Compass QuantAnalysis 5.

0
User Manual

Revision A (April 2017)

Legal and regulatory notices Bruker

Legal and regulatory notices

Copyright 2017
© Bruker Daltonik GmbH
All other trademarks are the sole property of their respective owners.
All Rights Reserved
Reproduction, adaptation, or translation without prior written permission is prohibited,
except as allowed under the copyright laws.
Document History
Compass QuantAnalysis 5.0 User Manual Revision A (April 2017)
Part number: #1845173
First revision: April 2017
Warranty
The information contained in this document is subject to change without notice.
Bruker Daltonik GmbH makes no warranty of any kind with regard to this material,
including, but not limited to, the implied warranties of merchantability and fitness for a
particular purpose.
Bruker Daltonik GmbH is not liable for errors contained herein or for incidental or
consequential damages in connection with the furnishing, performance or use of this
material.
Bruker Daltonik GmbH assumes no responsibility for the use or reliability of its software on
equipment that is not furnished by Bruker Daltonik GmbH.
Use of Trademarks
The names of actual companies and products mentioned herein may be the trademarks of
their respective owners.
Limitations on Use
For Research Use Only (RUO). Not for use in diagnostic procedures.
Hyperlink Disclaimer
Bruker Daltonik GmbH makes no express warranty, neither written nor oral, and is neither
responsible nor liable for data or content from the linked Internet resources presented in
this document.

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Bruker Contact

Contact
Contact your local Bruker representative for service and further information.

Germany USA
Bruker Daltonik GmbH Bruker Daltonics Inc
Fahrenheitstraße 4 40 Manning Road
28359 Bremen Billerica, MA 01821
Germany USA
Phone: +49 421 2205-0 Phone: +1 978 663-3660
Internet: [Link] Internet: [Link]

Service Support Service Support

Phone: +49 421 2205-350 Phone: +1 978 663-3660
Fax: +49 421 2205-106 Fax: +1 978 667-5993
Email: [Link]@[Link] Email: [Link]@[Link]

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Table of contents Bruker

Table of contents

Legal and regulatory notices 2

Contact 3
Table of contents 4
1 Preface 7
2 Getting Started 9
2.1 Installing and uninstalling QuantAnalysis 9
2.2 Compliance modes and UserManagement 9
2.2.1 Running QuantAnalysis in Compliance or Non-Compliance mode 9
2.2.2 UserManagement 10
[Link] QuantAnalysis operating rights in UserManagement 11
[Link] Auto- generated operator groups and their right assignments in
QuantAnalysis 12
2.2.3 Electronic records and electronic signatures 13
2.3 Audit trailing 13
2.4 Starting QuantAnalysis 14
2.5 Logging an operator into QuantAnalysis 14
2.6 Changing the operator's password 15
2.7 Locking and unlocking an operator 16
2.8 Locking and unlocking QuantAnalysis and all other Bruker Compass applications
supporting Compass Security Pack 16
2.9 Closing QuantAnalysis 17
3 QuantAnalysis user interface 19
3.1 Work Table window 20
3.2 Chromatogram/Spectrum window 26
3.3 Calibration window 29
3.4 Nested display of windows 33
3.5 Customizing the user interface 34
3.5.1 Modifying the Work Table layout 34
[Link] Hiding a Work Table column 34
[Link] Showing a hidden Work Table column 35
[Link] Changing the width of a Work Table column 35
[Link] Saving a Work Table layout 35

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[Link] Selecting a Work Table layout 36

3.5.2 Changing data display ranges 36
[Link] Changing the display range of the Chromatogram and Spectrum views 36
[Link] Changing the display range of the Calibration view 37
4 Creating and managing batch files 39
4.1 Creating a batch file 39
4.1.1 Creating a batch file from a sample table 39
4.1.2 Importing a sample table 43
4.1.3 Creating a batch file for a set of individually acquired data files 45
4.2 Filling and manipulating the Work Table for a batch file 47
4.2.1 Filling the Work Table automatically 47
4.2.2 Filling the Work Table manually 48
4.2.3 Copying Work Table entries multiple times 48
4.2.4 Moving a row within the Work Table 49
4.2.5 Deleting a row from the Work Table 50
4.2.6 Resetting the Work Table 50
4.2.7 Defining sample parameters 51
[Link] Defining the type of a sample 51
[Link] Defining the calibration level of a calibration or quality control sample 52
4.3 Saving a batch file 52
4.4 Opening a batch file 53
4.5 Showing the result history of a batch file 55
4.6 Signing a result of a batch file electronically 55
4.7 Deleting a result from a batch file 56
4.8 Showing the audit trail of a batch file 57
4.9 Closing a batch file 57
5 Creating quantitation methods 59
5.1 Creating a quantitation method 60
5.2 Saving a quantitation method 62
5.3 Opening a quantitation method 63
5.4 Viewing a quantitation method 63
5.5 Modifying a quantitation method 64
6 Processing batch files 65
6.1 Processing a batch file 66

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6.2 Calculation of calibration curves 67

7 Reviewing calibration and quantitation results 69
7.1 Reviewing calibration and quantitation results of a processed batch file 69
7.2 Plotting quantitation data of a processed batch file 72
8 Altering quantitation results of a processed batch file 73
8.1 Integrating a compound peak manually 73
8.2 Deleting a compound peak 75
8.3 Altering a calibration curve 75
8.3.1 Disabling a calibration point 76
8.3.2 Enabling a calibration point 76
8.3.3 Changing the curve fit of a calibration curve 77
8.3.4 Changing the mode of origin of a calibration curve 77
8.3.5 Changing the weighting of calibration points 78
9 Printing and sending reports 79
9.1 Printing a report 79
9.2 Sending a report as email 80
9.3 Sending a report to PDF document 80
9.4 Creating a custom report layout 81
10 Exporting batch files 83
Appendix A — Quick reference tables 85
A.1 QuantAnalysis toolbar 85
A.2 QuantAnalysis menus 86
A.3 QuantAnalysis shortcuts 88
Index 89

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Bruker 1 Preface

1 Preface
Welcome to Bruker Compass QuantAnalysis 5.0 (referred to as 'QuantAnalysis'), the
state-of-art Windows application for quantitation of analyses acquired on Bruker Daltonics
mass spectrometer instruments. QuantAnalysis is specifically designed to process
analyses acquired on the ion trap, the o- TOF/UHR- TOF and the FTMS mass
spectrometers.
QuantAnalysis is an advanced program dedicated for quantitation of MS and MSn
analyses. Dynamically linked views of the spreadsheet data, the chromatogram and
spectrum, and the calibration curve make quantitation faster and easier. Working in any of
the views e.g., selecting a different curve fit for calibration is immediately reflected in all
other views. QuantAnalysis processes batches acquired with Bruker Compass HyStar or
Agilent ChemStation. Printed reports in various layouts are available and custom layouts
can be created using the Bruker Compass ReportDesigner.
Quantitation with QuantAnalysis consists of acquiring data files from calibration solutions
and "unknown" samples. This can also involve quality control ('QS') and blank samples.
The acquisition of such data files is usually done within a sequence that is set up in the
HyStar or Agilent ChemStation application, but you can also use a series of individually
acquired data files. Quantitative data analysis is performed within QuantAnalysis after the
data acquisition.
With QuantAnalysis, you can quantify a single target compound (single component
quantitation) or multiple target compounds at once (multi-component quantitation). You
can calibrate with internal and external standards. QuantAnalysis can handle multiple
injections of the same sample and average the corresponding calibration data, as well as
handle quality control samples to validate the calculated calibration curves. Different
sample series, such as those with different matrices but the same target compounds, can
be quantified in sequence. By entering the data files in separate blocks, processing
produces a corresponding number of calibration curves individually calculated for each
block.
The task flow of quantitation includes the following major steps:
l Creating a batch file containing all the data files to be used in quantitation.

l Creating or opening the quantitation method to be used in processing the batch file.

l Processing the batch file.

l Reviewing the calibration and quantitation results for the processed batch file and, if

required, altering these results.

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l Saving the processed batch file.

l Printing a quantitation report.

The QuantAnalysis 5.0 User Manual describes how to work with QuantAnalysis 5.0.
For reference on QuantAnalysis 5.0 menus and commands, please refer to the
QuantAnalysis 5.0 Reference Manual.

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Bruker 2 Getting Started

2 Getting Started

2.1 Installing and uninstalling QuantAnalysis

The Bruker Compass QuantAnalysis 5.0 application installs automatically when the
Bruker Compass DataAnalysis 5.0 application is installed on your system. The
QuantAnalysis application is uninstalled automatically when you uninstall the DataAnalysis
application from your system.
To work with QuantAnalysis, a valid 'DataAnalysis 5.0' license must be present.

2.2 Compliance modes and UserManagement

2.2.1 Running QuantAnalysis in Compliance or Non-

Compliance mode
QuantAnalysis can be run in 'Compliance' or 'Non- Compliance' mode. Working in
Compliance mode can support you to meet FDA 21 CFR Part 11 (FDA's rule on electronic
signatures and records) requirements.
To run QuantAnalysis in Compliance mode, the Bruker Daltonics Compass Security Pack
application needs to be installed either on this computer or, preferably, on a central server.
When the 'Compass Security Pack' license is present, QuantAnalysis is automatically
running in Compliance mode. Otherwise, QuantAnalysis is running in Non- Compliance
mode.
Note Compliance mode in the context of Compass Security Pack exclusively means the
availability of Compass Security Pack tools and functionalities, which can be used
to support the user to meet 21 CFR Part 11 requirements. Neither Compliance
mode nor Compass Security Pack can assure full compliance with 21 CFR Part
11 requirements.
Compliance mode
The Compliance mode for QuantAnalysis offers the following features:
l Only operators created by the customer's UserManagement administrator can log into
QuantAnalysis after identification by operator ID and password.

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l The UserManagement administrator can administer access to QuantAnalysis by

assigning individual rights to the operators he creates. These rights determine the
actions the operator is allowed to perform in QuantAnalysis.
l Electronic signatures for signing electronic records are possible. Multiple signing of
results is allowed.
l All Bruker Compass applications supporting Compass Security Pack that are installed
on the operator's computer can be locked and unlocked by the operator.
Note Most of the features above apply to any Bruker Compass application supporting
Compass Security Pack.

Non-Compliance mode
When QuantAnalysis is running in Non-Compliance mode:
l Anybody can log into QuantAnalysis because no identification by operator ID and
password is needed.
l Operators who have different QuantAnalysis rights do not exist.
l QuantAnalysis and other Bruker Daltonics applications cannot be locked or unlocked.

2.2.2 UserManagement
When QuantAnalysis is running in Compliance mode , QuantAnalysis uses
UserManagement. UserManagement enables you to administer access to Bruker
Compass applications supporting Compass Security Pack and manage individual action
rights based on operator ID and password.
Creating operators and assigning rights to them is performed using the Bruker Compass
UserManagement Administration application. Only the customer's UserManagement
default administrator and perhaps further UserManagement administrators (if they have
the 'UserManagement Administration Tool: Administrate Operators' right) have the right to
create operators which should use QuantAnalysis and assign individual rights to them
concerning the actions these operators are allowed to perform in QuantAnalysis.
Before anybody apart from the UserManagement default administrator can log into
QuantAnalysis when in Compliance mode, the UserManagement administrator has to
create (an) desired operator (s) identified by operator ID and password. To become
effective an operator must be assigned to an operator group that has specific rights. The
UserManagement administrator can use the auto-generated operator groups or define
new groups to be able to customize the assignments of rights based on specific
requirements. All members within a group will have the same rights. In addition, the

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Bruker 2 Getting Started

UserManagement administrator can also modify the default password policy and timeout
settings as desired.
Note For detailed information on how to create operators and assign rights, please refer
to the UserManagement help tools.
UserManagement is client- server based. On the server PC the database defining
operators and their rights is installed, on the client PC the Bruker Compass applications
are installed.

[Link] QuantAnalysis operating rights in UserManagement

In UserManagement specific rights for performing actions in QuantAnalysis exist that can
be assigned to an operator group and, therefore, to an operator. If an operator tries to
perform an action without having the respective right, an error message will appear.
The rights existing in QuantAnalysis are listed below. In most cases, several actions are
associated with a single right, which an operator having this right is allowed to perform in
QuantAnalysis. An operator must at least have the Load/edit batches right to be able to
load and edit batch files in QuantAnalysis.

Right: Actions permitted concerning the following

subjects:
• Change parameter Changing quantitation method parameters and
calibration curve parameters.
• Delete result Deleting a result.
• Load method Loading quantitation methods.
• Load/edit batches Opening and editing batch files.
• Process batch Processing batch files using defined routines.
(Includes e.g. Process, Clear Areas, Delete Peak).
• Process batch manually Processing batch files manually. (Includes manually
integrating and deleting compound peaks)
• Save batch Saving processed batch files.
• Save method Saving quantitation methods.

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[Link] Auto-generated operator groups and their right assignments in

QuantAnalysis

In UserManagement, various so-called 'auto-generated' operator groups are predefined

with each of them having specific rights for performing actions in QuantAnalysis included.
The UserManagement administrator can assign a new operator to one of these auto-
generated groups if he does not want to define own groups but he cannot change the right
assignment of the predefined groups.
The following operator groups are predefined in UserManagement (in alphabetical order):
l Administrators (auto-generated)
l Operators (auto-generated)

l Project Managers (auto-generated)

l Scientists (auto-generated)

l Service (auto-generated)

The QuantAnalysis rights assigned to the auto-generated operator groups are shown
below (the figures show the respective sections in the UserManagement Administration
Tool). No difference exists between an operator of the 'Administrators (auto-generated)'
and the 'Project Managers (auto-generated)' group; both have all rights that are available
for this application. An operator of the 'Scientists (auto- generated) ' group lacks the
Change parameter , Delete result and Load method rights. An operator of the
'Operators (auto-generated)' group also lacks the Process batch manually right. The
'Service' group is used for service purposes of the manufacturer.
'Administrator' 'Project Manager'

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Bruker 2 Getting Started

'Scientist' 'Operator'

2.2.3 Electronic records and electronic signatures

When QuantAnalysis is running in Compliance mode, electronic records can be signed
electronically by operators who have the right to sign. An electronic signature consists of
operator ID and password. Optionally, the meaning of signing can be given, and multiple
signing of results is allowed.
Signing a result is done using the History command found in the Work Table window. You
can see whether the results of a batch have already been signed by seeing the batch's
result history displayed in the Result History or the Open dialog.

2.3 Audit trailing

A corresponding audit trail is recorded for each batch file that is set up. The audit trail lists
all changes that were made to the loaded batch file with corresponding date and time,
name of the operator who made the change and what was the change. This includes all
changes saved during previous processing operations performed on this batch file and
changes made during the current processing of this batch file, even if these changes have
not been saved yet. When the batch file is closed only changes actually saved during the
processing are stored in the audit trail.
You can view the audit trail of the loaded batch file using the Show Audit command found
in the Work Table window.

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2.4 Starting QuantAnalysis

You can start QuantAnalysis from the Windows Start menu. During installation of the
Bruker Daltonics applications package, a Bruker folder was created automatically in the
Start menu's All Programs folder. This folder contains the respective applications.
On starting QuantAnalysis, a dialog appears that requests you to log in unless you are
already logged in another Bruker Daltonics application (for both Compliance mode and
Non-Compliance mode ) or the corresponding option for skipping this dialog is set (for
Non-Compliance mode only).
After logging in, QuantAnalysis starts and the user interface displayed depends on the
settings stored for the current user logged into Windows.
To start QuantAnalysis:

1. Click > All Programs > Bruker > QuantAnalysis. This starts QuantAnalysis
and opens the QuantAnalysis application.
2. Log in if requested.

2.5 Logging an operator into QuantAnalysis

When QuantAnalysis is running in Compliance mode , only operators created by the
UserManagement administrator can log into QuantAnalysis (after being identified by their
operator ID and password). UserManagement can lock an operator who enters the wrong
password successively. The UserManagement administrator defines the maximum
number of false attempts allowed.
When QuantAnalysis is running in Non-Compliance mode, any operator can log in after
entering the operator ID. Identification by password is not required.
Note Only one operator can be logged into Bruker Compass applications supporting
Compass Security Pack on a specific computer at a time.
You must log in after starting QuantAnalysis unless you are currently logged in another
Bruker Daltonics application (for both Non-Compliance and Compliance mode). When
QuantAnalysis is running in Non-Compliance mode an option for automatic log in of the
specified operator can be set.
In Compliance mode: If QuantAnalysis is the first Bruker Compass application supporting
Compass Security Pack you want to log in after the UserManagement administrator has
defined you as a new operator, the program will require you to change your password.

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Bruker 2 Getting Started

The operator currently logged in is identified in the status bar when QuantAnalysis is
running.
To log into QuantAnalysis:
1. Start QuantAnalysis or when in a running session select Operator from the Help
menu. This opens the QuantAnalysis dialog that corresponds to the current mode in
which QuantAnalysis is running.
2. In Operator, enter your operator ID. The operator ID is not case-sensitive.
3. In Non-Compliance mode, check Always log in using this operator if you want to
log in automatically the next time without showing the log-in dialog again.
4. In Compliance mode, enter your password in Password.
Note Passwords are case-sensitive. Too many successive wrong inputs will cause
locking of the operator.
5. Click Log On. In Compliance mode, log in will be successful only if operator ID and
password are correct.
6. If you are required to change your password, change it and then repeat steps 4 and 5.

2.6 Changing the operator's password

When QuantAnalysis is running in Compliance mode, any operator who wants to log in
has to identify by password.
The program requires you to change your password when you first log into a Bruker
Compass application supporting Compass Security Pack after the UserManagement
administrator has defined you as new operator. You must also change your password
after the administrator has changed your password or forced a password change on you.
Apart from this, you can change your password as desired either during login or while
running a QuantAnalysis session.
A new password must conform to the password policy settings defined by the
UserManagement administrator; or the password will not be changed.
To change an operator's password:
1. Start QuantAnalysis or when in a running session, select OperatorOperator from the
Help menu. This opens the QuantAnalysis dialog.
2. In Operator, enter your operator ID.
3. Click Change Password. This opens the Change Password dialog.

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4. In Operator, the ID of the operator whose password can be changed is given. If the
password for another operator should be changed, click Cancel to return to the
QuantAnalysis dialog and repeat steps 2 and 3.
5. In Old password, enter your current password. The password is not displayed as you
type it.
Note Passwords are case-sensitive.
6. In New password, enter the new password. The new password must conform to the
password policy settings.
7. In Confirm new password, enter your new password again.
8. Close the message confirming a successful password change. If an error message
appears, repeat the corresponding steps.

2.7 Locking and unlocking an operator

An operator can be locked by UserManagement after too many wrong passwords are
entered in succession. The UserManagement administrator defines how many wrong
inputs are allowed. An operator can also be locked by direct UserManagement
administrator action. The operator will get information about being locked after locking has
occurred.
A locked operator cannot log into any Bruker Compass application supporting Compass
Security Pack. Only the UserManagement administrator can unlock a locked operator.

2.8 Locking and unlocking QuantAnalysis and all

other Bruker Compass applications supporting
Compass Security Pack
When QuantAnalysis is running in Compliance mode, you can lock QuantAnalysis and all
other Bruker Compass applications supporting Compass Security Pack installed on your
system. Only the previous operator or someone with the special right to unlock
applications is permitted to unlock a locked application.
Note The Lock All Applications command is only available when QuantAnalysis is
running in Compliance mode.
Note An automatic locking (= timeout) of all Bruker Compass applications supporting
Compass Security Pack will occur if one of these applications has not been used
for a certain period of time defined by the UserManagement administrator.

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To lock all Bruker Compass applications supporting Compass Security Pack:

1. Press the Ctrl+Alt+K keys or select Lock All Applications from the Help menu.
This opens the QuantAnalysis dialog that informs you that QuantAnalysis is currently
locked and how it can be unlocked.
To unlock all Bruker Compass applications supporting Compass Security Pack:
1. In the QuantAnalysis dialog, enter in Operator your operator ID. The dialog displays
the name of the previous operator who has locked Bruker Compass applications. The
respective ID will automatically be entered if the UserManagement administrator has
set the corresponding option. Anyone other than the previous operator who wants to
unlock the applications must enter their operator ID.
Note To do this, the operator must have the right to unlock applications.
2. If you want to change the password before logging in, click Change Password and
change it as instructed.
3. In Password, enter the password for the operator named in Operator.
Note Passwords are case-sensitive. Too many successive wrong inputs will cause
locking of the operator.
4. Click Log On. If operator ID and password are correct and if the respective operator is
allowed to unlock applications, QuantAnalysis is unlocked and the operator is logged
in.

2.9 Closing QuantAnalysis

You can close QuantAnalysis when you have finished your current session. On closing,
the current user interface settings are stored automatically for the current user logged into
Windows.
To close QuantAnalysis:
1. Do one of the following:
l Click the application's Close .
lFrom the File menu, select Exit.
l Press the Alt+F4 keys.

2. If required, answer the appearing confirmation request on saving the current

processing state of the open file.

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Bruker 3 QuantAnalysis user interface

3 QuantAnalysis user interface

The QuantAnalysis graphical user interface consists of the title bar, menu bar, toolbar
(hidden by default), status bar and three display windows: the Work Table window ,
Chromatogram/Spectrum window and Calibration window. These elements are used for
displaying and processing the quantitation data and results currently available for the open
batch file. When QuantAnalysis is running in Compliance mode the status bar displays the
full name of the current operator.
You can display the three windows individually or nested together to provide four different
display modes that you can toggle among by clicking the corresponding Nested, Work
Table, Chromatogram/Spectrum or Calibration tabs in the lower left corner of the
QuantAnalysis window.
The contents of the three windows are linked dynamically. Changes made in one window
are instantly updated in the other windows. For example: if you select another type of
calibration curve in the Calibration window, then the respective calibration curve is
recalculated and redisplayed as well as all the corresponding quantitation results listed in
the Work Table window. This allows you to adjust parameters, or corrections like manual
integration of single peaks, quickly and easily.

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Figure 3-1 QuantAnalysis user interface in Nested display mode showing the
quantitation results of the loaded, processed batch file in the Work Table
window, Chromatogram/Spectrum window and Calibration window

3.1 Work Table window

The Work Table window displays the current Work Table and information about the target
and ISTD compounds used in quantitation of the open batch file. It contains buttons for
customizing the Work Table layout and for processing the current Work Table contents. It
also provides buttons for performing the quantitation.

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Figure 3-2 Work Table window displaying data from a processed batch file

Work Table
The Work Table contains all the information that is associated with quantitating a batch of
samples. By defining and saving this table you create the batch file (*.btc) that provides
easy access to the complete series of files you may later use to review the results or to
reprocess them.
The Work Table has two major areas indicated by either dark gray or light gray column
headers. You can adjust the Work Table layout to specific quantitation tasks. Thus, the
columns that are displayed depend on the loaded Work Table layout and/or the current
user settings.
Sample-specific columns
The dark gray-headed columns are used to enter sample-specific data.
File Name. File name of the analysis acquired for the sample.
Sample Name. Name of the sample.
Sample Info. Information on the sample.
Vial. Number of the vial the sample was placed in.
Method Name. Name of the quantitation method to be used for the file. It must be given
for each file and it must be the same for all files within a batch of files.
Inj. Vol. Injected volume of the sample. The value cannot be zero.
Dil. Factor. Dilution factor used for the sample. The value cannot be zero (e.g. just use "1"
for all samples).

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Sample Type. Type of the sample. Each sample must be defined by selecting the desired
sample type from the corresponding drop-down list:
Sample. (Default) Sample to be quantified.
Calib. Sample to be used for setting up a calibration curve.
QC. Sample to be used in quality control for validation of a calibration curve.
Blank. Blank sample.
Calib. Level. Calibration level of the respective sample. This must be defined only for
'Calib' and 'QC' samples. 'Sample' and 'Blank' samples do not get a calibration level.
QuantAnalysis uses this level to read the corresponding concentration from the table
defined in the quantitation method used. The calibration level can be given in arbitrary
numbers (e.g. 1, 2, 3, ...) or as text in the case of 'QC' samples (e.g. low, medium, high).
Inj. No. Injection number. This value cannot be zero.
Acq. Date. Acquisition date.
Operator. Name of the operator.
Compound- and sample-specific columns
The light gray-headed columns are used to display the quantitation results. In the case of a
multi-component calibration, each of these columns exists multiple times, one time for
each compound. The target compound whose data are currently displayed is indicated in
the Cmpd list box found above the table.
Theor. Conc. Theoretical concentration of the indicated target compound in the sample if
it is a 'Calib' or 'QC' sample. The QuantAnalysis software enters the corresponding
values defined in the quantitation method used during processing of the batch file. The
operator can change the theoretical concentration after calculation by entering a new
value.
Theor. Conc. Unit. Unit of the theoretical concentration of the target compound in the
sample if it is a 'Calib' or 'QC' sample. The QuantAnalysis software enters the
corresponding values defined in the quantitation method used during processing of the
batch file. The operator can change the unit of the theoretical concentration after
calculation by entering a new value.
Conc. ISTD. Concentration of the internal standard in the sample.
Conc. ISTD Unit. Unit of the internal standard in the sample.
RT Target Cmpd. Retention time of the target compound in the sample.

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Area Target Cmpd (or Height Target Cmpd). Calculated peak area (or height) of the
target compound in the sample. Whether peak area or peak height is calculated
depends on the selected calibration mode ('Area' or 'Height').
S/N Target Cmpd. Signal-to-noise ratio of the target compound.
Area ISTD Cmpd (or Height ISTD Cmpd). Calculated peak area (or peak height) of the
internal standard in the sample. Whether peak area or peak height is calculated
depends on the selected calibration mode ('Area' or 'Height').
S/N ISTD Cmpd. Signal-to-noise ratio of the ISTD compound.
Ratio Area Target/ISTD (or Ratio Height Target/ISTD). Ratio between the peak area
(or peak height) of the target compound and the peak area (or peak height) of the
internal standard in the sample. Whether the ratio between peak areas or peak heights
is calculated depends on the selected calibration mode ('Area' or 'Height').
Calc. Conc. Calculated concentration of the target compound in the sample.
Note An 'n/c' (= not calculated) will be entered if no concentration value could be
assigned to the calculated peak area (or height) because there is not data point in the
calibration curve that fits this area or height value. This may happen with quadratic
calibration curves only.
Calc. Conc. Unit. Unit of the calculated concentration of the target compound in the
sample.
Accuracy . Calculated accuracy determined as the ratio between the calculated
concentration (evaluation of the peak area against the current calibration curve) of the
target compound and its (known) theoretical concentration. It will be calculated only for
'Calib' and 'QC' samples. This value allows you to assess easily the quality of the
integration results and calibration curve.

Target and ISTD compound fields

Cmpd. Active target compound whose corresponding data is currently shown in the Work
Table. In case of a multi-component calibration, you can click to display the complete
list of target compounds used and switch to another compound by selecting it from this
list.
Chro. Chromatogram trace to be used for the active compound in peak integration.
ISTD. ISTD compound used. If no internal standard is used in the respective batch file,
'<None>' is displayed.
Chro. Chromatogram trace to be used for the ISTD compound in peak integration.
Prev. Cmpd.. Switches to the previous compound if available.

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Next Cmpd.. Switches to the next compound if available.

Calib. Basis. Current calibration basis. The following options are available:
Area. Uses the calculated area of a target or ISTD compound peak.
Height. Uses the calculated height of a target or ISTD compound peak.
Calib. Mode. Current calibration mode. The following modes can be applied if several
calibration blocks and sample blocks were measured one after another within a
sequence.
Note For this, the Work Table has to be set up accordingly, e.g.
Calibration block 1
Sample block 1
Calibration block 2
Sample block 2
Calibration block 3
Sample block 3
Sequential. Calibrates the samples of sample block 1 based on the calibration function
calculated from calibration block 1, the samples of sample block 2 based on the
calibration function calculated from calibration block 2, etc.. This means that always the
previous calibration runs are used to calculate the calibration function.
Bracket. Calibrates the samples of sample block 1 based on the calibration function
calculated from calibration blocks 1 and 2, the samples of sample block 2 based on the
calibration function calculated from calibration blocks 2 and 3, etc. This means that
always the previous and the next calibration runs are used to calculate the calibration
function.
Average. Calibrates all samples based on the calibration function calculated from all
calibration blocks.

'Work Table layout' buttons

Opens the Select Work Table Layout dialog to select a layout.

Opens the Save Work Table Layout dialog to save the current layout.

Lists the currently hidden Work Table columns and redisplays the selected
column.

Hides the selected column(s).

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'Work Table contents processing' buttons

Resets the Work Table to the situation that existed before processing the
batch. This allows all Work Table fields to be editable again. This allows you
to remove incorrect entries from fields that otherwise cannot be edited after
batch processing was performed.

Deletes the selected row(s).

Plots data of a selected column . This function is only available for certain
columns.

'Showing batch file information' buttons

Opens the Audit Trail dialog for the open batch file.

Opens the Result History dialog which lists all results previously saved for
the open batch file.

'Importing and exporting' buttons

Opens the Import Sample Table dialog to import a sequence file.

Opens the Export Sample Table dialog to export the batch file as a Comma
Separated Values (*.csv) file. For a processed batch file its results table will
be exported; otherwise, the respective sample table file will be exported.

'Quantitation task flow' buttons

Opens the Open Batch dialog to open a batch file.

Starts the Method Editor to create the quantitation method to be used with
opening the General dialog.

Processes the batch file.

Saves the open batch file. If the current batch has not been saved before, the
Save Batch dialog is opened.

Opens the Print dialog to select the desired report layout and to set up and
print the selected report.

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'Toggling between files' buttons

Toggles to the previous or to the next data file contained in the open batch file and displays
the results corresponding to the currently selected target compound.

'Toggling between target compounds' buttons

Toggles in case of a multi-component calibration to the previous or to the next target

compound in the compound list of the currently selected data file and displays the
corresponding data.

3.2 Chromatogram/Spectrum window

After you have performed a quantitation, the Chromatogram/Spectrum window displays
the individual compound peaks and the corresponding averaged mass spectra calculated
for the target and ISTD compounds contained in the processed data files. Chromatogram
traces display in the Chromatogram view (above) and mass spectra display in the
Spectrum view (below).
You can browse through the results for all files and compounds. If compound peaks are
not recognized during the quantitation process or are not properly integrated, then the
integration can be corrected by means of the manual integration mode. This mode allows
you to reintegrate easily and individually each compound peak without having to reprocess
the entire batch of files.

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Figure 3-3 Chromatogram/Spectrum window after performing a quantitation: The

Chromatogram view displays a recognized target compound peak; the
Spectrum view displays the corresponding averaged mass spectrum

Chromatogram view
The Chromatogram view displays the chromatogram trace edited from the active data file
for the active target compound. If an ISTD compound is contained, its corresponding trace
will be displayed. If during the automatic integration process the corresponding compound
peak(s) has/have been recognized, this/these become(s) labeled with an index.
If a compound peak has not been recognized during automatic integration, you can switch
to the manual integration mode to manually integrate the respective peak in the
Chromatogram view.
You can adjust the display range of the Chromatogram view.
Spectrum view
The Spectrum view displays the averaged mass spectrum calculated for that peak that has
been detected for the selected target compound or the ISTD compound. Which mass
spectrum currently is displayed depends on the selected option (Target or ISTD).
You can adjust the display range of the Spectrum view.

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File Name
Displays the name of the active data file whose chromatogram and mass spectrum data
are displayed in the Chromatogram and Spectrum views. This file is highlighted in dark
green in the Work Table. You can toggle between the different data files of a batch using
the Prev. File and Next File buttons.
Analysis
Displays analysis data corresponding to the active data file.
Name. Sample name as entered in the Sample Name column of the Work Table.
Desc. Sample description as entered in the Sample Info column of the Work Table.
Type. Sample type as selected in the Sample Type column of the Work Table.
Target Compound
Displays the active target compound, the chromatogram trace used for its quantitation and
the retention time of the corresponding compound peak recognized from the active data
file. In addition, it shows the color used for displaying the respective chromatogram trace in
the Chromatogram view. In the case of a multi-component quantitation, you can toggle
between the various target compounds using the Prev. Cmpd and Next Cmpd buttons.
ISTD Compound
Displays the ISTD compound assigned to the active target compound, the chromatogram
trace used for its quantitation and the retention time of the ISTD compound peak
recognized from the active data file. In addition, it shows the color used for displaying the
respective chromatogram trace in the Chromatogram view.
Display MS
Note This parameter is displayed instead of Integrate when the manual integration
mode is not active.
Target. Displays the averaged mass spectrum calculated for the compound peak of the
selected target compound.
ISTD. Displays the averaged mass spectrum calculated for the compound peak of the
selected ISTD compound.
Integrate
Note This parameter is displayed instead of Display MS when the manual integration
mode is active.
Target. Hides the chromatogram trace edited for the ISTD compound and displays the
Manual Integration cursor for defining the target compound peak to be integrated.
ISTD. Hides the chromatogram trace edited for the target compound and displays the
Manual Integration cursor for defining the ISTD compound peak to be integrated.

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'Deleting peak' button

Deletes the currently displayed target or ISTD compound peak.

'Starting and stopping manual integration mode' buttons

Activates or deactivates the manual integration mode. This mode allows you to manually
integrate compound peaks that were not recognized in the automatic integration process.

'Toggling between files' buttons

Toggles to the previous or to the next data file contained in the open batch file and displays
the results corresponding to the currently selected target compound.

'Toggling between target compounds' buttons

Toggles in the case of a multi-component calibration to the previous or to the next target
compound contained in the target compound list and displays its corresponding data.

'Toggling between auto-scaling and no auto-scaling' buttons

Toggles between auto- scaling and non- auto- scaling of the ordinate in the
Chromatogram view (upper button) or Spectrum view (lower button).
Toggles between auto- scaling and non- auto- scaling of the abscissa in the
Chromatogram view (upper button) or Spectrum view (lower button).

3.3 Calibration window

After you have performed a quantitation, the Calibration window displays the calibration
curve for the active target compound that was calculated from the active calibration points
obtained for this compound. You can change the type of calibration curve to be calculated
or deactivate particular calibration points to exclude them from being used in calibration
curve calculation. In addition, you can change other parameters used to set up the
calibration curve.

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Note If you have made any changes in the parameter settings used for calculating the
calibration curve, the corresponding data is instantly recalculated, and the new
data is displayed both here and in the Work Table.
In addition, if you have performed a quantitation using an ISTD compound, you can display
the corresponding ISTD response data.

Figure 3-4 Calibration window after performing a quantitation: Display of calibration

curve and ISTD data

Calibration view
Displays the individual calibration points for the active target compound and the resulting
calibration curve that is calculated according to the parameters set up for the current
curve. The curve is automatically recalculated if you change one of these parameters.
The calibration points are displayed as filled black points ( ) or as filled white points ( ) if
there were multiple injections of a sample and QuantAnalysis calculates averaged
calibration points. You can exclude a calibration point from being used in the calibration
curve calculation by disabling it. Disabled points are indicated by an open circle ( ) instead
of the filled point. If necessary, you can re-enable a disabled calibration point and include it
back in the calibration curve set up.

When you move the mouse cursor near a calibration point, it changes either to or to

depending on whether the point is currently enabled or disabled. Additionally, a data

tip will appear for a few seconds displaying information about the respective calibration
point (calibration level, accuracy, theoretical concentration).
Depending on the current settings in the Calibration window, other data may be displayed
in the Calibration view if the corresponding buttons (see below) are activated:

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l The current calibration coefficients are shown when the Show Coefficients button is
active.
l If you have performed a quantitation with an internal standard, the integration results for
the ISTD compound are displayed as green squares ( ) when the Show ISTD Areas
button is active. A green line in the middle of the view marks the averaged integration
result. Additional green lines above and below denote the limits of single ('+1σ', '-1σ')
and triple ('+3σ', '-3σ') standard deviation from the value.
Note It may happen that a standard deviation line is not shown since it is outside the
view.
l If you have defined QC samples, the corresponding results are displayed as blue
rhombs ( ) when the Show QC Samples button is active.
l If a QC sample is located in the batch file between the data files of calibration samples,
the calibration files are separated into two blocks and QuantAnalysis calculates a
separate calibration curve for each block separately . You can toggle between the
different calibration curves for a target compound using the Next Block and Previous
Block buttons, which in this case will be active.
You can adjust the display range of the Calibration view.
(Target compound list)
Displays the selected target compound whose calibration data is displayed in the
Calibration view.
In the case of a multi-component quantitation, click to select the target compound

whose calibration curve you wish to display from this list or use and

.
(ISTD compound)
Displays the ISTD compound assigned to the selected target compound. The calibration
points calculated for this ISTD are displayed in the Calibration view as dark green squares.
Curve Fit
This parameter sets the type of calibration curve to be calculated for the selected
compound. To change the curve fit, select another option from this list.
Average RF. Mean "Response Factor" (RF).
Linear. Linear equation.
Quadratic. Quadratic equation.
Cubic. Cubic equation.

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Clicking applies the current Curve Fit setting for the selected compound to all
compounds.
Origin
This parameter sets how the point of origin (data point 0;0) will be included in calibration
curve calculation of the selected compound. To change the mode of origin, select another
option from this list.
Exclude. Calculates the calibration curve only from the data points.
Include. Calculates the calibration curve from the data points and the point of origin.
Force. Calculates the calibration curve from the data points and forces it through the
point of origin.
Clicking applies the current Origin setting for the selected compound to all
compounds.
Weighting
This parameter sets how the data points will be weighted in calibration curve calculation of
the selected compound. To change the weighting of calibration points, select another
option from this list. The following weightings are possible: None (Default), 1/X, 1/X^2,
1/Y, 1/Y^2, In-In, log-log.
Clicking applies the current Weighting setting for the selected compound to
all compounds.
'Toggling between target compounds' buttons

Toggles in the case of a multi-component calibration to the previous or to the next target
compound in the compound list of the currently selected data file and displays the
corresponding data.
'Toggling between blocks' buttons

Toggles in the case of a multiple calibration curve setup between the calibration curves
calculated for the previous and the next block of calibration samples for the selected target
compound.
'Showing specific data' buttons
Activating one of these buttons (button becomes pressed) results in the corresponding
data being displayed in the Calibration view

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Toggles between displaying and not displaying the current calibration

coefficients.

This tool is not yet implemented.

This tool is not yet implemented.

Toggles between displaying and not displaying QC sample data.

Toggles between displaying and not displaying ISTD data and areas.
'Changing scaling' buttons

Increases the Calibration view's ordinate and abscissa scaling by a factor of 5 each
time you click this button (e.g. if abscissa and ordinate each display a range from 0 to
10, then clicking this button once results in abscissa and ordinate becoming re-
scaled to only display a range from 0 to 2).

Decreases the Calibration view's ordinate and abscissa scaling by a factor of 5 each
time you click this button.

Resets a changed Calibration view's ordinate and/or abscissa scaling to full display
of all data.

3.4 Nested display of windows

In the Nested display mode, the Work Table, Chromatogram/Spectrum and Calibration
windows are nested together and displayed simultaneously. You can adjust the Nested
display, and therefore the data currently shown, by dragging the corresponding window
borderlines.
Note After the first start of QuantAnalysis the Nested display may seem to show only one
of these three windows. In this case, rearrange the borderlines to an appropriate
view.

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3.5 Customizing the user interface

3.5.1 Modifying the Work Table layout

The layout of the Work Table can be adjusted for the kind of quantitation you want to
perform. Various standard layouts set up for external and internal quantitation tasks are
available. Additionally, you can create your own layouts optimized for a specific kind of
quantitation, which you can save and reload anytime you are going to do this kind of
quantitation.

[Link] Hiding a Work Table column

You can hide a Work Table column you currently do not need for the quantitation you wish
to perform. Using multiple selection, you can hide multiple columns at once.
Note Make sure that the columns Sample Type and Calib Level are always displayed.

To hide a single column:

1. Click on the header of the desired column.
2. Click .
To hide a series of neighboring columns:
1. Do one of the following:
l Hold down the Shift key and click the headers of the first and last columns in the

desired series.
l Position the mouse cursor on the header of the first column in the desired series

and drag it, with the left mouse button held down, to the header of the last column.
2. Click .
To hide multiple individual columns:
1. Hold down the Ctrl key and click the headers of each desired column.
2. Click .

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[Link] Showing a hidden Work Table column

You can show a currently hidden Work Table column again.

To show a hidden column:

1. Click . A drop-down field appears listing all currently hidden Work Table
columns.
2. Click the desired column name. This displays the respective column

[Link] Changing the width of a Work Table column

You can change the current width of a Work Table column e.g., if an entry is not shown in
full length.
To change the width of a column:
1. Position the mouse cursor on the left or right border of the desired column head to
display the Column Width cursor .
2. Drag the border with the left mouse button held down until the desired width is
reached.

[Link] Saving a Work Table layout

The current layout of the Work Table can be saved, e.g. after you have optimized it for a
particular kind of quantitation. This allows you to select this Work Table layout whenever
you want to perform this type of quantitation. Work Table layout files are saved in the
QuantAnalysis Layout File format (*.qal).
To save the current Work Table layout:

1. Click . This opens the Save Work Table Layout dialog for saving a
layout file. The QuantLayouts folder opens by default.
2. If you do not want so save the layout in the default folder, navigate to that drive and
folder in which you want to store the layout file.
3. Depending on whether you want to save the layout under a new or an existing file
name, do one of the following:
l If you want to save the layout file under a new name, enter the new name in File

name
l If you want to save the layout file under an existing name, select this name from the

folder list.

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4. Click Save.

[Link] Selecting a Work Table layout

You can select a Work Table layout suitable for the kind of quantitation you want to
perform. This can be one of the standard layouts available for external or internal standard
quantitation tasks or a self-created layout. Loading another layout changes the current
Work Table layout according to the settings of the new layout. Work Table layout files are
saved in the QuantAnalysis Layout Files format (*.qal).
To select a Work Table layout:

1. Click . This opens theSelect Work Table Layout dialog for selecting a
file of the *.qal format. The QuantLayouts folder opens by default.
2. If the layout file you want to load is not contained in the QuantLayouts folder, navigate
to the folder that contains the desired file.
3. Double-click the desired layout file or select the desired layout file and click Open.

3.5.2 Changing data display ranges

The display range of the Chromatogram and Spectrum views of the
Chromatogram/Spectrum window and of the Calibration view of the Calibration window
can be adjusted.

[Link] Changing the display range of the Chromatogram and Spectrum

views

You can adjust the display range of the Chromatogram or Spectrum view in the
Chromatogram/Spectrum window to the optimal display of the data you are interested in.
You can toggle the ordinate and abscissa between auto-scaling and no auto-scaling: auto-
scaling means that the display range of an axis is automatically adjusted to display the
maximum measured values. If auto- scaling is disabled, the first displayed data or the
scaling that was used at the moment of auto-scaling deactivation specifies the display
range for the subsequently displayed data. Whether auto-scaling of an axis is enabled or
not, you can see from the status (pressed or released) of the corresponding auto-scaling
button.
In addition, you can displace, increase or decrease the display range of ordinate or
abscissa and, if desired, reset a changed scaling to full display of data.

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To toggle between auto-scaling and no auto-scaling of ordinate or abscissa:

1. Click or that corresponds to the axis you wish to toggle to auto-scaling or no
auto-scaling.
To displace the display range of ordinate or abscissa:
1. Position the mouse cursor left of the ordinate or below the abscissa to display the
Vertical or Horizontal scaling cursor.
2. Drag the cursor with the left mouse button held down either right, left, up, or down until
the respective axis is displaced as desired. Then release the mouse button. During
dragging, the scaling and the values displayed are continuously updated to show the
effect of displacement.
To increase or decrease the display range of ordinate or abscissa:
1. Position the mouse cursor left of the ordinate or below the abscissa to display the
Vertical or Horizontal scaling cursor.
2. Drag the cursor with the right mouse button held down either downwards, to the left
(for increasing), upwards or to the right (for decreasing), until the desired display
range is reached. Then release the mouse button. During dragging, the scaling and
the values displayed are continuously updated to show the effect of the changes.
To reset a changed ordinate or abscissa scaling to full display of data:
1. Position the mouse cursor left of the ordinate or below the abscissa to display the
Vertical or Horizontal scaling cursor and double-click the left mouse button.
This resets the axis.

[Link] Changing the display range of the Calibration view

You can adjust the display range of the Calibration view in the Calibration window to the
optimal display of data you are interested in. You can change the ordinate and abscissa
scaling either continuously by using the mouse or by predefined steps using the
appropriate buttons. By using the mouse you can independently adjust the display range
of the ordinate and abscissa.
To displace the display range of the ordinate or abscissa:
1. Position the mouse cursor left of the ordinate or below the abscissa to display the
Vertical or Horizontal scaling cursor.

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2. Drag the cursor with the left mouse button held down either to the right, left, up, or
down until the axis is displaced as desired. Then release the mouse button. During
dragging, the scaling and the values displayed are continuously updated to show the
effect of displacement.
To continuously increase or decrease the display range of ordinate or abscissa:
1. Position the mouse cursor left of the ordinate or below the abscissa to display the
Vertical or Horizontal scaling cursor.
2. Drag the cursor with the right mouse button held down either downwards, to the left
(for increasing), upwards or to the right (for decreasing), until the desired display
range is reached. Then release the mouse button. During dragging, the scaling and
the values displayed are continuously updated to show the effect of the changes.
To increase or decrease the display range of ordinate and abscissa in defined
steps:
1. Do one of the following:

l Click to increase the display range of ordinate and abscissa by a factor of 5.

l Click to decrease the display range of ordinate and abscissa by a factor of 5.

To reset a changed axis scaling to full display of data:
1. Do one of the following:
l Position the mouse cursor left of the ordinate or below the abscissa to display the

Vertical or Horizontal scaling cursor and double-click the left mouse

button. This resets the axis.

l Click . This resets both ordinate and abscissa.

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4 Creating and managing batch files

4.1 Creating a batch file

To perform a quantitation, first you have to create a Batch Files format file (*.btc) file, which
must contain all the data files that have been acquired from the various calibration and
"unknown" sample solutions. Optionally, a batch file can contain further data files from
quality control and/or blank samples. Additionally, the batch file must contain specific
information about the data files including their sample type, calibration level, and
calibration action.
How you create a batch file depends on how the data files to be used in quantitation were
acquired. Data acquisition can be done within a sample table set up in either the Bruker
Compass HyStar or the Agilent ChemStation application. In this case, you can import the
respective sample table with automatically entering some of the data required for batch
creation in the QuantAnalysis Work Table. Alternatively, you can use a series of
individually acquired data files; in this case, you have to enter all data required manually.
QuantAnalysis can handle data files obtained by multiple injections of the same sample.
The program identifies such samples by having the same calibration level but different
injection numbers.
Furthermore, QuantAnalysis allows set up of separate calibration curves for different
sample series with e.g. different matrices but the same target compound in one batch
sequence. This requires the respective data files to be entered in the batch file as separate
blocks.
Once a batch file has been set up, you can create or open a quantitation method suitable
for processing the respective batch file and then process the batch file.

4.1.1 Creating a batch file from a sample table

A batch file can be created from an Agilent ChemStation sample table stored in Comma
Separated Values Files format (*.csv) or a HyStar sample table extract stored in HyStar
Sample Table Extract format (*.seq). You can import the respective sample table into
QuantAnalysis, enter additional information required to perform a quantitation and save
the data as a batch file (*.btc).
You can import the sample table into a new (untitled) batch file or an existing batch file that
already contains a sample table. In the latter case, you have the choice between

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appending the new sample table to the existing one, and replacing the existing by the new
one.
Note To import a sample table in an existing batch file the respective batch file must be
open and unprocessed.
On importing a sample table, specific information is automatically entered in the Work
Table. This includes the names of the data files in the sample table, corresponding sample
names, vial positions, and injection volumes. The resulting batch file automatically gets a
name, which depends on how the sample table is imported. If the sample table is imported
in an existing batch file with the Append option set, the name of the batch file is not
changed. If it is imported with the Replace option set, the batch file gets the name of the
imported sample table with the extension changed to *btc. The same applies to a sample
table that is imported in a new (untitled) batch file. You can change this name, if desired.
To perform quantitation, QuantAnalysis needs additional information, which you have to
enter manually, e.g. the sample type and calibration level for each data file used. After
entering all necessary and any additional information in the Work Table, review the Work
Table. Check that the entries in the File Name , Sample Name, Sample Info, Vial ,
Method Name, Inj. Vol., and Sample Type columns are complete. After processing the
batch file these columns cannot be edited again so that changes you try to make in these
fields will be ignored. If you notice a mistake in one of these particular fields after batch
processing, you can reset the Work Table to the situation before processing.
To create a batch file from a sample table:
1. Click the Work Table tab to switch to full-screen display for the Work Table.
2. Depending on whether you want to import the sample table in a new (untitled) or an
existing batch file, do one of the following:
l If you want to import it into a new batch file while a batch file is already open, select

New from the File menu and, if needed, answer the pop-up confirmation request
on saving the open file. This closes the respective file and clears the Work Table.
l If you want to import it into an existing batch file, open the desired batch file if not

already open.
3. Click to import the sample table from which you want to create a batch
file. This automatically enters specific information stored in the sample table into the
File Name, Sample Name, Sample Info, Vial, Method Name, Inj. Vol, Dil. Factor,
Sample Type, Calib Level, Inj. No., Acq. Date and Operator columns. You have to
check these entries and, if necessary, change them.

4. Click to select a Work Table layout suitable for the type of quantitation
you want to perform. Alternatively, adjust the current Work Table layout accordingly.

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Tip You can save an optimized layout to use it for further quantitations.
5. In the Method Name column, check that a method is assigned to each data file. Within
a batch of files, this method name must be the same for all. Change any differing
method names.
6. In the Inj. Vol. column, check that an injection volume is given for each sample that
must differ from zero. Change incorrect values.
7. In the Dil. Factor column, check that the given dilution factors differ from zero.
Change incorrect values.
8. In the Sample Type column, for each sample define its sample type.
9. In the Calib Level column, for each 'Calib' or 'QC' sample define its calibration level.
In case of multiple injections of the same sample, you must assign the same calibration
level to these samples.
Note In the actual software version, the concentrations belonging to the different
calibration levels have to be defined later during creating the quantitation
method.
10. In the Inj. No. column, check that the given numbers differ from zero and change
incorrect values.
In case of multiple injections of the same sample QuantAnalysis, on importing a
sample table, only reads the total number of injections for the same sample and
therefore sets all Inj. No. fields belonging to the same sample to this total number, e.g.
'3'. You have to change these fields manually to '1', '2', and '3' for the corresponding
data files having the same Calib Level.
11. After entering all necessary and any additional information in the Work Table, review
the Work Table. Check that the entries in the File Name, Sample Name, Sample
Info, Vial, Method Name, Inj. Vol., and Sample Type columns are complete. After
processing the batch file, these columns cannot be edited anymore so that changes
you try to make in these fields will be ignored.
Note If you notice a mistake in one of these particular fields after batch processing,
you can reset the Work Table to the situation before processing and repeat the
respective entries.
12. Check that all data files belonging to 'Calib' type samples are placed together within
the sequence of the batch, as it is needed for the calibration curve setup you wish to
perform.
Please consider to the following fact: The program will calculate separate calibration
curves if more than one block of 'Calib' type samples exist, separated within the
sample by a 'Sample', 'QC' or 'Blank' type sample. This means:

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l If the calibration points from all 'Calib' type samples contained in a batch should be
entered into one calibration curve, then all 'Calib' type samples must be entered as
one block (e.g. see the example below: all 'Calib' samples have been entered as
one block consisting of the rows 2 to 5). This means e.g., if you want to do an
external calibration and you have done alternating runs of unknown and calibration
samples you cannot enter the files in the same order as you have run them.
Therefore, after importing the sample table you must sort all 'Calib' type samples
within one block.
l If more than one calibration curve should be setup for a batch, the respective 'Calib'

type samples must be placed into different blocks, which must be separated by at
least one 'Sample', 'QC' or 'Blank' type sample. This will be necessary e.g. if you
want to quantify different sample series with e.g. different matrices but the same
target compound in one sample.
You can rearrange the data files within the sample, if necessary, by moving the Work
Table rows accordingly.
13. Check that within the Work Table there are no rows left blank since QuantAnalysis
considers the first row that contains no File Name entry to be the end of the batch. If
there are blank rows, delete them.
14. Save the batch file using either the Save or the Save As command from the File
menu.
Note Batch file saving can be performed even earlier within this procedure. In this
case, afterwards continue filling the Work Table and save the modified batch
file again.

The following example shows an Agilent ChemStation sample table imported into
QuantAnalysis. In the upper figure, you can see the Work Table entries automatically
made on importing the sample table. The lower figure shows the Work Table as finally set
up. The respective sample consists of four standard solutions containing the target
compound, Alprazolam d0, at concentrations of 2, 10, 20, and 100 pg/µl, and the ISTD
compound, Alprazolam d5 (penta-deuterated derivative), at a constant concentration of 10
pg/µl. Two solutions containing 5 or 50 pg/µl d0 and 10 pg/µl d5 function as "unknown"
samples. Additionally, three injections of a blank solution were used.

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Figure 4-1 Work Table entries automatically filled in by importing an Agilent

ChemStation sample table (example)

Figure 4-2 Finally set up Work Table as needed for processing the batch file created
from the imported Agilent ChemStation sample table (example)

4.1.2 Importing a sample table

You can import an Agilent ChemStation sample table stored in Comma Separated Values
Files format (*.csv) or a HyStar sample table extract stored in HyStar Sample Table Files
Extract format (*.seq) into QuantAnalysis in order to create a batch file for this sample. You
can either set up a new batch file for the respective sample table. On the other hand, you
can append the sample table to a sample table already contained in the loaded batch file or
replace the sample table present by the imported one.
Note To import a sample table into an existing batch file the respective batch file must be
open and still unprocessed.
On importing the sample table, all data files this sample consists of and the corresponding
sample data already contained in the sample table are automatically entered in the Work

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Table of the new created or existing batch file. The resulting batch file automatically gets a
name, which depends on how the sample table is imported. If the sample table is imported
into an existing batch file with the Append option set, the name of the batch file is not
changed. If it is imported with the Replace option set, the batch file gets the name of the
imported sample table with the extension changed to *btc. The same applies to a sample
table, which is imported into a new (untitled) batch file regardless of whether Append or
Replace is set.
To import a sample table:
1. Depending on whether you want to import the sample table into a new (untitled) or an
existing batch file, do one of the following:
l If you want to import it into a new batch file while a batch file is already open, select

New from the File menu and, if needed, answer the pop-up confirmation request
on saving the open file. This closes the respective file and clears the Work Table.
l If you want to import it into an existing batch file, open the desired batch file if not

already open.
2. Click . This opens theImport Sample Table dialog.
3. Select the type of sample table files to be shown in the folder list.
4. Navigate to that folder that contains the sample table you want to import.
5. If a batch file is open, select how to proceed with the sample table when importing it.
This setting is of no importance if the sample table should be imported into a new batch
file.
l Select Append, if the imported sample table should be appended to the present

one.
l Select Replace, if the imported sample table should replace the present one.

6. Double-click the desired sample table or select it and click Open.

7. Save the resulting batch file under a desired file name.

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4.1.3 Creating a batch file for a set of individually acquired

data files
You can also create a batch file for a set of individually acquired data files, which must be
contained in the same directory.
In contrast to creating a batch file from a sample table file, it is not possible to import data in
the Work Table. Thus, you have to enter all necessary information manually. However,
you can make your work easier e.g. by copying Work Table entries multiple times using
either copy and paste or performing an 'Excel-like fill' of columns.
After entering all necessary and any additional information in the Work Table, review the
Work Table. Check that the entries in the File Name, Sample Name, Sample Info, Vial,
Method Name, Inj. Vol., and Sample Type columns are complete. After processing the
batch file these columns may not be edited anymore so that entries you try to make in
these fields will be ignored. If you notice a mistake in one of these particular fields after
batch processing, you can reset the Work Table to the situation before processing.
To create a new batch file:
1. Click the Work Table tab to switch to full-screen display for the Work Table.
2. If a batch file is already open, selectNew from the File menu and, if needed, answer
the pop-up confirmation request on saving the open file. This closes the respective file
and clears the Work Table.

3. Click to select a Work Table layout suitable for the type of quantitation
you want to perform. Alternativelyadjust the current Work Table layout accordingly.
Tip You can save an optimized layout to use it for further quantitations.
4. In the File Name column, enter the names of the individual data files. Make sure that
all data files needed are copied into the same directory.
Note The file names must be entered together with the file extension.
In placing 'Calib' type samples within the sequence of a batch, please consider the
following fact: the program will calculate separate calibration curves if more than one
block of 'Calib' type samples exist, separated within the sample by a 'Sample', 'QC' or
'Blank' type sample. This means:
l If the calibration points from all 'Calib' type samples contained in a batch should be

entered into one calibration curve, then all 'Calib' type samples must be entered as
one block (e.g. see the example below: all 'Calib' samples have been entered as
one block consisting of the rows 1 to). This means e.g., if you want to do an external
calibration and you have done alternating runs of unknown and calibration samples
you cannot enter the files in the same order as you have run them. You must sort

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them accordingly.
l If more than one calibration curve should be setup for a batch, the respective 'Calib'

type samples must be placed into different blocks which must be separated by at
least one 'Sample', 'QC' or 'Blank' type sample. This will be necessary e.g. if you
want to quantitate different sample series with e.g. different matrices but the same
target compound in one sample.
You can rearrange the data files within the sample if required, by moving the Work
Table rows accordingly.
5. In the Sample Info column, enter that sample information that corresponds to the
respective data file.
6. In the Method Name column, check that a method is assigned to each data file. Within
a batch of files, this method name must be the same for all. Change any differing
method names.
7. In the Inj. Vol. column, enter the injection volumes. They must differ from zero.
8. In the Dil. Factor column, enter the dilution factors. They must differ from zero.
9. In the Sample Type column, select for each sample its sample type.
10. In the Calib Level column, select for each 'Calib' or 'QC' sample its calibration level.
In case of multiple injections of the same sample, you must assign the same calibration
level to these samples
Note In the actual software version, the concentrations that belong to the different
calibration levels have to be defined later during creating the quantitation
method.
11. In the Inj. No. column, enter the corresponding injection numbers.
12. After entering all information that is necessary, or that you want to see additionally in
the Work Table, review the Work Table. Check that the entries in the File Name ,
Sample Name, Sample Info, Method Name, Inj. Vol., and Sample Type columns
are complete. After processing the batch file, these columns cannot be edited
anymore so that changes you try to make in these fields will be ignored.
Note If you notice a mistake in one of these fields after batch processing, you can
reset the Work Table to the situation before processing and alter the respective
entries.
13. Check that within the Work Table there are no rows left blank since QuantAnalysis
considers the first row that contains no File Name entry to be the end of the batch.
Delete blank rows if existing.
14. From the File menu, select Save As and save the entries in a new batch file.

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Note You can save and, therefore, create the batch file even earlier within this
procedure. In this case, afterwards continue filling the Work Table and save the
modified batch file using the Save command from the File menu.

Figure 4-3 Batch file for a set of individually acquired data files created by manually
entering data

4.2 Filling and manipulating the Work Table for a

batch file
Before processing a batch file, the Work Table must be filled with all data that is needed for
performing the respective quantitation. Which data actually has to be entered depends on
the type of quantitation to be performed e.g. whether internal standards are used.
Some data can be entered automatically when importing a sample table but all other data
needed for quantitation must be entered manually either by typing in or selecting the
respective data. You can manipulate the Work Table by moving or deleting rows. When a
batch file has already been processed, you can reset the Work Table to its state before
processing.

4.2.1 Filling the Work Table automatically

When a sample table is imported, automatically particular Work Table entries are made by
the program. The corresponding data is stored in the respective sample table, which
includes the names of the data files as well as the corresponding sample names, vial
positions, and injection volumes.
To perform a quantitation, QuantAnalysis needs additional information, which has to be
entered manually e.g. the sample type and calibration level for each data file used.

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4.2.2 Filling the Work Table manually

Depending on whether you create a batch file from a sample table or for a set of
individually acquired data files you have to enter manually some data needed for
quantitation into the Work Table.
Entering data manually is done by first clicking the desired Work Table field and then either
typing in the respective data (e.g. file name, sample name, etc.) or selecting the desired
option from the corresponding list box (in the case of sample type or calibration action).
You can make your work easier by copying Work Table entries multiple times.

4.2.3 Copying Work Table entries multiple times

You can copy a Work Table entry multiple times by performing an 'Excel-like fill' of a Work
Table column or using copy and paste.
Note This 'Excel-like fill' is only active before the batch file is processed.

To perform an 'Excel-like fill' of a Work Table column:

1. Click the field you want to copy multiple times.
2. Position the mouse cursor on the square in the lower right corner of the field so that it
changes to .
3. Drag the cursor with the left mouse button held down downwards until the desired
number of fields is reached.
4. Release the left mouse button. This results in the marked fields become filled
according to the entry shown in the selected field even if the respective fields already
contain entries. In case of the Vial column, the vial numbers will be incremented
automatically. This is also the same for the File Name column when the selected file
name contains a number.

Figure 4-4 'Excel-like fill' of the File Name column

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To perform copy and paste:

1. Click the field whose contents you want to copy. This selects the respective entry.

2. Click or select Copy from the Edit menu. This copies the selection and puts it
onto the clipboard.
3. Click the field in which you want to paste the copied entry.

4. Click or select Paste from the Edit menu. This inserts the current clipboard
contents in the selected field.

4.2.4 Moving a row within the Work Table

You can move a row in the Work Table up or down in order to sort the Work Table.
To move a Work Table row:
1. Position the mouse cursor in the number field of the row you want to move so that the
Select Row cursor appears and click the left mouse button. This selects the
respective row.
2. Position the mouse cursor on the number field and with the left mouse button held
down drag the cursor up or down to the desired new position. During dragging, the
current insertion position that the selected row will be moved to is indicated by a red
line. On releasing mouse button, the row is moved to the selected new position.

Figure 4-5 Moving a Work Table row upwards by one position

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4.2.5 Deleting a row from the Work Table

You can delete a row from the Work Table. This must be done e.g. in case you have left a
row blank within a batch (because the first row that contains no entry in the File Name
field is considered to be the end of the batch), or if you have entered a sample by mistake
which should not be contained in a batch file to be created.
Using multiple selection, you can delete multiple rows at once. All entries currently
contained in the selected row(s) are removed from the Work Table.
To delete a single row:
1. In the Work Table, click the number field of the row you wish to delete. This selects the
respective row.
2. Click .
To delete a series of neighboring rows:
1. Do one of the following:
l Hold down the Shift key and, in the Work Table, click the number fields of the first

and last row in the desired series.

l Position the mouse cursor on the number field of the first row in the series and drag

it with the left mouse button held down to the number field of the last row.
2. Click .
To delete multiple individual rows:
1. Hold down the Ctrl key and, in the Work Table, click the number fields of each desired
row.
2. Click .

4.2.6 Resetting the Work Table

You can return the Work Table of an already processed batch file to its state before
processing. This allows you to correct a mistake in the Work Table after processing the
respective batch file and then repeat processing.
When resetting the Work Table, all data entered during batch processing is cleared from
the table and those columns which after batch processing cannot be edited anymore are
released for being edited again.

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To reset the Work Table:

1. Click .

4.2.7 Defining sample parameters

For performing a quantitation, you have to define specific sample parameters for the data
files (samples) involved.
First you must define the sample type, i.e. you have to select whether a respective data file
should serve either as a sample to be quantified, as calibration sample, as a quality control
sample or as a blank sample.
Depending on the sample type you have assigned to a data file, you may further define the
corresponding calibration level and calibration action.

[Link] Defining the type of a sample

QuantAnalysis can handle four different sample types:

l 'Sample' "Unknown" sample that is to be quantified.
l 'Calib' Sample of known concentration that is used to set up a calibration curve.
l 'QC' Quality control sample that is used to validate the calibration curve.
l 'Blank' Blank sample that is used for system control.
By default, the sample type is set to Sample. When you wish to assign another type to a
sample, select it from the corresponding list.
To select the type of a sample:
1. In the Work Table's Sample Type column, click the field that corresponds to the
sample whose sample type you want to define. A drop-down button appears.
2. Click the drop-down button to open the sample type list.

3. Click the desired sample type.

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[Link] Defining the calibration level of a calibration or quality control

sample

You can define the calibration level of a calibration ('Calib') or quality control ('QC')
sample. The program uses this level to read the corresponding concentrations from the
table defined in the quantitation method in the Method Editor's Target Compounds
dialog.
In case of multiple injections of the same sample, QuantAnalysis identifies such samples
from the entries in the Calib Level and Inj. No. columns.
The calibration level can be given in arbitrary units (e.g. 1, 2, 3, ...) or in the case of quality
control sample as text (e.g. low, medium, high ...).
To define the calibration level of a sample:
1. In the Work Table's Calib Level column, click that field that corresponds to the
calibration or quality control sample whose calibration level you want to define.
2. Enter the desired calibration level as either arbitrary unit (1, 2, 3 ...) or text (for quality
control samples, only).

4.3 Saving a batch file

You can save a not yet processed or an already processed batch file to the Batch Files
format (*.btc). For an unprocessed batch file, the corresponding Work Table is saved
whereas for an already processed batch file, the quantitation method used and the
quantitation results obtained are also saved in the batch file.
When creating a new batch file you have to save the new file. Use the Save As command
from the File menu and select an already existing or a new file name. Later changes made
to this batch file can be saved using the Save command from the File menu.
Note The batch file has to be saved to that folder that contains the data files to be
quantified.
Saving a batch file under a new file name will result in a subfolder with the specified batch
file name being set up in the chosen target folder and a corresponding result file being
saved to this batch folder. In the following, each saving operation you perform on this batch
file will result in a new, additional result being stored to this batch file folder. Existing result
files are not overwritten. The batch file folder contains all result files currently available for
the respective batch file as well as further corresponding files.

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Automatic batch saving will be performed only before the process operation really starts.
In case of a still unprocessed batch file, the Save Batch dialog will appear automatically to
select a file name for saving the batch. This allows you to save the processed batch file
under another file name while keeping the original batch file unprocessed. If you process
an already processed batch file again, the batch file will automatically be saved under the
same file name. Moreover, if you want to close QuantAnalysis or open another or a new
batch file, the program will ask you about saving yet unsaved changes made to the
currently open batch file.
To save a batch file using a new or already existing name:
1. From the File menu, select Save As. This opens the Save Batch dialog.
2. Navigate to that folder that contains the data files to be quantified.
3. Depending on how you want to save the batch file, do one of the following to specify its
file name:
l To save under a new name, enter the desired name in File name.

l To save under an existing name, enter the name in File name or select it from the

folder list.
4. Click Save
5. If you have selected an already existing file name, affirm the appearing confirmation
request on overwriting the existing file.
6. Completing the Save Batch dialog results in saving the batch file under the specified
name. In case this dialog has appeared automatically after starting batch processing,
the respective batch file is first processed and then saved.
To save a batch file using the same name:

1. Click or . Alternatively, select Save from the File menu.

4.4 Opening a batch file

QuantAnalysis uses Windows conventions for opening batch files. You can open a batch
file from either within QuantAnalysis or Windows Explorer. QuantAnalysis supports the
drag-and-drop functionality, i.e. you can open a batch file by dragging its file name from
Windows Explorer into the QuantAnalysis window.
QuantAnalysis writes a new, additional result file on each saving operation you perform on
a batch file. Thus, for each batch file one or several result files are available. If more than
one result is available for the batch file you want to open you can select either any of its
previously saved results or the last saved result to be loaded. Only one batch file can be

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open at a time. Loading a previous result is only possible with the Open command from the
File menu. When opening a batch file from Explorer or using the File menu's Recent File
List, always its last saved result is loaded.
If you open an unprocessed batch file, its current processing state displays in the Work
Table window while the Chromatogram/Spectrum window and the Calibration window
are empty. If you open an already processed batch file, all windows automatically show the
respective corresponding data saved in the batch file.
Only one batch file can be open at a time.
To open a batch file from within QuantAnalysis:
1. Start QuantAnalysis.

2. Click or . Alternatively, select Open from the File menu. This opens
the Open Batch dialog.
3. Navigate to that folder that contains the batch file you want to open.
4. Select the desired batch file from the folder list or enter its name in File name.
5. If more than one result is available in the chosen batch file's Result History, and if you
do not want to load the last but a previous result, select the desired result from this list.
Otherwise, the last result is loaded.
6. Double-click the desired batch file or select it and click Open.
Tip You can quickly open a batch file you have recently worked with by clicking the
respective recent file name at the bottom of the File menu. This loads the last
saved result of the selected batch file.
Tip If you want to open another result of the currently open batch file you can also use
the History button in the Work Table window to load it.

To open a batch file from Windows Explorer using drag and drop:
1. Start QuantAnalysis.
2. Start Windows Explorer.
3. Navigate to the folder that contains the batch file you want to open.
4. Click the desired batch file and drag it with the left mouse button held down in the
QuantAnalysis window. Then release the mouse button. This loads the last saved
result of the selected batch file.

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4.5 Showing the result history of a batch file

You can show the result history for the open batch file. Depending on whether
QuantAnalysis is running in Non-Compliance or Compliance mode, the Result History
dialog displays different information and allows for different operations. Generally, all
results that have been saved since batch file creation are listed along with corresponding
information about saving date and time, operator who saved as well as whether or not a
result was deleted. When in Compliance mode, also information about already signed
results is displayed. An arrow indicates the currently loaded result.
From the Result History dialog, you can load or delete a certain result. When
QuantAnalysis is running in Compliance mode, you can also sign a certain result.
To show a batch file's result history:

1. In the Work Table window, click . This opens theResult History dialog.
2. To return to the Work Table window, click Close.

4.6 Signing a result of a batch file electronically

When QuantAnalysis is running in Compliance mode, an electronic record (= result of a
batch with corresponding method) of the open batch file can be signed electronically.
Electronic signatures consist of operator ID and operator password. Only operators who
have received from their UserManagement administrator the right to sign electronic
records can sign. Multiple signing of results is allowed.
To sign a result there is no need for the signing operator to be logged into DataAnalysis.
Thus, even if currently an operator is logged in who does not have the right to sign, signing
can be performed without a previous change of the operator.
Already signed results are indicated in the batch file's result history by a 'yes' under
Signed. This applies to the Result History dialog as well as to the result history list
displayed in the Open dialog provided that QuantAnalysis is currently run in Compliance
mode.
To sign a result of a batch file:

1. In the Work Table window, click . This opens the Result History dialog.
2. From the result list, select the result you want to sign.
3. Click Sign. This opens the Sign Electronic Record dialog.
4. In Operator, enter the operator ID.

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5. In Password, enter the corresponding password.

6. In Meaning, enter the meaning of this signing, if desired.
7. Click Sign. If operator ID and password meet, and the respective operator has the
right to sign, the selected result is signed. The Result History dialog returns with a
'yes' being entered for this result under Signed and additional information being
shown by the Signature parameters.
8. To return to the Work Table window, click Close.

4.7 Deleting a result from a batch file

Since QuantAnalysis creates and stores a new, additional result file on each saving
operation you perform on a batch file, several results can be available for one batch file
probably representing different states of the same batch file. Results that are not needed
any longer can be deleted again.
Deleted results will be listed further on in the batch files Result History dialog indicated by
a 'yes' under Deleted but will not appear any longer in the Open dialog.
When QuantAnalysis is running in Compliance mode , only an operator who has the
respective right can perform deleting a result.
To delete a result from a batch file:
1. From the result list, select the result you want to delete.

2. In the Work Table window, click . This opens the Result History dialog.
3. Click Delete.
4. Affirm the appearing confirmation request. This deletes the selected result and enters
a 'yes' for this result under Deleted.
5. To return to the Work Table window, click Close.

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4.8 Showing the audit trail of a batch file

For each batch file the corresponding audit trail is recorded which could be shown when
the batch file is open.
The audit trail lists all changes made to the batch file with corresponding date and time,
who (operator name) made the change and what happened. This includes all changes
that were saved in previous processing of this batch file as well as all current changes
already made during the running processing of this batch even if the changed state has not
been saved yet. When the batch file is closed, only those changes that were saved during
the running processing are stored in the audit trail.
To show the audit trail for the open batch file:

1. In the Work Table window, click . This opens the Audit Trail dialog.
2. To return to the Work Table window, click Close.

4.9 Closing a batch file

You can close an open batch file. Depending on what you intend to do hereafter there are
several ways to close a batch file.
To close an open batch file:
1. To close the open batch file do one of the following:

l Click or select Open from the File menu if you want to open another batch file.

l Click or select New from the File menu if you want to create a new batch file.

l Click if you want to import a sample table for creating a new batch file.
l From the File menu, select Exit if you want to close the current QuantAnalysis
session.
2. In each case, answer the appearing confirmation request on saving the current
processing state of the batch file to be closed.

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5 Creating quantitation methods

Batch files are processed by using a defined quantitation method which is stored in the
QuantAnalysis part of the method embedded in the batch file.
Methods consist of application-specific method parts. Each method contains at least one
method part and each method part can be contained in a method only once. Often,
methods contain several method parts e.g., for data acquisition (e.g. the trapControl part)
and data processing (e.g. the DataAnalysis and QuantAnalysis parts).
To process a batch file the quantitation method needs to contain all information required to
detect the respective target and ISTD compound peaks on the various data files of the
batch and to calculate the corresponding quantitation results. The method defines the
chromatogram trace(s) to be used in peak detection, the target and ISTD compounds
present in the samples, corresponding chromatographic and concentration data, as well
as the integration parameters to be used in peak detection and mass spectrum calculation.
After editing a quantitation method, you can save the parameter settings into a new or an
existing method. As long as you do not save the settings into a method, the settings will be
saved only in the batch file when this is saved. Thus, saving quantitation parameter
settings into a method allows using them for future quantitations making results
comparable. When saving into an existing method, the previous QuantAnalysis part of the
method will be overwritten with the new one. When saving into a new method, the new
created method will contain the QuantAnalysis part only.
In Compliance mode, methods can be saved as SOP or non-SOP methods (SOP =
standard operating procedure) if the UserManagement administrator has turned on SOP
method handling. Methods with an SOP flag cannot be modified. Only operators who have
the special right can mark SOP methods. All operators who are allowed to load methods
can load SOP methods but only operators with a special right can also load non- SOP
methods. The UserManagement administrator can define a default SOP method folder for
saving/loading methods; in this case, operators need a special right to also use non-default
method folders.

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5.1 Creating a quantitation method

You can create a quantitation method to be used in processing the open batch file. After
setting up the method, you can save it as QuantAnalysis processing part into a method
which allows you to use these settings in future quantitations.
In Compliance mode, methods can be saved as SOP or non-SOP methods if SOP method
handling is turned on. Only operators who have the special right can mark methods with
the SOP flag.
A method wizard will guide you through the setup of the quantitation method. During set
up, you have to define general quantitation parameters, the chromatogram trace(s) to be
edited, the target and ISTD compound(s) present, corresponding chromatographic and
concentration data, and the integration parameters to be used for peak detection and
mass spectrum calculation.
To create a quantitation method:

1. Click or . Alternatively, select Edit from the Method menu. This starts
the Method Editor.
2. In the General dialog define general settings. Do the following steps:
a. In Default Injection Volume and Accuracy Limit [%], enter the desired values.
b. Check Apply dilution factor to ISTD compounds, if the dilution factor set in
the Work Table's Dil. Factor column should be also applied to ISTD compounds.
c. Check Load calibration from DataAnalysis results if the mass spectra in an
analysis being loaded in QuantAnalysis should automatically be calibrated using
the calibration coefficients stored in the last DataAnalysis result of the respective
analysis.
3. Click Next.
4. In the Chromatograms dialog define the chromatogram trace(s) for the compound(s)
to be quantified.
a. Define a chromatogram trace by making the corresponding entries in the Type,
Filter, of , Masses , Width , Polarity , Color , Smth Width (Gauss[sec]) and
Cycles boxes.
b. Click Add. This enters the respective trace in Traces.
c. Repeat (a) and (b) for each chromatogram trace you want to use in peak
detection.

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5. Click Next.
6. In the ISTD Compounds dialog define the ISTD compound(s) you want to use in the
respective quantitation. Do the following steps:
Note If no ISTD compound is to be used, skip this dialog and continue with step 8.
a. Define an ISTD compound by making the corresponding entries in Name, CAS
No. (optionally), Chrom. , Retention time [min] , Window [min] , Default
concentration, and Concentration units.
b. Click Add. This enters the respective compound in ISTD Compounds.
c. Repeat (a) and (b) for each ISTD compound you want to use.
7. Click Next.
8. In the Target Compounds dialog define the target compound(s) you want to use in
the respective quantitation.
a. Define a target compound by making the corresponding entries in Name, CAS
No. (optionally), Chrom. , ISTD, Retention time [min], Window [min] , and
Concentration units . In Standard conc. enter the calibration levels and
corresponding concentrations for this target compound in the calibration samples.
b. Click Add. This enters the respective compound in Target Compounds.
c. Repeat (a) and (b) for each target compound you want to use.
9. Click Next.
10. In the Integration Parameters dialog define the parameter settings to be used in
detecting and integrating the respective target and ISTD compound peaks on the
defined chromatogram traces as well as in calculating the corresponding mass
spectra. Do the following steps:
Note Normally, the default values already allow good integration results, but if
necessary the parameters can be given independently for each individual
chromatogram trace. In case there are peaks within the same chromatogram
which differ a lot in width or intensity, it is quite often not possible to integrate all
peaks in a correct way when using only one set of integration parameters.
Optimizing the integration parameters then will minimize the need for manual
integration of peaks after batch processing.
a. In Chromatogram, select the chromatogram trace for which you want to define
the integration parameter settings.
b. Check Apply to all chromatograms if the integration parameter settings should
be applied to all chromatograms.
c. Make the desired entries for the Peak detection and Mass spectrum
calculation parameters.
d. Repeat (a) and (b) for each chromatogram trace defined.

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11. Click Finish. This closes the method editor.

12. Save the quantitation method if you want to use its parameter settings for further
quantitations.

5.2 Saving a quantitation method

You can save a new or modified quantitation method as QuantAnalysis processing part
into a new or existing method. When saved into an existing method, the previous
QuantAnalysis part of the method will be overwritten by the new one. Saving into a new
method will create a new method with only the QuantAnalysis part contained. Saving a
quantitation method into a method allows using its parameter settings in future quantitation
operations.
In Compliance mode, methods can be saved as SOP or non-SOP methods if SOP method
handling is turned on. Only operators who have the special right can mark methods with
the SOP flag. SOP methods cannot be modified. If a default SOP method folder has been
defined, the method must be saved to that default folder except the operator has the right
to use non-default method folders.
To save a quantitation method:
1. From the Method menu, select Save As . This opens the Save QuantAnalysis
Method Part As dialog.
2. Navigate to the folder where the method should be saved. When in Compliance mode
with SOP method handling being turned on and an SOP method folder being defined
this must be the default folder if you do not have the right to use non-default method
folders.
3. Depending on how you want to save the quantitation method, do one of the following
to specify its file name:
l To save it into the method attached to the open batch file or another existing

method, select the respective method from the folder list or enter its name in
Method name. This does not apply to SOP methods.
l To save it into a new method, enter the desired new name in Method name.

4. In Method part name, if desired, enter a name for the QuantAnalysis part. This can
be entered in a sense of a comment. If you do not enter a name, the QuantAnalysis
part will be saved with a part name same as the method name specified.
5. In Comment, if desired, enter a comment for the method. This comment applies to the
entire method, not only to the QuantAnalysis part.

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6. When in Compliance mode with SOP method handling being turned on: Check the
SOP method box if you want to save the method with the SOP flag. This is only
allowed if you have the right to mark methods as SOP.
7. Click Save.
8. If you have chosen an existing file name, confirm the appearing request to overwrite
the QuantAnalysis part of the original method.

5.3 Opening a quantitation method

You can open a quantitation method and attach it to the loaded batch file. This overwrites
the QuantAnalysis processing part of the method currently embedded in the batch file.
When in Compliance mode with SOP method handling being turned on, all operators can
load SOP methods but only operators who have a special right can also load non-SOP
methods. If a default SOP method folder has been defined, only methods placed in that
default folder can be loaded except the operator has the right to also use non- default
method paths.
You can view the parameters settings of the currently open quantitation method after
starting the method editor.
To open a quantitation method:

1. Click or select Open from the Method menu. This opens the Open Method
dialog.
2. Navigate to the folder that contains the method with the desired QuantAnalysis part.
When in Compliance mode with SOP method handling being turned on and an SOP
method folder being defined, you can only load a method placed in that default folder if
you do not have the right to use non-default method folders.
3. Select the method or enter its name in Method name.
4. Click Open.

5.4 Viewing a quantitation method

You can view the parameter settings of the open quantitation method. These are
displayed in the method editor.

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To view a quantitation method:

1. Open the quantitation method you want to view.

2. Click or . Alternatively, select Edit from the Method menu. This starts
the method editor and opens the General dialog.
3. Click Next or Back to browse through the method editor's dialogs and view the
current parameter settings.
4. Click Finish to close the method editor.

5.5 Modifying a quantitation method

You can modify a quantitation method according to your needs by changing its current
settings. When finished, the modified method can be saved as QuantAnalysis part into a
new or an existing method.
When in Compliance mode with SOP method handling being turned on you cannot modify
methods for which the SOP flag is set. Modification is only possible after the SOP flag has
been cleared. This can be done by saving the method without the SOP method option
being set using the same file name.
To modify a quantitation method:
1. Open the quantitation method you want to modify.

2. Click or . Alternatively, select Edit from the Method menu. This starts
the method editor and opens the General dialog.
3. Click Next (and/or Back) to reach the dialog whose current settings you want to
change.
4. Change the current settings as required.
Note Take care, that changes you have made in the Chromatograms , ISTD
Compounds or Target Compounds dialogs must be entered by clicking the
appropriate button (Change or Add) before leaving the respective dialog by
clicking Next or Back. Otherwise these changes will be lost.
5. Click Finish when you have finished modifying the respective method.
6. Save the modified method.

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6 Processing batch files

After creating a batch file and defining the quantitation method to be used with this batch
file you can process the respective batch files.
Processing a batch file means that the data files (analyses) contained in this batch are
processed according to the parameter settings defined in the selected quantitation method
and that the concentrations of the specified target compounds are calculated from the
calibration curves set up.
l When processing starts, QuantAnalysis first evaluates the information and gives an
error message if important information is missing.
l After evaluation, the data files are loaded and analyzed. If the Load calibration from
DataAnalysis results option is set in the method used, the mass spectra in the loaded
analyses will be calibrated using the calibration coefficients stored in the respective last
DataAnalysis result.
l The chromatogram traces specified in the Method Editor's Chromatograms dialog are
created for each data file.
l Compound peaks are detected and integrated accordingly to the settings in the Method
Editor's Target Compounds , ISTD Compounds and Integration Parameters
dialogs.
l Calibration curves are calculated using the calibration levels set in the Work Table and
the corresponding target compound standard concentrations defined in the Target
Compounds dialog.
l From these calibration curves, the target compound concentrations of the unknown
'Sample' samples are calculated and entered in the Work Table.
A green bar at the bottom of the screen shows the progress of this process. The entire
process usually takes only a few seconds.
The quantitation results are automatically saved during data analysis. You can review the
quantitation results and, if required, alter them e.g., by modifying calibration curves or
manually integrating compound peaks. You can plot particular quantitation data, print
specific quantitation reports and export quantitation data to use them in other applications.

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6.1 Processing a batch file

You can process the open batch file according to the current parameter settings defined in
the selected quantitation method and save the quantitation results and the method used
with the respective processed batch file.
When starting batch processing, the respective batch file is automatically saved before
processing starts. For a yet not processed batch file, the Save As dialog will appear which
allows you to save the processed batch file under a new file name and, thus, keep the
original batch file unprocessed for performing further processing operations on it, e.g. by
using another quantitation method. For an already processed batch file no saving dialog
will appear.
Processing a batch file usually takes only a few seconds. A green bar at the bottom of the
screen shows the progress of this process. After processing is finished, you can review the
quantitation results obtained.
To process a not yet processed batch file:
1. Open the unprocessed batch file you want to process.
2. Open the quantitation method you want to use or create a new method.
3. Click .
4. In the appearingSave As dialog, select or enter the file name the processed batch file
should be saved with
Note The batch file must be saved in that folder that contains the data files to be
quantified.
Note This dialog will appear only on processing a not yet processed batch file.
5. Click Save. This starts batch processing.
6. Save the processed batch file.
To reprocess an already processed batch file:
1. Open the unprocessed batch file you want to process.
2. Open the quantitation method you want to use or create a new method.
3. Click . This starts batch processing.
4. Save the processed batch file.

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6.2 Calculation of calibration curves

Calibration curves will be calculated using the following formulae:
Calculation of the theoretical concentration
The theoretical concentration is calculated using the following formula:

With:
: Theoretical concentration calculated and displayed in the Work Table.

: Standard concentration for this level of the target compound entered in the
quantitation method.
: Dilution factor entered in the Work Table.
: Injection volume for this analysis entered in the Work Table.

: Default injection volume entered in the quantitation method.

Calculation of the internal standard concentration

The concentration of the internal standard is calculated in the same way. The dilution
factor is applied only if it is enabled in the quantitation method. This will result in the
following X, Y pairs shown in the calibration plot:

resp. with internal standard calculation.

For calibration mode height (instead of area) the calibration is performed equivalently.
Calculation of the calibration curve
The calibration curve is calculated using these X, Y pairs, resp. the average value for the
same.
Weighting is applied in the calculation of the calibration curve by applying the inverse of the
weight factor as standard deviation at each individual point.
Calculation of the concentration of an unknown sample
The concentration of an unknown sample is calculated by solving the calibration curve with
the area, respectively the height, of the peak. Then the dilution factor and injection volume
is applied using the above equation.

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7 Reviewing calibration and quantitation

results

7.1 Reviewing calibration and quantitation results

of a processed batch file
For reviewing calibration and quantitation results we recommend that you switch to the
Nested display. This shows all results simultaneously displayed in the Work Table window,
Chromatogram/Spectrum window and Calibration window.
Note If necessary, adjust the relative size of the windows by dragging the respective
window borders.

Figure 7-1 Quantitation results obtained for a batch file

Determining which file or target compound is currently active

One of the lines in the Work Table is highlighted in green to indicate that the respective
data file is the "active" (selected) one. The respective Data File name is also displayed at
the top of the Chromatogram/Spectrum window.
The "active" target compound is listed in the Work Table's
as well as under Target Compound in the

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Chromatogram/Spectrum window and in the corresponding list box of the Calibration

window.
The Chromatogram/Spectrum window will display the chromatogram peak and mass
spectrum that corresponds to the currently selected ("active") target compound of the
"active" data file. It also displays the respective ISTD compound peak if an internal
standard was assigned to this target compound. The Calibration window shows the
calibration curve that was calculated for the selected target compound along with
corresponding ISTD and quality control data provided such data are present and their
display is activated.
Toggling between different files and target compounds
You can toggle between different data files or different target compounds. The one
currently selected is the "active" one whose corresponding data is displayed.

Use and from either the Work Table window or the Chromatogram/Spectrum
window to toggle between different data files.

Use and from either the Work Table window,

Chromatogram/Spectrum window or Calibration window to toggle between different
target compounds.

Or use from the Work Table window to select

the desired target compound directly. This is helpful in cases where the quantitation
contains lots of compounds.
Viewing the quantitation data for a target compound
The quantitation data obtained for a target compound is listed in the corresponding
columns of the Work Table window. This includes the retention times and areas of the
target compound peaks, and the calculated concentrations and the accuracy values for the
calibration samples. In case of a quantitation with an internal standard the areas of the
ISTD compound peaks and the area ratios of target and ISTD compound peaks are also
given.
In some instances, no entries are made in one of the data file rows for the calculated area,
concentration, and accuracy for a selected target compound. This indicates that the
respective target compound or corresponding ISTD compound was not found in the peak
integration operation, and the corresponding values could not be calculated. If this occurs,
try to integrate the respective compound manually.
Area values for manually integrated compounds display in blue, accuracy values, which lie
outside the specified accuracy limit, display in red.

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The quantitation data displayed in the Work Table are automatically recalculated when the
corresponding calibration curve is altered or a target or ISTD compound peak is manually
integrated.
You can plot specific quantitation data obtained for the data files of a batch.
Viewing the peak integration results for a target compound
The peak integration results for the selected target compound of the active data file and the
calculated corresponding mass spectrum are displayed in the Chromatogram/Spectrum
window.
If internal standard was assigned to the target compound, its corresponding peak is also
shown in the Chromatogram view. For viewing the corresponding mass spectrum, you
have to select the ISTD for Display MS.
Note We recommend that you check the peak integration results for improperly
integrated peaks. Give special attention to chromatogram traces of the 'Sample'
type. If necessary, correct the integration of a target or ISTD compound peak in the
manual integration mode.
Viewing the calibration curve for a target compound and corresponding ISTD
and quality control data
The calibration curve for the selected target compound is displayed in the Calibration
window.
You can display additional information by activating the following buttons:

Shows the ISTD areas if an internal standard was assigned to the selected
target compound.

Shows quality control samples provided such samples have been defined.

Shows the curve coefficients for the calculated calibration curve.

When setting up multiple calibration curves, use and to

toggle between the calibration curves that were calculated for the previous block and the
next block of calibration samples for the selected target compound.
You can alter the calculated calibration curve for a target compound by disabling
calibration points as well as with respect to its curve fit, mode of origin and/or weighting of
calibration points. Each of these changes will result in recalculating the calibration curve
immediately and redisplaying it. The corresponding quantitation data listed in the Work
Table are recalculated accordingly.

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7.2 Plotting quantitation data of a processed batch

file
You can plot specific quantitation data obtained for the individual data files of a batch file by
plotting the contents of the corresponding Work Table column. This function is restricted to
specific columns.
To plot the contents of a Work Table column:
1. Click the header of the desired Work Table column (e.g. Cal. Conc.).
2. Click . The Plot Column window appears displaying the respective plot.
3. To change the current plot type, click the desired option Bar, Line or Area.
4. Click Close to close the current plot.

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8 Altering quantitation results of a

processed batch file
You can alter the obtained quantitation results after a batch file was processed.
Quantification results can be altered by manually integrating or deleting target or ISTD
compound peaks. The calculated calibration curves can be altered by deactivating single
calibration points or changing their weighting, by changing the curve fit or the mode of
origin. Each of these changes will result in an automatic recalculation the corresponding
quantitation results in the Work Table.
Furthermore, you can reprocess an already processed batch file e.g. with using another
quantitation method.

8.1 Integrating a compound peak manually

You can manually integrate a target or ISTD compound peak that was not recognized
during the automatic integration process performed on the corresponding chromatogram
or which has been improperly integrated. A compound peak that has not been recognized
during automatic integration is indicated in the Work Table by its corresponding Area (or
Height) Target (or ISTD) Cmpd field being left empty.
When the Manual Integration mode is active, manual integration can be performed in the
chromatogram view of the of Chromatogram/Spectrum window. The corresponding
quantitation results are immediately updated in the other windows. Compound peak areas
that were obtained through manual integration are displayed in blue in the Work Table.
To manually integrate a compound peak:
1. Click the Chromatogram/Spectrum tab to switch to full- screen display for the
Chromatogram/Spectrum window.
2. Click to activate the Manual Integration mode. This can
result in the following:
l In the case of a quantitation with internal standard, the chromatogram trace

currently not selected in Integrate (Target or ISTD) is not displayed. If you wish to
integrate this hidden chromatogram, click the corresponding option to display it and
hide the other one.
l For an already integrated peak, its current start and end positions are indicated by

two handles.

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3. Select the data file containing the compound peak to be integrated by clicking or

. The currently active data file is shown right beside File name.

4. Select the compound whose peak you wish to integrate by clicking or

if there is more than one target compound. The currently active target
compound is shown in Target Compound, the corresponding ISTD compound, if
available, in ISTD Compound. This displays the corresponding chromatogram trace
(s) edited for this/these compound(s) in the chromatogram view.
5. Adjust the display range of the chromatogram view to display the peak you are
interested in.
6. Depending on whether the peak you wish to integrate has already been integrated or
not, proceed as follows:
l In the case of an already integrated peak, position the mouse cursor near (3 pixel)

to the handle whose position you want to change so that it changes to . Then
drag the respective handle with the left mouse button held down to the desired
position (data point) and release the mouse button. If desired also change the
position of the second handle.

Figure 7-2 Integrating a compound peak manually

In the case of an unintegrated peak, position the mouse cursor at the beginning of
l

the peak and click the left mouse button. This causes two peak handles to be
displayed. Then drag these handles to desired positions as described above.
The (new) calculated peak area is automatically entered in the corresponding Work
Table field.
7. Repeat steps 3 to 6 for all peaks you want to integrate manually.

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8. Click to deactivate the Manual Integration mode. The peak

handles will disappear and a hidden chromatogram trace is redisplayed.
9. Save the changed processed batch file, if desired.

8.2 Deleting a compound peak

You can delete a target or ISTD compound peak from the open batch file. This removes
the corresponding data from the Work Table and, therefore, from being used in
quantitation. On deleting a peak, all corresponding quantitation results are immediately
updated in the other windows.
Tip If you have deleted a compound peak from a batch file you can include it again in
quantitation by integrating it manually This will add the peak again.
To delete a compound peak:
1. Click the Chromatogram/Spectrum tab to switch to full- screen display for the
Chromatogram/Spectrum window.
2. Select the compound peak you want to delete by displaying it in the chromatogram

view. For this use , , or .

3. Click . This opens the Confirm Delete dialog.
4. In the case of a quantitation with internal standard, select which peak (Target Peak or
ISTD Peak) you want to delete.
5. Click OK.
6. Repeat steps 2 to 5 for all compound peaks you want to delete.

8.3 Altering a calibration curve

You can alter a compound's calibration curves in several ways. Altering the calibration
curve, such as by disabling single calibration points or changing its origin, automatically
results in recalculating and redisplaying the curve. The corresponding quantitation results
are displayed immediately in the Work Table, which is updated accordingly.

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8.3.1 Disabling a calibration point

You can disable individual calibration points on the calibration curve to exclude them from
the calibration curve calculation. An enabled calibration point is displayed as a black point
( ), or in case of an average value from multiple injections, as a white point ( ). In the latter
case, you must disable all calibration points of the respective level individually.
When you disable a calibration point, the current calibration curve is automatically
recalculated and redisplayed, and the Work Table is updated immediately.
To disable a calibration point:
1. In the Calibration window, display the calibration curve you want to alter. To do this,

select the respective target using and . In case of a

multiple injection quantitation, additionally select the respective calibration block using

and .
2. Move the mouse cursor near to the calibration point ( or ) you want to disable so that

it changes to .
3. Click the left mouse button. The black point will turn into an open circle ( ).
4. Save the changed processed batch file, if desired.

8.3.2 Enabling a calibration point

You can re-enable a disabled calibration point and include it again in the calibration curve
calculation. A disabled calibration point is indicated by an open circle ( ).
When you re-enable a previously disabled calibration point, in the current calibration curve
is automatically recalculated and redisplayed, and the Work Table is updated immediately.
To enable a disabled calibration point:
1. In the Calibration window, display the calibration curve you want to alter. To do this,

select the respective target using and . In case of a

multiple injection quantitation additionally select the respective calibration block using

and .
2. Move the mouse cursor near the desired disabled calibration point ( ) so that it

changes to .

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3. Click the left mouse button. The open circle will turn into a filled black point ( ).
4. Save the changed processed batch file, if desired.

8.3.3 Changing the curve fit of a calibration curve

The calibration curve for the selected target compound can be altered by changing the
Curve Fit currently selected. You can choose between Linear,Average RF, Quadratic
or Cubic curve fit.
Changing the curve fit causes the current calibration curve to be automatically recalculated
and redisplayed. The corresponding quantitation results are displayed immediately in the
Work Table Instantaneously, which is updated accordingly.
To change the curve fit of a calibration curve:
1. In the Calibration window, display the calibration curve you want to alter. To do this,

select the respective target using and . In case of a

multiple injection quantitation, additionally select the respective calibration block using

and .
2. From the Curve Fit list box, select the desired fit.
3. Save the changed processed batch file, if desired.

8.3.4 Changing the mode of origin of a calibration curve

The calibration curve for the selected target compound can be altered by changing the
Origin currently selected. You can select between Exclude, Include or Force.
Changing the mode of origin causes the current calibration curve to be automatically
recalculated and redisplayed. The corresponding quantitation results are displayed
immediately in the Work Table Instantaneously, which is updated accordingly.
To change the mode of origin of a calibration curve:
1. In the Calibration window, display the calibration curve you want to alter. To do this,

select the respective target using and . In case of a

multiple injection quantitation, additionally select the respective calibration block using

and .

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2. From the Origin list box, select the desired mode of origin.
3. Save the changed processed batch file, if desired.

8.3.5 Changing the weighting of calibration points

The calibration curve for the selected target compound can be altered by changing the
Weighting currently selected. You can choose between different types of weighting.
Changing the weighting of calibration points causes the current calibration curve to be
automatically recalculated and redisplayed. The corresponding quantitation results are
displayed immediately in the Work Table Instantaneously, which is updated accordingly.
To change the weighting of calibration points of a calibration curve:
1. In the Calibration window, display the calibration curve you want to alter. To do this,

select the respective target using and . In case of a

multiple injection quantitation, additionally select the respective calibration block using

and .
2. From the Weighting list box, select the desired weighting.
3. Save the changed processed batch file, if desired.

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9 Printing and sending reports

Several standard report layouts for printing specific quantitation data are available. They
are installed on your system automatically when you install QuantAnalysis. You can use
these default layouts or you can also create your own layouts using the Bruker Daltonics
ReportDesigner. You can preview a report before printing it to allow you to decide whether
to print it. In addition, you can send a report as an email to a recipient or save it as PDF
document.

9.1 Printing a report

You can print a quantitation report. Several standard report layouts for printing specific
quantitation data are available. All layouts can be printed in portrait and landscape format.
Before printing a report, you can preview it. This allows you to first look at the respective
report and then to decide whether it should be printed.
To print a report with previewing it:

1. Click . This opens the Print dialog.

2. In Name, select the printer you want to use.
3. Click Properties and select in Orientation the format (Portrait or Landscape) you
want to use for printing. If needed, change page set up options. Then click OK.
Note The options available depend on the selected printer.
4. In Instrument, the instrument used is selected by default. If you want to select a report
layout appropriate for another instrument, uncheck Select automatically and select
the desired instrument.
5. In Layout, select the layout for the report you want to print.
6. If you wish to preview the report before printing it, click Preview.
7. To print the report, click OK in the Print dialog, or if in the preview, click the preview's
. This prints the report on the selected printer.

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9.2 Sending a report as email

You can print a selected report to a PDF file and send this as an attachment of an email to
a specified email address. If desired you can preview the report before sending it.
To send a report as email:
1. From the File menu, select Send To and then Mail Recipient. This opens the Send
To Mail Recipient dialog.
2. In Email Address, enter the email address of the recipient to whom you want to send
the report.
3. In Name, select the printer you want to use.
4. Click Properties and select in Orientation the format (Portrait or Landscape) you
want to use for printing. If needed, change page set up options. Then click OK.
Note The options available depend on the selected printer.
5. In Instrument, the instrument used is selected by default. If you want to select a report
layout appropriate for another instrument, uncheck Select automatically and select
the desired instrument.
6. In Layout, select the layout for the report you want to preview.
7. Click Send. This creates the selected report, saves it as PDF document and sends it
to the email address. If no email address is specified, the email program will prompt for
it.

9.3 Sending a report to PDF document

You can to print a selected report to a PDF file and save it to a chosen target folder. If
desired you can preview the report before saving it as PDF document.
To send a report to a PDF document:
1. From the File menu, select Send To and then PDF Document. This opens the Send
To PDF Document dialog.
2. In PDF file name, enter path and name for the PDF document to be saved. To enter
the path, you can click and select the target folder using the appearing dialog.
3. In Name, select the printer you want to use.
4. Click Properties and select in Orientation the format (Portrait or Landscape) you
want to use for printing. If needed, change page set up options. Then click OK.
Note The options available depend on the selected printer.

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Bruker 9 Printing and sending reports

5. In Instrument, the instrument used is selected by default. If you want to select a report
layout appropriate for another instrument, uncheck Select automatically and select
the desired instrument.
6. In Layout, select the layout for the report you want to print.
7. Click Save. This saves the PDF document with the specified file name in the chosen
target folder.

9.4 Creating a custom report layout

The Bruker Compass ReportDesigner application allows you to create your own report
layouts for printing specific reports. You can either modify an existing report layout
available on your system or set up a completely new layout.
Note It is recommended not to modify the standard layout but to save the modified layout
under a new file name. Otherwise, there is a risk that your changed standard layout
version may be overwritten by a later system upgrade.

To start ReportDesigner:

1. Click . This opens the Print dialog.

2. In Report Layout, select the layout based on which you want to create a new layout.
Alternatively, you can select the respective layout in ReportDesigner after it is started.
3. Click ReportDesigner. This starts ReportDesigner and loads the layout currently
selected in Layout.

For help on creating report layouts please refer to the ReportDesigner Help.

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9 Printing and sending reports Bruker

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Bruker 10 Exporting batch files

10 Exporting batch files

You can export the data in the open batch file in Comma Separated Values Files format
(*.csv) to allow you to load the file in Microsoft Excel. The data actually exported depends
on whether the respective batch file has already been processed. Processed batches are
exported in the form of results tables while in unprocessed batches, the sample table is
exported as *.csv file.
To export a batch file:

1. Click . This opens the Export Sample Table dialog for exporting a
Comma Separated Values file (*.csv ).
2. Navigate to that folder the batch file should be exported to.
3. In File name, enter the name of the file you want to export.
4. Click Save.

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10 Exporting batch files Bruker

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Bruker Appendix A — Quick reference tables

Appendix A — Quick reference tables

A.1 QuantAnalysis toolbar

QuantAnalysis 5.0 provides in its toolbar the following buttons:

Button Menu > Command Shortcut Used to ...

File > New Ctrl+N Create a new batch

File > Open Ctrl+O Open an existing analysis.

File > Save Ctrl+S Save active batch using the same file name.

Edit > Cut Ctrl+X Cut the selection and put it onto the
clipboard.
Edit > Copy Ctrl+C Copy the selection onto the clipboard.

Edit > Paste Ctrl+V Paste clipboard contents at selected

position.
Method > Open Open and attach quantification method.

Method > Edit Edit parameters of open quantification

method.
Help > Help Topics F1 Start QuantAnalysis Help.

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Appendix A — Quick reference tables Bruker

A.2 QuantAnalysis menus

QuantAnalysis 5.0 provides the following menus and commands:

File menu Command Used to ...

New Create a new batch.
Open Open an existing batch.
Save Save the active batch using
the same file name.
Save As Save the active batch using
another file name.
Send To popup Send report.
Recent files List the last processed
batches.
Exit Close QuantAnalysis.

Edit menu Command Used to ...

Undo - not yet implemented -
Cut Cut the selection and put it
onto the clipboard.
Copy Copy the selection onto the
clipboard.
Paste Paste clipboard contents at
selected position.

View menu Command Used to ...

Toolbar Show or hide toolbar.

Status Bar Show or hide status bar.

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Bruker Appendix A — Quick reference tables

Method menu Command Used to ...

Open Open and attach a
quantification method.
Save As Save quantification method.
Edit Edit parameters of open
quantification method.

Help menu Command Used to ...

Help Topics Start QuantAnalysis Help.
License Show license information.
Operator Log in specified operator.
Lock All Lock QuantAnalysis and all
Applications other Bruker Compass
applications supporting
Compass Security Pack.
About Compass Show program information.
QuantAnalysis

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Appendix A — Quick reference tables Bruker

A.3 QuantAnalysis shortcuts

QuantAnalysis 5.0 provides the following shortcuts:

Shortcut Menu > Command Used to ...

Alt+F4 File > Exit Close QuantAnalysis.
Ctrl+Alt+K Help > Lock All Lock QuantAnalysis and all other Bruker Compass
Applications applications supporting Compass Security Pack
Ctrl+C Edit > Copy Copy the selection onto the clipboard
Ctrl+N File > New Create a new batch.
Ctrl+O File > Open Open an existing batch.
Ctrl+S File > Save Save the active batch using same file name.
Ctrl+V Edit > Paste Paste clipboard contents at selected position.
Ctrl+X Edit > Cut Cut the selection and put it onto the clipboard.
Ctrl+Z Edit > Undo - not yet implemented -
F1 Help > Help Topics Start QuantAnalysis Help.

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Bruker Index

Mode of origin 77
Index Viewing 29
Calibration levels 52
Calibration points
Disabling 76
A Enabling 76
Agilent ChemStation sample table, Calibration results, reviewing 69
importing 43 Calibration samples 51
Altering Calibration view
Calibration curves 75 Changing display range 37
Processed batch file 73 Description 29
Audit trailing 13 Calibration window 29
Auto-generated operator groups 12 Changing
Calibration curves 75
B Column width 35
Display range of Calibration view 37
Batch files Display range of Chromatogram and
Altering 73 Spectrum views 36
Closing 57 Display ranges 36
Creating 39 Password of operator 15
Creating for set of individually acquired Quantitation methods 64
data files 45 Work Table layout 34
Creating from sample table 39 Chromatogram view
Deleting results 56 Changing display rang 36
Exporting 83 Description 26
Opening 53 Chromatogram/Spectrum window 26
Plotting quantitation data 72 Closing
Processing 65-66 Batch files 57
Result history 55 QuantAnalysis 17
Saving 52 Compliance mode 9
Showing audit trail 57 Compound peaks
Showing result history 55 Deleting 75
Signing results 55 Integrationg manually 73
Bruker Daltonik GmbH 3 Copying Work Table entries 48
Creating
C Batch file for set of individually acquired
data files 45
Calculation of calibration curves 67 Batch file from sample table 39
Calibration curves Batch files 39
Altering 75 Custom report layouts 81
Calculating 67 Quantitation methods 60
Changing curve fit 77 Curve fit 77
Changing weighting of calibration Custom report layouts 81
points 78
Disabling calibration points 76
Enabling calibration points 76

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Index Bruker

D Logging into QuantAnalysis 14

Defining M
Calibration level 52
Sample parameters 51 Manually integrating compound peaks 73
Sample type 51 Menus 86
Deleting Modifying
Compound peaks 75 Quantitation methods 64
Results from batch files 56 Work Table layout 34
Work Table rows 50 Moving Work Table rows 49
Disabling calibration points 76
N
E Nested display of windows 33
Electronic records 13 Non-Compliance mode 9
Electronic signatures 13
Enabling alibration points 76
O
Exporting batch files 83 Opening
Batch files 53
F Quantitation methods 63
Filling Work Table Operator
Automatically 47 Changing password 15
Copying entries 48 Locking 16
Manually 48 Logging in 14
Formulae for calibration curve calculation 67 Unlocking 16
Operator rights in QuantAnalysis 11
H
P
Hiding Work Table colums 34
HyStar sample table extract, importing 43 Peak integration results for target
HyStar sample table extract; importing 43 compound 69
Peaks
I Deleting 75
Integrating manually 73
Importing Plotting quantitation data 72
Sample table 43 Previewing reports 79
Work Table entries 47 Printing reports 79
Installing QuantAnalysis 9 Processing batch files 65-66
Integrating compound peaks manually 73
Q
L
Quality control samples 51
Locking QuantAnalysiis
Bruker Compass applications 16 Electronic records 13
Operator 16 Electronic signitures 13

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Bruker Index

QuantAnalysis Importing 43
Audit trailing 13 Sample type 51
Auto-generated operator groups 12 Saving
Closing 17 Batch files 52
Installing 9 Quantitation methods 62
Locking 16 Work Table layout 35
Logging in 14 Sending reports
Menus 86 As email 80
Operator rights in QuantAnalysis 11 To PDF file 80
Running in Compliance or Non- Shortcuts 88
Compliance mode 9 Showing
Shortcuts 88 Audit trail of batch file 57
Starting 14 Result history of batch file 55
Toolbar 85 Work Table columns 35
Uninstalling 9 Signing results 13
Unlocking 16 Signing results of batch files 55
User interface 19 SOP method handling 59
UserManagement 10 Spectrum view
Quantitation data for target compound 69 Changing display range 36
Quantitation methods Description 26
About 59 Starting QuantAnalysis 14
Creating 60
Modifying 64 T
Opening 63
Saving 62 Toggling between
Viewing 63 Data files 69
Quantitation results, reviewing 69 Target compounds 69
Toolbar 85
R
U
Reports
Creating custom layouts 81 Uninstalling QuantAnalysis 9
Previewing 79 Unlocking
Printing 79 Bruker Compass applications 16
Sending as email 80 Operator 16
Sending to PDF file 80 User interface 19
Resetting Work Table 50 UserManagement 10
Reviewing
Calibration results 69 V
Quantitation results 69
Viewing
Calibration curves 69
S
Peak integration results 69
Sample table Quantitation data 69
Creating batch file from 39 Quantitation methods 63

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Index Bruker

W
Work Table
Changing column width 35
Copying entries 48
Deleting rows 50
Description 20
Filling automatically 47
Filling manually 48
Hiding columns 34
Modifying layout 34
Moving rows 49
Resetting 50
Saving layout 35
Selecting layout 36
Showing columns 35
Work Table window 20

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