, 1-10
add button, 3-2 generating a report, 2-53
adding, 2-4, 3-4 generating report from, 4-2
configuring, 2-7, 3-18 generating report from (tutorial), 4-10
definition, 1-11 maintaining tables, 3-28
properties, 3-18 saving, 2-52
Properties list, 3-18 shipped examples, A-1
Property Pages d.b., 3-18 toolbar editing, 2-52
report object placement in using tables, 2-53
table, B-2 Word editing, 2-53
selecting type, 3-5 reports
Repeating Section Wizard, 2-7, 3-4 definition, 1-17
Configure Peak Reporting Layout page, Qual, 2-10 generating, 1-9, 2-53, 3-30, 4-1
Configure Peak Reporting Layout page, Quan, 2-14 from report template, 4-2
finishing, 2-14 from report template (tutorial), 4-10
key features, 1-3 from Xcalibur, 4-11
Repeating Section Generated page, Qual, 2-8 method, 2-3
Repeating Section Generated page, Quan, 2-11 sample, 2-2
Select How To Order page, Qual, 2-8 saving, 1-17, 4-3
Select How To Order page, Quan, 2-12 selecting type, 2-2
Select Peak To Exclude page, Quan, 2-11 summary, 2-3
Select Type of Peak to Repeat On page, 3-5 type, 2-2
starting, 2-7 type, selecting, 2-2
repeating section, Qual reports section, 1-12
adding, 3-5 resizing graphic objects, 3-29
configuring, 2-7 resolved document, 1-17
configuring page layout, 2-10 result (.rst) file, 4-4
definition, 1-11
5IFSNP
&-&$530/$03103"5*0/ ________________ Finnigan Xcalibur: Getting Productive with Merlin __________________ III
Index
________________________________________________________________________ 'JOOJHBO9DBMJCVS
summary report, 2-3

S by sample Quan, 2-3
system requirements, 1-5
sample report, 2-2
Qual, 2-2
Quan, 2-2 T
Quan and Qual, 2-2
saving Table Manager, 3-28
report templates, 2-52 key features, 1-4
reports, 1-17, 4-3 Maintain Template Tables d.b., 3-28
scan filters table objects
Chromatogram, 2-35 add button, 3-3
sections adding, 3-6
adding, 3-4 adding table columns, 2-16
configuring, 3-17 configuring, 2-15, 3-20, 3-28
definition, 1-10 configuring user columns, 2-17
non-repeating, 1-12 data source files required, B-4
repeating, 1-11 definition, 1-14
selecting, 2-4 descriptive tables, B-4
sequence (.sld) file, 4-6 maintaining, 3-28
smoothing notification of location, 2-15
Spectrum, 3-10 ordering columns, 2-19
software requirements, 1-5 properties, 3-20
source file, data Properties list, 3-21
Xcalibur, 1-17 Property Pages d.b., 3-21
Spectrum Control Properties d.b., 3-8 repeating section placement, B-4
Axis page, 3-13 Table Objects button, 3-3
Enhance page, 3-10 Table Wizard
Labels page, 3-12 Add to Generated Report page, 2-15
Normalization page, 3-14 Configure User Column page, 2-17
Options page, 3-9 finishing, 2-20
Peak page, 3-15 key features, 1-4
Plot Type page, 3-9 Select Table Fields page, 2-16
Style page, 3-11 Set Table Sort Filter page, 2-19
Spectrum report object starting, 2-15
adding, 3-8 templates, report, 1-6
configuring, 3-8, 3-26 templates, Word, 1-6
Merlin Spectrum Control Properties d.b., 3-8 terminology, 1-10
properties, 3-26 text objects
Properties list, 3-26 add button, 3-2
Property Pages d.b., 3-27 adding, 3-6
selecting axis details, 3-13 data source files required, B-2
selecting enhance details, 3-10 definition, 1-13
selecting labels, 3-12 descriptive tables, B-2
selecting normalization options, 3-14 field codes, 1-13
selecting options, 3-9 labels, 1-13
selecting plot type, 3-9 repeating section placement, B-2
selecting style details, 3-11 Text Objects button, 3-2
specifying peak to display, 3-15 time range
starting Chromatogram, 2-35
Merlin, 1-6 toolbar
Word, 1-6 Add Repeating Section button, 3-2
Structure Report Wizard, 2-2 Design Mode button, 3-2
Confirm Report page, 2-6 editing report template, 2-52
creating report templates, 2-1 Exit Design Mode button, 3-2
finishing, 2-6 Graphic Objects button, 3-3
Select Objects page, 2-5 key features, 1-3
Select Report page, 2-2 Merlin Operations, 3-2, 3-30
Select Sections page, 2-4 overview, 3-2
starting, 2-2 Properties button, 3-2
style Table Objects button, 3-3
Chromatogram, 2-38 Text Objects button, 3-2
Spectrum, 3-11 using, 3-1
IV ___________________Finnigan Xcalibur: Getting Productive with Merlin_________________ 5IFSNP

&-&$530/$03103"5*0/
Index
'JOOJHBO9DBMJCVS ________________________________________________________________________
tutorial using tables, 2-53

copy of report generated, C-1 Word templates
generating report from report template, 4-10 BaseGRD.dot, 1-5
Merlin.dot, 1-2
W
X
wizards, 1-3
Word Xcalibur
adding breaks, 2-53 data source files, 1-17
adding headers and footers, 2-53 generating report from, 4-11
design mode, 3-2 report
editing report template, 2-53 definition, 1-17
5IFSNP
&-&$530/$03103"5*0/ ________________ Finnigan Xcalibur: Getting Productive with Merlin __________________ V

Xcalibur Custom Reports With Merlin

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Xcalibur Custom Reports With Merlin

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'JOOJHBO¥

Printing History: Revision A printed in May 2003.

Published by Technical Publications, Thermo Electron Corporation, San Jose, California.

EDITOR, TECHNICAL PUBLICATIONS

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

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

Typographical Conventions ................................................................................................................... xi

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

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

1.2 Using Merlin ............................................................................................................................. 1-6

1.3 Overview of Report Templates ............................................................................................... 1-10

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

2.2 The Merlin Repeating Section Wizard ..................................................................................... 2-7

2.3 The Merlin Table Wizard........................................................................................................ 2-15

2.4 The Merlin Chromatogram Wizard ........................................................................................ 2-21

2.5 The Merlin Component Calibration Curve Wizard ................................................................ 2-46

2.6 After Using the Wizards… ..................................................................................................... 2-50

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

ii ____________________Finnigan Xcalibur: Getting Productive with Merlin_________________ 5IFSNP

3.2 Adding Sections and Report Objects to a Template ................................................................. 3-4

3.3 Configuring Repeating Sections and Report Objects ............................................................. 3-17

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

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

3.6 Merlin Operations Menu......................................................................................................... 3-30

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

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

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

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

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

Welcome to Merlin, the custom reports application of Xcalibur®! Merlin is

Changes to the Manual and Online Help

vi ___________________Finnigan Xcalibur: Getting Productive with Merlin_________________ 5IFSNP

viii __________________Finnigan Xcalibur: Getting Productive with Merlin_________________5IFSNP

ppm parts per million

Note. Exponents are written as superscripts. In the corresponding online

x ____________________Finnigan Xcalibur: Getting Productive with Merlin_________________ 5IFSNP

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

Boxed information can be of the following types:

xii ___________________Finnigan Xcalibur: Getting Productive with Merlin_________________ 5IFSNP

1.2 Second Level Topics

Third Level Topics

Fourth Level Topics

Fifth Level Topics

xiv __________________Finnigan Xcalibur: Getting Productive with Merlin_________________ 5IFSNP

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

1.1 Overview of Merlin

Key Features of Merlin

Merlin Report Structure Wizard

The Merlin toolbar

Figure 1-1. Merlin Toolbar

Merlin Repeating Section Wizard

Merlin Table Wizard

Merlin Chromatogram Wizard

Merlin Component Calibration Curve Wizard

Merlin Table Manager

Merlin Data Source Identifier

Merlin Data Source Browser

Shipped Merlin Report Templates

Upgrading From a Previous Version

System / Software Requirements

1.2 Using Merlin

Creating and Generating Reports with Merlin

Creating a Report Template

'JOOJHBO¥

ii ____Finnigan Xcalibur: Getting Productive with Merlin_ 5IFSNP

vi ___Finnigan Xcalibur: Getting Productive with Merlin_ 5IFSNP

viii __Finnigan Xcalibur: Getting Productive with Merlin_5IFSNP

x ____Finnigan Xcalibur: Getting Productive with Merlin_ 5IFSNP

xii ___Finnigan Xcalibur: Getting Productive with Merlin_ 5IFSNP

xiv __Finnigan Xcalibur: Getting Productive with Merlin_ 5IFSNP

1-10 Finnigan Xcalibur: Getting Productive with Merlin_ 5IFSNP

1-12 Finnigan Xcalibur: Getting Productive with Merlin_ 5IFSNP

1-14 Finnigan Xcalibur: Getting Productive with Merlin_ 5IFSNP

1-16 Finnigan Xcalibur: Getting Productive with Merlin_ 5IFSNP

2-10 Finnigan Xcalibur: Getting Productive with Merlin_ 5IFSNP

2-12 Finnigan Xcalibur: Getting Productive with Merlin_ 5IFSNP

2-14 Finnigan Xcalibur: Getting Productive with Merlin_ 5IFSNP

2-16 Finnigan Xcalibur: Getting Productive with Merlin_ 5IFSNP

2-18 Finnigan Xcalibur: Getting Productive with Merlin_ 5IFSNP

2-20 Finnigan Xcalibur: Getting Productive with Merlin_ 5IFSNP