USER GUIDE

Clarity Software ENG

Code/Rev.: M021/90H
Date: 2024-05-14

DataApex Ltd.
Phone: +420 251 013 400 Petrzilkova 2583/13
clarity@dataapex.com 158 00 Prague 5
www.dataapex.com Czech Republic
Clarity®, DataApex® and ® are trademarks of DataApex Ltd. Microsoft® and WindowsTM are
trademarks of Microsoft Corporation.
DataApex reserves the right to make changes to manuals without prior notice. Updated manuals can be
downloaded from www.dataapex.com.

Author: DR
User Guide Table of Contents

Contents
1 Installation 1
1.1 Installing Clarity Software 1
1.2 Updating Clarity Software 6
1.3 Installing Colibrick 13
1.4 Installing a Rockey USB dongle 14
1.5 Connecting a chromatograph analogue output to Clarity 16
1.6 Installing Multicom 17
2 Configuring the Chromatography Station 20
2.1 Obtaining information about Clarity configuration 20
2.2 Setting the number and type of instruments 21
2.3 Adding a new device 22
2.4 Configuring a device 24
2.5 Setting the options for sending the method to the instrument 26
2.6 Assigning digital input and output to start acquisition 27
2.6.1 Data Inputs & Outputs 28
2.6.1.1 External Start Digital Input 28
2.6.1.2 Ready Digital Output 29
2.6.1.3 Settings Examples 29
2.7 Setting a custom image and a name for an instrument 30
2.8 Tablet mode 30
3 Configuring the User Accounts 33
3.1 Configuring the User Accounts 33
3.2 Creating a new user account 34
3.3 Deleting a user account 35
3.4 Sharing user settings among users 36
3.5 Restricting access 37
3.6 Setting a password for the first time 38
3.7 Changing a user password 39
3.8 Logging in without a password 40
4 Proposed workflow for routine analysis 41
5 Method Setup 42
5.1 Setting up a method 42
5.2 Setting up a slow flow rate increase and decrease on your LC pump 47
5.3 How to make a mark in a chromatogram during acquisition 50
6 Data Acquisition 53
6.1 Running a single analysis 53

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6.2 Pre-evaluating a chromatogram during acquisition 54

6.3 Creating and running a sequence 54
6.4 Shutdown after sequence is finished 55
7 Device Monitor 58
7.1 How to set parameters during run 58
7.2 How to directly control LC gradient pumps during run 59
8 Chromatogram Editing 61
8.1 How to integrate chromatogram 61
8.1.1 Setting the integration interval 65
8.1.2 Modifying Global parameters 66
8.1.3 Modifying the beginning and the end of a peak 69
8.1.4 Removing a peak from integration manually 69
8.1.4.1 Baseline - Lock 70
8.1.4.2 Peak - Hide (and Show) 70
8.1.5 Changing the position of a peak separating line 70
8.1.6 Separating rider peaks by tangent 71
8.1.7 Adding a new peak manually 73
8.2 Saving the chromatogram method as a template method 74
8.3 Adding a peak to a group 75
8.4 Removing a peak from a group 76
8.5 Adding text and lines to a chromatogram 77
9 Calibration 80
9.1 Creating a new calibration 80
9.2 Adding a new calibration level 84
9.3 Applying a calibration to a chromatogram 85
9.4 Setting the calibration in the method 87
9.5 Calibrating with manually entered Response Factors 88
9.6 Recalibrating a calibration 91
9.7 Automatic recalibration using a sequence 93
9.8 Creating model calibration to use in calibration cloning 95
9.9 Calibrating using clone on first recalibration 96
9.10 Calibration adjustments 98
9.11 Calibration - Advanced Topics 106
9.11.1 Compensating for response drift using bracketing 106
9.11.2 Creating a Multisignal Calibration 111
9.11.3 Improving quantification with the standard addition method 121
9.11.3.1 How the concentration is calculated 125
9.11.4 Using a reference peak to improve compound identification 126
9.11.5 Normalized Area % Calculation 127

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User Guide Table of Contents

9.11.6 Normalized Amount % Calculation 127

9.11.7 Using Calculate By to determine the amount of a compound with no
standard available 130
9.11.8 Calibration with ISTD 131
9 Batch Processing 135
9.12 Reprocessing whole sequence 135
9.13 Reprocessing whole sequence while using calibration cloning 136
9.14 Reprocessing by selected method 137
9.15 Performing Post Run Options from Batch dialog 138
10 Results and Calculations 140
10.1 User Columns 140
10.2 User Variables 142
10.3 Signal to Noise Ratio Calculation 146
10.3.1 Noise Parameter Evaluation 146
10.3.2 Calculating Signal to Noise Ratio 147
10.4 How to calculate Relative Retention Time 148
10.4.1 Relative Retention Time calculation based on an existing peak 148
10.4.2 Relative Retention Time based on the Unretained Peak variable 150
10.5 How to calculate Peak to Valley Ratio 151
10.6 How to handle not-found compounds in your calculations 153
10.7 How to Display Older Results when Linked Calibration is Modified 155
10.8 Calculating percentage content of a compound in a solid sample 157
10.9 Comparing the results from several chromatograms 159
10.10 Confirming the identity of a compound by using the signal ratio 161
11 Data Reports 164
11.1 Setting up a report style for printing 164
11.2 Printing or previewing a report 165
11.3 Creating a report style (example) 169
11.4 Printing the summary table 175
12 File Management 177
12.1 Setting up project directories 177
12.2 Creating a new project 177
12.3 Creating customized file names automatically 179
12.4 Storing files into project subfolders 181
13 Import and Export Data 183
13.1 Importing a chromatogram into Clarity 183
13.2 Exporting a chromatogram from Clarity to a different chromatography
data station 184
13.3 Exporting data from Clarity 185

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13.4 Exporting data for LIMS 186

13.5 Exporting sequence 191
13.6 Importing sequence 192
13.7 Exporting a chromatogram as a picture 194
14 Mathematical Operations 195
14.1 Extract chromatogram's signal using Mathematical Operations 195
14.2 Subtraction of various chromatograms using Mathematical Operations 195
14.3 Copying of chromatogram using Mathematical Operations 196
15 Archive and Restore 199
15.1 Archiving a project (Creating an Archive) 199
15.2 Restoring a project from an archive 200
15.3 Archiving specific files (Creating an Archive) 201
15.4 Restoring a file from an archive 202
16 Managing the Chromatography Station 204
16.1 Enabling instruments to be used by Clarity2Go application 204
16.2 Locking/Auto Locking a Clarity Instrument 206
16.3 Unlocking a Clarity Instrument 208
16.4 Taking control over Clarity Instrument 209
16.5 Monitoring Events and Operations in Clarity 210
16.6 Controlling Clarity from an external application 213
17 Clarity in Network 214
17.1 Clarity in network overview 214
17.2 Multiple Clarity stations in a network 214
17.2.1 Migrating Clarity Project into a Network 217
17.3 Using remote desktop to control Clarity 219
18 Utilities 223
18.1 Checking that the software has been installed correctly (Installation
Qualification - IQ) 223
18.2 Editing Clarity profiles for different analyses using the Launch Manager 224
18.3 Creating a duplicate configuration using the Launch Manager 226
19 Extensions 231
19.1 GPC operations 231
19.1.1 Creating a GPC calibration 231
19.1.2 Applying a GPC calibration to a chromatogram 233
19.1.3 Setting a GPC calibration in the template method 234
19.2 PDA Operation 235
19.2.1 How to set Clarity instrument to display PDA data 235
19.2.2 How to open PDA chromatogram 236
19.2.3 How to work with PDA chromatogram 237

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User Guide Table of Contents

19.2.4 How to set PDA method 241

19.2.5 How to display peak purity 242
19.2.6 How to work with PDA library 243
19.2.7 How to search in PDA library 244
19.2.8 How to view specific spectra in overlay 246
19.3 MS Operation 248
19.3.1 Creating and filling your own MS library 248
19.3.2 Integration of signals in MS 250
19.3.3 MS Search and improving Match probability 250
19.3.3.1 MS Search - library search for compounds in MS 251
19.3.3.2 Improving Match probability 252
19.4 SST operations 252
19.4.1 Using SST for quality control 252

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User Guide Table of Contents

To facilitate the orientation in the User Guide manual and Clarity chromatography station, different
fonts are used throughout the manual. Meanings of these fonts are:
Open File (italics) describes the commands and names of fields in Clarity, parameters that
can be entered into them or a window or dialog name.
WORK1 (capitals) indicates the name of the file and/or directory.
ACTIVE (capital italics) marks the state of the station or its part.
Chromatogram (blue underlined) marks clickable links referring to related chapters.
The bold text is sometimes also used for important parts of the text and the name of the Clarity
station. Moreover, some sections are written in format other than normal text. These sections are
formatted as follows:

Note: Notifies the reader of relevant information.

Caution: Warns the user of possibly dangerous or very important information.

▌ Marks the problem statement or trouble question.

Description: Presents more detailed information on the problem, describes its causes,
etc.
Solution: Marks the response to the question, presents a procedure how to remove it.

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User Guide 1 Installation

1 Installation
Topics covering installation of Clarity software, Colibrick, Multicom, etc. Also the
connection between Clarity and chromatograph is explained.

1.1 Installing Clarity Software

These are the basic steps you have to follow for the First installation of Clarity.

First installation of the software (since version 9.0)

1. Install the software BEFORE connecting any hardware.
More Info:
l The software can be installed by inserting the installation USB and running
install.exe or by downloading the installation from the Downloads at our
website.
l On administered systems use „Run as Administrator“ from intended User
account. Administered systems are managed by an administrator and users
using the PC may not have administrator privileges. Insufficient privileges
may result in:
l Clarity not being installed.
l When installed from Administrator account, the installation directory
may be read only for users with limited privileges and the station will
be inoperable.

2. Select the language.

3. Confirm the License Agreement. It is possible to continue only in case you agree
with the statement.

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User Guide 1 Installation

4. Choose the destination folder. The user must have Read/Write/Modify access to
the installation directory.

5. Set location for your data files. C:\CLARITY\DataFiles is set by default. Notice
that Data location folder name cannot contain following characters / : * ? " < > |
and also cannot start or end with a space and cannot end with a dot.

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User Guide 1 Installation

6. Enter the User code corresponding to your hardware key or select Enter User
Code later to start 30-day Trial.
Note: The user code can be found on the back side of the card provided with
the Installation USB. Alternatively, you can contact DataApex support to
obtain one.

7. Select the type of installation. Make sure that control module for your device is
selected to be installed.
Note: In most cases "Typical" should be selected. "Custom"/"Full" installation is
necessary e.g., for Agilent and other devices controlled via ICF, DANI
devices and few others.

Note: List only contains names of original devices. If you can't find your device,
even though it is stated as controlled, it is most likely an OEM version of
different device.

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User Guide 1 Installation

8. Select the Start Menu folder for the shortcut or create a new one. After clicking
Install installation process will start.

9. Wait for installation to finish. In the end you might be prompted to confirm
installation of several hardware drivers.
10. When installation is finished Notes and Tools window will be opened.

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User Guide 1 Installation

11. Finally the last window will offer you several actions which may be executed after
the installation is completed.
More Info:
l The Launch Manager allows you to start Clarity using different profiles that
correspond to different configurations and combinations of instruments,
projects, methods, etc. For example, different users or groups of users can
have the chromatography station configured on the same computer.
l The Installation Qualification - IQ (Make IQ report option) is a procedure that
confirms that the software has been installed successfully and that the files
are in the correct version.

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User Guide 1 Installation

1.2 Updating Clarity Software

These are the basic steps you have to follow to update Clarity.
1. Check for the updates: click Help - Check for Updates... or download new
version of the software from the Downloads at our website.
2. Run the installer.
More Info:
l On administered systems use „Run as Administrator“ from intended User
account. Administered systems are managed by an administrator and users
using the PC may not have administrator privileges. Insufficient privileges
may result in:
l Clarity not being installed.
l When installed from Administrator account, the installation directory
may be read only for users with limited privileges and the station will
be inoperable.

3. Select the language.

4. Confirm the License Agreement. It is possible to continue only in case you agree
with the statement.

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User Guide 1 Installation

5. Previous version of Clarity will be detected. Decide whether to update or

preserve this version.
Note: In both cases your data and configuration will be preserved.

Note: Selecting Install to different location will result in presence of two different
Clarity version at once (current version will be left as it is and new version
will be installed elsewhere).

6. If you select to Update existing installation it is necessary to confirm the User

code (code from current version will be pre-filled).
Caution: Each major version (change of the first version number) since version 9.0
requires new User Code. Make sure that you have a valid User Code for
newly installed version before proceeding further. For more information
see https://www.dataapex.com/upgrade.

Caution: Downgrading is not supported and might be problematic in some cases.

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User Guide 1 Installation

7. Clarity will proceed with uninstallation, following window appears.

8. Continue to Choose Components step and click Uninstall.

Caution: When Remove All DEMO Projects is selected all files within them will be
lost, including any data you saved into their folders. DEMO projects
should never be used to store your data.

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User Guide 1 Installation

9. Wait for uninstall to finish and click Finish in the following window.

10. Choose what to do with existing data and configuration files.

Caution: It is recommended to select Keep the configuration and important data
files to preserve all of your settings and data. Other two options might
lead to losing important files and should be only used under special
circumstances.

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User Guide 1 Installation

11. Set destination folder for your data files. If data location is changed all data from
current version will be moved accordingly.

12. Select type of installation. Installation type which was used for current version
will be preselected. Make sure that control module for your device is selected to
be installed
Note: In most cases "Typical" should be selected. "Custom"/"Full" installation is
necessary e.g., for Agilent and other devices controlled via ICF, DANI
devices and few others.

Note: List only contains names of original devices. If you can't find your device,
even though it is stated as controlled, it is most likely an OEM version of
different device.

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User Guide 1 Installation

13. Select the Start Menu folder for the shortcut or create a new one. After clicking
Install installation process will start.

14. Wait for installation to finish.

15. When installation is finished Notes and Tools window will be opened.

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User Guide 1 Installation

16. Finally the last window will offer you several actions which may be executed after
the installation is completed.
More Info:
l The Launch Manager allows you to start Clarity using different profiles that
correspond to different configurations and combinations of instruments,
projects, methods, etc. For example, different users or groups of users can
have the chromatography station configured on the same computer.
l The Installation Qualification - IQ (Make IQ report option) is a procedure that
confirms that the software has been installed successfully and that the files
are in the correct version.

Caution: When upgrading from Clarity 6.2 or older to Clarity 7.0 or newer be aware
that there is change in the installation structure - the content of the
original installation folder is separated to three new subfolders BIN, CFG
and DataFiles. The respective files are moved automatically during
update to the new locations if you selected Update existing installation. In
the rare cases this fails, some files may need to be moved manually.

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User Guide 1 Installation

1.3 Installing Colibrick

Colibrick is an external 24-bit A/D converter designed for acquisition of data from
any chromatograph. It uses the USB communication channel and it is powered from
the PC.

1. First install Clarity.

More Info:
l The driver is by default installed in Typical installation of Clarity. It can be
found in Hardware section of Choose Components step.
l The Colibrick device is identified by its S/N. If you exchange it by another one
later, it will be also necessary to reconfigure it in the Clarity - System
Configuration dialog.
2. Connect Colibrick to a USB port in your computer. It will be detected
automatically.

3. Connect the CANNON SUB D 27-pin connector on the (INT7) cable to Colibrick
back panel.

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User Guide 1 Installation

4. Connect the cables (Starting, Digital output and Analog Signal) to the
chromatograph as explained in Connecting a chromatograph analogue output to
Clarity.
5. Start Clarity and then add the Colibrick channels to specific Clarity instruments
as explained in Adding a new device.
6. Check the LED's on the front panel to find out about the status of Colibrick and
whether it has been installed properly.

More Info:
l Ready (orange) LED status Indicates correct installation.
l Data (blue) LED status Indicates connection to the chromatography data
station.
l Digital Input (green) LEDs status
l LED ON - the input status is High (logical "1") or not connected.
l LED OFF - the input status is Low (logical "0") or connected to the
ground (GND).
l Digital Output (red) LEDs status
l LED ON - the output status is High (logical "1"), the relay contact is
opened.
l LED OFF - the output status is Low (logical "0"), the relay contact is
closed.

1.4 Installing a Rockey USB dongle

Currently supplied RkNDUSB HW keys use the HID (Human interface device)
technology and do not require any drivers.
For old RkUSB keys the drivers will be installed automatically during the installation
of Clarity. For this reason it is important to install Clarity before plugging the key. If
the installation did not proceed as expected or you may have an old version of
Windows, follow the procedure below.

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User Guide 1 Installation

1. First install Clarity.

2. Connect the USB dongle to a USB port on the computer.
3. Install the Rockey drivers by running INSTDRV.EXE in C:\CLARITY\BIN\HW_
DRIVERS\ROCKEY\. The following window will appear.
4. Select the Install USB driver option and click on Next to finish the installation.

5. Verify that the driver has been installed correctly. Meaning that the Device
Manager ⓐ has the item "Universal Serial Bus Controllers" - "Rockey4 USB"
ⓑ.

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User Guide 1 Installation

If this does not work, try the following procedure after the installation of Clarity:
After connecting the dongle, Windows will detect a new Plug and Play device and
the Found New Hardware Wizard will appear.
1. Select "Search for a suitable driver for my device."
2. Select "Specify a location" and then select the C:\CLARITY \BIN\HW_
DRIVERS\ROCKEY\folder. The rest of the installation will be carried out
automatically.

Note: On Windows 10 and Windows 11, the driver for older HW keys (Rockey4USB.sys)
can only be installed if Memory Integrity/Core isolation function of Windows
Security is turned off. This function is turned on by default. If an incompatible
driver is already installed on the computer, it cannot be turned on. But if it is
enabled, the driver installation fails with Error code 39.

1.5 Connecting a chromatograph analogue output to Clarity

The Clarity Station cable (INT7) connects the station to the chromatograph and it is
a set of Starting, Digital output and Analog Signal cables connected to a CANNON
SUB D 27-pin connector.

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User Guide 1 Installation

1. Install your external A/D converter like Colibrick (refer to Installing Colibrick) or
an A/D converter card (refer to the specific HW manual).
2. Switch off your chromatograph.
3. Connect the bare wires to the chromatograph depending on your equipment,
configuration and the following guidelines.
More Info:
l The Signal cables "DET 1" to "DET 4" carry the main signal from the
chromatograph to the computer. The connection can be asymmetrical or
symmetrical.
l The Starting cables "IN1" to "IN4" come in pairs, one part connected to the
27-pin connector and ending on a female RCA connector and the other with a
male RCA connector and free leads for connection to a starting contact or a
button for a manual start.
l The Digital Output cables "OUT 1R" to "OUT 4R" end on free leads and they
can be used for synchronizing autosamplers.
Caution: The shielding must be connected. It works not only as the shielding, but also as
the analogue ground against which measurement takes place. In the case of asymmetrical
output of a detector (only two leads/terminals/pins/screws) the shielding must be
connected to the white lead! No lead of the signal cable may remain unconnected.
4. Connect the CANNON SUB D 27-pin connector to the A/D convertor.
5. Switch on your computer and your chromatograph.

1.6 Installing Multicom

MultiCOM is a USB to RS232 converter developed for controlling via the RS232
serial interface. It is connected to the PC via the USB port and has 6 serial 9-pin
ports. It also has a free USB port for the connection of the USB hardware key.

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User Guide 1 Installation

1. First install Clarity. Multicom driver is by default installed in Typical installation of

Clarity. It can be found in Utils section of Choose Components step.
2. Connect Multicom to a USB port in your computer. It will be detected
automatically. LED diodes will be turned on one by one.
3. Connect your devices to the Multicom RS232 ports.
4. Start Clarity and then add each device to a specific Clarity instrument as
explained in Adding a new device.
5. Select the appropriate port from the list during the device setup.
Note: When using functions like Autodetect and Check LED diode of selected
port will blink. This can be used to find the desired port number on
Multicom.

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User Guide 1 Installation

6. Check the LEDs on the top panel to find out about the status of Multicom and
whether it has been installed properly.
More Info:
Green LED status:
l OFF – not connected to USB, the driver is not installed or Multicom is in
suspend mode.
l ON (Constant) – idle state, no communication.
l BLINKING:
l Two short consecutive blinks – only sending data from USB to
the COM port.
l Turned off twice consecutively – only receiving data from the
COM port into USB.
l Constant blinking – both sides are receiving and sending data.

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User Guide 2 Configuring the Chromatography Station

2 Configuring the Chromatography

Station
Chapters covering settings in the System Configuration dialog.

2.1 Obtaining information about Clarity configuration

To find out information on the supported control modules and Extensions, used A/D
converters and purchased Instrument licenses follow this procedure:
1. Open the About box: Select Help - About… on the Main window.
2. Switch to the System Files tab ⓐ . Note that it may take a while for Clarity to
generate the report.
3. In the first table ⓑ there is info about:
l Clarity SW version
l Number of purchased instrument licenses
l Extensions available
l The allowed control modules
l Acquisition and hardware devices
4. Go to the files table ⓒ to find information about the drivers and its status.
If the status is other than OK there may be an issue with the driver. The
version of the drivers developed by DataApex should be the same as that of
Clarity.

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User Guide 2 Configuring the Chromatography Station

2.2 Setting the number and type of instruments

1. Enter the System Configuration dialog: select System - Configuration… on
the Main window.
2. In the Number of Instruments field ⓐ you can set a number of instruments,
based on bought licenses or you can use non- bought Instrument as the
Offline one.
Note: The Offline instruments can be used in the same way as your standard
ones except for data acquisition.
3. Set the Instrument Type field ⓑ according to the type of instrument you are
using e.g., GC or LC.
Note: The rest of the instrument types - GPC, PDA, EA, NGA, etc., need to
have the particular Extension license purchased.

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User Guide 2 Configuring the Chromatography Station

2.3 Adding a new device

1. Enter the System Configuration dialog: select System - Configuration… on the
Main window.

2. If the device you want to add is not in the list, click on Add ⓐ and the following
window will open. Here you can filter the list by typing some text in the filter field

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User Guide 2 Configuring the Chromatography Station

or filter by Name, Vendor, etc ⓑ .

Note: If the status of the module is not installed, double-click the line with this
device to see why the module is not installed and how to remedy the
situation.
3. Select the device and click on Add ⓒ or double-click the line.

4. Add new devices to the appropriate instrument: drag and drop the device from
the left pane ⓓ to the Instrument pane on the right ⓔ or select the device and
click on ⓕ.

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User Guide 2 Configuring the Chromatography Station

5. If you need to help with configuring a device, go to the topic Configuring a

device.

2.4 Configuring a device

1. Enter the System Configuration dialog: select System - Configuration… on the
Main window.
2. Select the Instrument 1..4: click on the corresponding tab ⓐ .

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User Guide 2 Configuring the Chromatography Station

3. To configure a device, double- click it or click the Setup... button ⓑ after

selecting it. A device setup dialog will appear. Setup dialogs are specific to each
device.
For more information on how to configure a specific device, go to the specific
manual or use the Help button.

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User Guide 2 Configuring the Chromatography Station

2.5 Setting the options for sending the method to the

instrument
In a default Clarity installation, each time you change the method on Instrument,
you need to send it manually to configured devices. Let's describe how to change
that behavior so the method will be automatically sent to devices after each time
you change the method.
Caution: We do not recommend to set the automatic sending of method on
HPLC instruments since you may mistakenly send a method to configured pumps
with wrong flow or pressure limits!
1. Enter the System Configuration dialog: select System - Configuration… on the
Main window.
2. In the group Miscellaneous Settings click on Method Options button ⓐ .

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User Guide 2 Configuring the Chromatography Station

3. Choose one of the option of the method sending.

If you select the Send Method to Instrument option, the method selected in Single
analysis window will be sent every time you log into the instrument or this method is
modified, or when the sequence is finished.

2.6 Assigning digital input and output to start acquisition

There are basically three means when Clarity decides to start the acquisition:
1. User presses Run button in Single Analysis (user probably did manual injection
and notifies Clarity that its time to start)
2. Clarity is outside of run, but one of the controlled detectors starts to provide data
marked as run data.

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User Guide 2 Configuring the Chromatography Station
3. Clarity gets the digital input marked as START from device over:
a. Communication line (LAN, serial (RS-232), USB/GPIB)
b. Wire as TTL signal (this connection requires an external A/D converter or
other device offering digital input to Clarity)
The last case (3) is most typical way and this chapter describes how to assign
digital input and output in Clarity for the most common wiring of devices (typically an
autosampler). The setting is performed in System Configuration dialog through Ext.
Start Dig. Input and Ready Dig. Output functions.

2.6.1 Data Inputs & Outputs

l Settings are specific for each particular instrument.
l ⓐ : Only devices configured on the Instrument are offered in device list.
l ⓑ : Input number list allows to select input number. Available inputs are specific
for particular instrument and correct number depends on actual wiring.

2.6.1.1 External Start Digital Input

The device (in most cases the sampler) provides the injection state to Clarity over
its digital output. This may be a real digital output on the device or just a simulated
one (Clarity does not distinguish between the two). Selecting a right Ext. Start Dig.
Input is necessary, because Clarity watches the state of the selected input all the
time and reacts on its change.
More Info:
Various devices are providing a lot of different inputs, and these may be used for other
reasons, not only for analysis starting. The user needs to select the proper input which will
allow the starting. For devices with virtual inputs, and in most cases also samplers with real
outputs on the hardware, Start is signaled on output number 1.
After receiving START signal from a sampler, that notifies Clarity about performed
injection, Clarity sends instruction to Start Acquisition to other modules (detector,
column oven etc.) of the system .

2.6.1.1.1 Possible synchronization issues

Missing start of analysis
Situation could happen when there is configured compact HPLC (without sampler)
and external sampler or controlled sampling valve. The sampler or valve lets Clarity
know, broadcasts the analysis start and the HPLC needs to get the information from
Clarity, otherwise it will never start running.

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User Guide 2 Configuring the Chromatography Station
For some chromatographs, the settings of the module and its behavior are set in the
module's configuration based on the actual wiring, and it is upon the person
installing Clarity and setting up the configuration to set the whole system correctly.

For correct option always consider the source of the analysis start first (sampler,
sampling valve, Start button on a instrument) and ask a question "What will happen
if Clarity does not signal anything? Will the instrument run anyway?"
l If Yes - option should be set to This Device Starts the Run in Clarity
l If No - option should be set to Clarity Starts This Device

2.6.1.2 Ready Digital Output

Note: Settings Ready Dig. Output in System Configuration dialog is relevant only for Active
Sequence using sampler without AS Control module. Conversely is not relevant
for controlled samplers used with AS Control module (signal over communication
line), neither for Passive Sequence.

Ready Dig. Output defines the device and its specific pin through which Clarity
informs other parts of the system that injection can be performed. After starting a
sequence, controlled modules READY states are verified, Clarity triggers the
Ready Dig. Output and changes its state, thus broadcasting to other modules of the
system that sequence can be run. READY signal is received by the sampler that
performs the injection and sends START signal. Then Clarity detects START signal
and triggers again Ready Dig. Output and change its state, thus preventing the
sampler to perform another injection.

Caution: Using the Event Table in Method Setup other actions can be configured changing
the parameters of Digital Output. Note, that if the same Digital Output is modified, it
may cause conflicts in synchronization. Avoid using these inputs and outputs in the
Event Table.

2.6.1.3 Settings Examples

Default assignment of the Ext. Start Dig. Input and Ready Dig. Output functions can
be found in the manual for the corresponding hardware.
For most common wiring of autosampler see chapter Connecting Autosamplers
(AS) or respective subsections in Getting Started manual.
l AS + GC set - Active Sequence
l AS + LC set - Active Sequence
l AS + GC set - Passive Sequence
l AS with Clarity control module - Active Sequence + A/D converter
l AS with Clarity control module - Active Sequence + digital acquisition

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User Guide 2 Configuring the Chromatography Station

2.7 Setting a custom image and a name for an instrument

1. Enter the System Configuration dialog: select System - Configuration…on the
Main window.

2. Click on the Instrument 1..4 tab to select the instrument ⓐ .

3. Type the name of the instrument in the Name field ⓑ .
4. Click on the image of the Instrument ⓒ to invoke Instrument Image Setup
dialog.

5. Check the Custom Image check-box and then on to select your image. Click
OK to save your changes.
6. Repeat for every Instrument you wish to change the name or the pictures.

2.8 Tablet mode

This procedure shows how to activate and use a Tablet mode. The Tablet mode
represents a specific windows layout that should simulate a single-window

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User Guide 2 Configuring the Chromatography Station
application. It is designed for devices with small displays. The optimum resolution is
1920 x 1080.
In Tablet mode, Instrument window is narrower than in standard layout and is
positioned on the left side of the monitor, other windows open on top of each other
and fill the remaining space on the monitor. Tablet mode allows the use of higher
scale in Windows (up to 200 %) which improves work with the software and
readability of parameters.

Enabling Tablet mode

1. In Clarity Main window menu, click View and select Tablet Mode item.
Note: Switching to Tablet mode is possible only when instruments are closed.

2. After logging in to the Instrument, new windows open in tablet layout. Instrument
window is positioned to the left side of the monitor, other windows open on top of
each other and fill the remaining space on the monitor.
More Info:
Instrument window cannot be fully maximized. Its width can be expanded up to a
maximum of 50% of the monitor width and is stored.
Other windows always fill the remaining space of the display.
Method Setup and Single Analysis windows are opened maximized.
If the scale in Windows is set to more than 100%, some of the icons and analysis
status line can break into a new line.

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User Guide 2 Configuring the Chromatography Station

3. Icon of an active window is highlighted by a blue frame in the Instrument

windowⓐ .

Disabling Tablet mode

1. In Clarity window menu, click View and select Tablet Mode item (active tablet
mode is highlighted by a tick icon).
2. After logging in to the Clarity Instrument, new windows will open in layout
used before activating the Tablet mode.

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User Guide 3 Configuring the User Accounts

3 Configuring the User Accounts

Chapters describing how to use User Accounts in Clarity, how to restrict some
operations for defined users and how to set shared settings for a group of users.

3.1 Configuring the User Accounts

The User Accounts can be configured from the User Accounts dialog. It allows you
to configure the settings for each user (Name, Password, Access Rights and Digital
Certificates).
1. Open the User Accounts dialog: click on or choose System - User Accounts.
2. To create a new user, follow the procedure explain in Create a new user account
More Info:
l Leave blank (do not create any user) for unprotected mode - everyone
working with station will share a common desktop file, and actions will be
logged to audit trail under 'administator' name.
l The desktop file (user profile) stores information about the last used project,
table and graph settings, etc.

3. Set the minimum password length and life time ⓑ .

4. Fill in the User Access Rights section ⓒ . More is explained in Restricting
access chapter.

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User Guide 3 Configuring the User Accounts

3.2 Creating a new user account

1. Open the User Accounts window: click on or choose System - User
Accounts.
2. To create a new user, click the button Newⓐ and fill in the new User Name ⓑ .
3. Enter the desktop file name ⓒ . If you left the Desktop file field empty, the
desktop file [USERNAME].DSK will be automatically created.
Note: This file contains settings about the size, location and visibility of the
windows as well as all the amendable Instrument parameters which are
not part of system files.
4. Fill in a user description if you want to. ⓓ
5. Click OK to accept the changes.

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User Guide 3 Configuring the User Accounts

3.3 Deleting a user account

1. Open the User Accounts window: click on or choose System - User
Accounts.
2. To delete a user, select the user in the User List and then click the Delete button
ⓐ.
3. Click the OK button to accept the changes.

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User Guide 3 Configuring the User Accounts

3.4 Sharing user settings among users

In Clarity user settings e.g., setting of User Columns, the width of the columns in
tables, customization of the toolbars are saved in the desktop files *.DSK.
1. Open the User Accounts dialog: click on or choose System - User Accounts.
2. Select the user to have a shared desktop file.
3. Then type the name of the desktop file to be shared to the User Details
sectionⓐ .
More Info:
This file contains settings about the size, location and visibility of the Instrument
windows as well as all the amendable Instrument parameters which are not part of
system files (shown columns in tables, etc.).
4. Repeat for every user you want to have the shared desktop setting.
5. Click OK to accept the changes.

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User Guide 3 Configuring the User Accounts

3.5 Restricting access

In Clarity it is possible to:
l Restrict other users' access to your files
l Restrict user's access to instruments
l Restrict user's access to Clarity procedures

1. Open the User Accounts dialog: click on or choose System - User Accounts.
2. Configure the file access rights for other users ⓐ .
3. Check the instruments the user will have access to ⓑ .
4. Check the Clarity procedures the user will have access to ⓒ .
5. Click OK to accept the changes.

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User Guide 3 Configuring the User Accounts

3.6 Setting a password for the first time

1. If the user has been created already and the password was left blank, then the
first time you click on any of the instruments in the Main window, after selecting
the user and clicking OK in the Login Dialog, you will be asked to enter a new
password.

2. Type in and confirm the new password and then click OK.

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User Guide 3 Configuring the User Accounts

3. Alternatively or if you are creating a new user, you can follow the same
procedure as explained in section Changing a user password and create a new
one.

3.7 Changing a user password

1. Open the User Accounts window: click on or choose System - User
Accounts.
2. Select the user in the Users List and then click Change password ⓐ .
3. Type the new password, confirm it and then click OK.

Alternatively you can change password by following these steps:

1. Open the User Accounts Details window by choosing System - User Details,
select the user and enter current password.
2. Click on Change Password ⓑ and enter and confirm the new password.

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User Guide 3 Configuring the User Accounts

3.8 Logging in without a password

1. Create a new user account without setting up a password as explained in section
Creating a new user account or remove the password, if it was previously set, in
an previously created account as explained in Changing a user password.
2. Click on the Instrument you wish to open in the Main window.
3. Select the user name and click OK while leaving a blank password.

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User Guide 4 Proposed workflow for routine analysis

4 Proposed workflow for routine

analysis
Below there is description of a procedure that can be used for performing routine
analysis of uniform samples. Steps are described in more details in linked topics.
1. Measure typical sample.
2. Adjust the integration of the chromatogram as needed. Details are described
in How to integrate chromatogram topic.
3. Save the method including this adjusted integration. Details are described in
Saving the chromatogram method as a template method topic.
4. Create model calibration that will be used in calibration cloning. Details are
described in Creating model calibration to use in calibration cloning topic.
5. Set the calibration cloning in the sequence, method (and potentially in the
calibration). Details are described in Calibrating using clone on first
recalibration or Compensating for response drift using bracketing, Improving
quantification with the standard addition method.
6. Create a sequence. Do not fill the levels of standard samples and post run
actions.
7. Run the sequence
8. Review the data. In case some minor adjustments are needed adjust the
integration.
9. Fill in the Levels and Post Run actions to the sequence file.
Note: If you need to sign the documents and print the report with the
signature do not fill the Print actions in the sequence now. After the
recalibration is performed, manually sign every chromatogram and
then use Batch dialog - Post run options to print the reports with
signatures.
10. In Batch dialog perform Complete Processing of the sequence. Details are
described in Reprocessing whole sequence topic.
11. Now you have the sequence recalibrated, reports printed and possibly other
Post Run actions performed.

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User Guide 5 Method Setup

5 Method Setup
Following chapters include useful tips regarding the Method Setup and working with
method.

5.1 Setting up a method

The method essentially contains information on how the analysis will be performed,
how the resulting signal will be processed and what events will be triggered and
when.
Any method can be created or edited in the Method Setup window. To use the
method for measurement it has to be sent to the instrument and for sequence
measurement method has to be set at each row.

Template Method vs. Chromatogram Method

l The sent method is used as a template for new chromatograms and its
contents are copied into the chromatogram file after acquisition or batch file
reprocessing. You can open the different sections of the sent method setup
from the icons in the Instrument window or with the command Method - ......
on the toolbar.
l The changes to the chromatogram method do not affect the template
method and they are performed in the lower pane of the Chromatogram
window.
l The calibration file is linked to the template method and to the chromatogram
method by its name.

Method Setup window

l The title of the Method Setup dialog displays a method that is currently
opened. If you make any changes, the method becomes (MODIFIED).
l The upper part of the Method Setup dialog displays a set of icons with which
it's possible to create a new method, open existing method, save method,
save method as, open Report Setup, open method audit trail, send method
by e-mail or open help.
l Upon pressing the OK button it will be automatically saved and Method
Setup dialog will close.
l Tabs shown in Method Setup window are dependent on devices actually
configured on the Instrument, e.g. MS Method, PDA Method, LC Gradient
can be only visible when proper instrument type and device is set.

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User Guide 5 Method Setup

Send Method
l Only a method that is saved can be sent.
l Pressing the Send Method button will result in two actions:
l Method will be sent to all connected hardware and thus
displayed in the information table of the Instrument window -
just as before.
l Method will be set as Method for Single Analysis - you can
start the single analysis form the instrument window using the
icon.
l When measuring sequence, each row can have different method. It is set
while creating or editing the sequence tab in the Method Name column.

Method Development
Method currently used for acquisition or present on already locked row of the
sequence can't be edited, and can be viewed in read-only mode only.
When developing a method, you can configure the following settings among others:
1. Set the measurement conditions.
Here you can disable or enable Autostop and set the run time for the
analysis ⓐ as well as configure the external signal start and stop settings
ⓑ (default setting Start Only should be used in majority of applications).
Autostop can be set within interval 0.2 - 9999 min, such value is not
influenced and does not influence any device specific time program settings
on different tabs (like LC Gradient or GC). When time defined in Autostop
passes, acquisition is finished, chromatogram is created, remaining time
from time programs will be spent in so called Control state.
You can also describe some parameters of the method and add a note ⓒ .
Such information is purely informative and do not influence analysis in any
way. They are saved into the resulting chromatogram and are showed in the
Chromatogram window.

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User Guide 5 Method Setup

2. Set the Data Acquisition parameters.

It allows you to select, enable/disable the detector signals ⓐ and to set
measurement parameters e.g., the signal range and sample rate ⓑ . At any
time at least one detector has to be Enabled.
Layout of this tab, together with possible parameters to be set, are
dependent on the configured devices (control modules) on the Instrument.

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User Guide 5 Method Setup

3. Set the Signal Integration parameters.

When using a multi-detector configuration, there is an integration table for
each detector (i.e. signal), thus every resulting signal can be integrated in a
different way.
Every resulting chromatogram acquired with such method will be integrated
automatically accordingly the integration tab.
If you aren’t able to edit tab parameters the current detector probably isn’t
Enabled.

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User Guide 5 Method Setup

Note: Integration parameters are often modified manually after the first acquired
chromatogram directly in the Chromatogram window. Then you can manually
rewrite them into any method in the Method Setup dialog or you can use the
Method - Save as Template menu command in the Chromatogram window to
easily copy them into your method. For more details see the chapter Saving the
chromatogram method as a template method on pg. 74..
4. Set the calculation options.
l
You can create New... calibration file or Set... the one created previously ⓐ
and configure the different settings related to it.
l When calibration file is set, resulting chromatograms will be calibrated
according to it and calibration standards will be used to automatically re-
calibrate the attached calibration file.
l
Clone... ⓑ button will create a copy of a current calibration file. In the
following Save As dialog you can select the name and location of the new
calibration file. The copy will then be linked to the method.
l If it is desired to have no calibration in the method you can use the None
button ⓒ .
l In this tab you can also choose how you want the results to appear in the
results ⓓ and set calculation type ⓔ .
l
Name of calibration clone ⓕ must be set here to use calibration cloning in
sequences, refer to chapter "Calibrating using clone on first recalibration" on
page 96.

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User Guide 5 Method Setup

5. Configure the settings in the additional tabs.

Method Setup also has tabs specific to currently configured devices and
Event Table tab, used for configuring what events will be triggered and
when e.g., shutting down Clarity after the sequence is finished.
However, there are some limitations:
l Event Table is for specific purposes, not needed for standard analyses.
l Does not have control against infinite loops.
l Must be filled per row, Fill Down/Fill Series can't be used in Event Table.

Note: For more information on any of the settings above, press F1 in such Clarity
window to go the corresponding section of the Help or use the Clarity Reference
Guide.

5.2 Setting up a slow flow rate increase and decrease on

your LC pump
You can protect your chromatograph column from sudden pressure changes by
setting up a Sequence together with three different methods, Startup, Shutdown
and Analysis to ensure a slow flow rate increase and decrease on your LC pump.
This procedure is mainly recommended for pumps controlled by Zebrick D/A
converter or UNI Ruby scripts due to less strict pressure limit controls in these
control types.
l Set the Instrument Method Sending option to "Do not send Method to
Instrument", opposite to the topic Automatic sending of a method to an
instrument after each change.

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User Guide 5 Method Setup

Startup Method
1. From the Instrument window open the Method Setup window using the Method -

Method Setup command or the Method Setup icon.

2. Create New Method and Save it under the name Startup.
3. Navigate to the Method Setup - LC Gradient tab.
4. Set the Idle State to Initial - Standby ⓐ .
5. In the Gradient Table, ⓑ set the Initial Flow to 0 and on the second row set the
Flow to its Standby Flow value ⓒ and the Time to obtain the appropriate flow
rate increase for your column.
6. Click OK to accept the changes.

Analysis Method
7. Repeat steps 2 to 6 but this time:
l Save the Method under the name Analysis.
l Set the Idle State to Initial ⓓ .
l Set the Initial Flow, Flow on the second row ⓔ and Standby Flow
value ⓕ to the value of Standby Flow from Startup method.
l Set the Time to the total duration of your analysis ⓖ .

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User Guide 5 Method Setup

Shutdown Method
8. Repeat steps 2 to 6 but this time:
l Save the Method under the name Shutdown.
l Set the Idle State to Initial - Standby ⓗ .
l On the second row, set the Flow to 0 and the Time to obtain the
appropriate flow rate decrease for your column ⓘ .
l Set the Standby Flow to 0 ⓙ .

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User Guide 5 Method Setup

Sequence
9. Set up a Sequence as explained in Running a Sequence and:
l On the first row set the Sample Type column as Bypass and the
Method Name to Startup.
l On the last row set the Sample Type column as Bypass and the
Method Name to Shutdown.
l Set as many rows as you need in between according to the
conditions of your analysis or sequence and set the Method Name to
Analysis.

5.3 How to make a mark in a chromatogram during

acquisition
To create a mark in a chromatogram, you can use the Event Table tab from the
Method Setup dialog and any hardware with digital input (such as Colibrick A/D
converter) or the Virtual Digital Input Output Loop module. With the proper settings,
triggering the digital input is recorded as an event, creating a mark (a vertical line

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User Guide 5 Method Setup
labeled with name and RT) in the Data Acquisition and Chromatogram windows.
The digital input can be triggered by pressing the start button when using HW or by
pressing the corresponding Digital Output in the Device Monitor when using the
Virtual Digital Input Output Loop module.
The following settings are necessary:
l HW with a digital input or the Virtual Digital Input Output Loop module configured
to an Instrument.
l Method Setup
l Measurement tab - External Start/Stop enabled and set to Start Only
l Event Table tab - set according to the image below, where:
l Name = the label of the event
l Source = the module providing the digital input
l Input = digital input recording the event

l To display the marks, enable the Show Events option in the Graph Properties
dialog accessible from the Data Acquisition and Chromatogram windows (the
dialog can be invoked by right-clicking the graph area in the respective window
and clicking Properties...).

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User Guide 5 Method Setup

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User Guide 6 Data Acquisition

6 Data Acquisition
Chapters describing how to perform a measurement using Single Analysis or
Sequence and how to evaluate chromatograms during run.

6.1 Running a single analysis

1. Open the Single Analysis dialog by selecting Analysis - Single or clicking on
icon in the Instrument window.
2. Fill in the sample information into the Sample ID and/or Sample fields ⓐ .
3. Fill in the Chromatogram File Name ⓑ . It is recommended to use variables to
do so, for example, %q (Sample ID) and %n (counter) or %R (date and time) to
prevent file name conflicts. Name preview is displayed above the field. For more
info regarding variables see "Chromatogram File Name" in the Clarity Reference
Guide.
4. Select the Method ⓒ which should be used for measurement. It is also possible
to edit it by clicking Edit Method.
5. What should happen after analysis like automatic report printing can be set on
the Post Run Settings tab.

6. Start the analysis by clicking the Run button ⓓ . Analysis can also be triggered
by External Start from the chromatograph. The Instrument will get to the

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User Guide 6 Data Acquisition
RUNNING state and the Single Analysis dialog will close. The state is visible in
the status line in the Instrument window.
7. It is possible to monitor the analysis from Data Acquisition window, see Pre-
evaluating a chromatogram during acquisition for more.

6.2 Pre-evaluating a chromatogram during acquisition

1. Open the Data Acquisition window by select Window - Data Acquisition or click
on in the Instrument window.

2. To create a temporary chromatogram, select Analysis - Snapshot or click on

ⓐ . Every time you take a snapshot, a temporary chromatogram will be created
again from the beginning up to the point where you clicked.
Caution: To preserve a snapshot it has to be saved under new name, otherwise it
will be overwritten once analysis is finished and final chromatogram is
created.

6.3 Creating and running a sequence

1. Open the Sequence window by selecting Analysis - Sequence or click on the
icon in the Instrument window.
2. Create a new sequence file by click ⓐ . or open an already created sequence
ⓑ . If you already have a sequence ready skip to step 11.
3. Save the new sequence by selecting File - Save As… and give it a name in the
saving dialog.
4. Check the checkbox in the first (empty) row in the Run column ⓒ . The row will
be pre-filled with default basic information on the analysis.
5. Fill in the Sample ID and/or Sample columns ⓓ .
6. Fill in the File Name ⓔ . It is recommended to use variables to do so, for
example, %q ( Sample ID) and %n (counter) or %R (date and time) to prevent
file name conflicts. Hold the mouse pointer over the file name field to see

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User Guide 6 Data Acquisition
resulting name. For more info regarding variables see "Chromatogram File
Name" in the Clarity Reference Guide.
7. The SV (Starting Vial) and EV (End Vial) rows ⓕ will be pre-filled with numbers
corresponding to the sample position in the autosampler tray, if you are using an
autosampler. It is possible to change these as needed, injection from multiple
vials can be made on one sequence row.
8. Fill in volume of the injection in the Inj. Vol. column ⓖ .
9. Select the method to be used in the Method Name column.
10. Tick any of the Open, Open Calib., Print etc., columns ⓗ in case you wish to
open measured chromatogram in chromatogram or calibration window or print
the results after each measurement of a sample.
Caution: To correctly include chromatograph graphs in the reports it is necessary
to check both Open and Print checkboxes. It is also necessary to fill in
Report Style when Print or Print to PDF is used.
11. Repeat the steps 4-10 for rows you need to add to the Sequence Table.
Note: It is possible to display additional columns by right-clicking the sequence
table, selecting Setup Columns and moving items from Hide Columns to
Show Columns list by Show button.
12. Check the validity of the sequence by selecting Sequence - Check Sequence or
clicking on icon. In valid sequences, all rows will show the symbol in
the Status column. Invalid sequences will issue a warning message with the
cause of the problem.
13. Save the sequence by selecting File - Save or clicking on icon.
14. Run the prepared sequence by selecting Sequence - Run or clicking on icon
ⓘ.
Note: The sequence state will change to WAITING FOR INJECTION or
INJECTING state, depending on READY state of other controlled
modules. The state is visible at the bottom of the Sequence window.

6.4 Shutdown after sequence is finished

After the sequence is finished, it might be sometimes convenient to send (and run)
shutdown method and/or perform shutdown. As the behavior of used controlled
devices may be quite specific, there are multiple options how to get them to a
desired standby state. For example some detectors may be able to perform run with
lamps off or switch them off after end of a run, while others will not get to ready state

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User Guide 6 Data Acquisition
without lamp on. Proper combination of the possible actions needs to be set
accordingly.
1. To setup shutdown open the Sequence Options in your opened sequence by
selecting Sequence - Options or clicking on icon.
2. Now, you need to decide whether you only need to send shutdown method to
controlled devices to prepare them for shutdown (step 3), or if you need also to
run such method, e.g. for lowering the gradient (steps 3 and 4). As mentioned in
the beginning of chapter this setting is highly depended on individual control
module capabilities.
3. Send shutdown method: checkbox: Check this checkbox to be able to select and
send shutdown method to controlled devices. You can also edit such method, if
needed. This option will only send the selected method to devices.
4. Run shutdown method checkbox: Use this option to run selected method.
Resulting chromatogram will be saved to the current project as
[SEQUENCENAME - SHUTDOWN - METHODNAME - %R.PRM], where %R
stands for current date and time.
Note: Use Bypass to omit injection from the vial, or Unknown for injection from
specified vial. Valid Vial position and Injection volume may be required by
some autosamplers, even if the injection will not be performed (i.e. when
method is not run or Bypass injection is selected).
5. Perform shutdown checkbox: Use this option to shutdown all controlled devices.
Shutdown command is sent after sending and completed run of the shutdown
method. Note that the reaction of some devices to the Shutdown may be
amended in their respective Setup window in System Configuration.

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User Guide 6 Data Acquisition

Note: The parameters of the After sequence is finished section are also executed when
the user stops the sequence by Stop command or the sequence is stopped by
an error. If it is necessary to stop the running sequence without sending (and
running) the shutdown method, use the Abort command.

Note: When the sequence is already finished and the shutdown is also already
performed, if new lines are added to the finished sequence and such sequence is
then resumed, the whole After sequence is finished will be applied again.

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User Guide 7 Device Monitor

7 Device Monitor
The Device Monitor window serves firstly to show the current status of each control
module and secondly for direct control of the device. The layout and possible
control options greatly vary based on the used control modules.
The window can be personalized. To change the order of individual monitors right
click on the module’s name ⓐ and choose desired action in the context menu ⓑ .
The individual monitor panel can be collapsed or expanded using the arrow icon ⓒ
in the header of the panel.

7.1 How to set parameters during run

Besides performing some service commands outside run, in some cases it is
possible to perform some actions also during run. This is individual for specific
control modules and could be found in the help or manual of respective control
module. Control module helps are located at the bottom of the Contents tab of
Clarity help which can be invoked by pressing F1. Manuals are available at
www.dataapex.com/downloads.
Caution: Manuals are not available for all controlled devices. Control modules developed
by third parties are only supplied with help file.
Common actions available for the pumps are described in next chapter.

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User Guide 7 Device Monitor

7.2 How to directly control LC gradient pumps during run

To control the configured LC pumps directly from Clarity, the Device Monitor
contains the LC Monitor ⓐ section common to up to four pumps (i.e., a maximum
of four solvents). Any combination of isocratic and gradient pumps can be used. If
more than four pumps are needed, any additional pump has to be added as an
auxiliary pump.
Note: The tooltip over each component shows the name of the pump ⓑ .
In the LC Monitor section of the Device Monitor, it is possible to:
l Stop Flow (the pump is stopped without stopping analysis) and Set Flow (a
custom flow rate and composition can be set). Both of these buttons can be used
outside or during analysis. Beware that when used during analysis, the gradient
from the method cannot be restored and the set flow will be used for the rest of
acquisition.
l Resume Idle switches the pump to the idle state as defined in Method Setup - LC
Gradient tab.

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User Guide 7 Device Monitor

Further commands are available for selected pumps (typically those controlled
by Clarity in real time). They are enabled only during runs with a gradient
program.
l Hold halts the gradient at its current state. The button changes to Resume which
can be used to resume the gradient from the point where it was halted.
l Modify Gradient invokes the LC Control Manual Flow dialog (similar to the
Method Setup - LC Gradient) which can be used to adjust the gradient for the
current analysis. This does not influence the method used for analysis in any
way.

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User Guide 8 Chromatogram Editing

8 Chromatogram Editing
This chapter focuses mainly on adjusting integration. For proposed general
workflow see chapter How to integrate chromatogram
Clarity Tips&Tricks videos covering Integration topics can be found in Clarity
Integration playlist.

8.1 How to integrate chromatogram

In order to have the integration of routine samples automated as much as possible
it is necessary to optimize integration parameters and then save them to the
method that is used for measurements. Two integrations algorithms (Wave and
Legacy) with slightly different approach are available, if you are not able to achieve
satisfactory integration in one of them try using the other one. Integration Algorithm
can be changed on Integration tab in Method Setup/Chromatogram.
1. Open one typical chromatogram for your analysis.

2. Set Integration Interval as needed. More details are in Setting Integration

Interval topic.

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User Guide 8 Chromatogram Editing

3. Set Global Peak Width parameter. Choose the narrowest peak which should
be integrated in your chromatogram and select his start and end. This setting
is used for calculation of Global Bunching.
4. Set Global Bunching parameter. This is a filter which is calculated based on
Global Peak Width and sample rate.
a. Alternatively, for chromatogram with high noise, it is possible to use
other filters - FFT Filter, Savitzky- Golay Filter or Moving Average
Filter.
5. Set Global Threshold parameter. This is influenced by the Global Bunching
or other filter set previously. Select an interval containing only noise, not
peaks. A more detailed description of the global parameters is covered by
topic Modifying Global parameters.

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6. (Optional) Set Detect Negative parameter. This has two potential uses, firstly
when you want to integrate also negative peaks. Secondly it may help when
signal has inconsistencies such as dips. This will prevent the integration
algorithm from placing peak starts/ends into them.

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7. Set Global Baseline Slope parameter. Change this parameter after you have
all the peaks integrated, it servers to optimize their start/end positions.
Note: Global Slope is available only in Wave Integration Algorithm.

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8. If you still aren't satisfied with the integration there are another possibilities
for manual changes.
a. Try to use Interval parameters such as Baseline Together, Baseline
Valley, Forward Horizontal etc..
b. Or try to use Peak parameters such as Peak Start, Peak End, Peak
Both, Add Positive etc..
Note: Add Positive operation should be used as a last resort because is
prone to every Retention time shifts. Peak Start and Peak End should
be preferred parameters as they are defined relative to peak apex.
9. When you are happy with the integration. Save method as Template and use
it for further measurements of these sample types.
10. If you have already measured some chromatograms and want to use this
integration in them you can do it using Batch - Reprocess by Method.

8.1.1 Setting the integration interval

1. Signal outside of the interval is not integrated, this function is mainly useful for
omitting solvent peaks etc.

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2. To set the interval on which to apply the integration use Chromatogram -
Integration - Integration Interval or icon ⓐ . It is possible to set multiple
intervals within a single chromatogram.
3. You can check, modify the interval or delete this operations in the Integration
Table ⓑ .

Note: If you want to exclude specific interval from the integration refer to Remove peak
from integration.

8.1.2 Modifying Global parameters

Peaks are only integrated if they exceed a minimum width and height. Slope
parameter influences position of starts and ends of peaks. These optimizations can
be achieved both globally or locally in a specified interval. It is always
recommended to maximally utilize global parameters before using any local one.
Global Bunching works as a smoothing filter, it has to be used only globally to whole
chromatogram.

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Global Peak Width:

l
To adjust minimum width use Chromatogram - Global Peak Width or use
icon ⓐ and select the narrowest you want to integrate.

Global Threshold:
l
To adjust minimum height use Chromatogram - Global Threshold or use
icon ⓐ and select an interval containing only noise, not peaks.

Global Bunching:
l Works as a smoothing filter that automatically averages number of data
points in order to preserve at least 30 data points per narrowest peak. It is
dependent on Global Peak Width value. To use it select Chromatogram -
Global Bunching or use the icon ⓐ after you done adjusting the Global
Peak Width parameter.

Global Slope:
l To adjust minimum slope, where the peak should start/end use
Chromatogram - Global Slope or use icon ⓐ and select the point where
the peak should start/end.

Note: Available only in Wave Integration Algorithm.

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If you are still not happy with the integration suggested by selection from the graph
you can modify the parameter values in the Integration Tableⓑ .

For setting the Local variants of Global parameters:

1. Setting local parameters is similar to the global ones, the only difference is
that they are only applied on selected time interval rather than entire
chromatogram.
2. To set local parameter use context menu Chromatogram - Integration and
select parameter you need. Similarly you can find the icon in the bottom part
of the vertical toolbar ⓒ . Select the time interval in the graph. Small dialog
appears ⓓ , here you can further specify the time interval and mainly select
the value of the parameter. You can use Suggest Value button ⓔ to select
the value from the graph same as for global parameter.
3. Again, all values can be further modified in the Integration Table if needed.

Note: Global bunching is a filter that is always applied to the whole chromatogram. To
filter data locally use other filers from Chromatogram - Integration menu.

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8.1.3 Modifying the beginning and the end of a peak

1. To change the position of peak beginning and/or end use Chromatogram - Peak
- Start and/or Chromatogram - Peak - End alternatively use and/or icons
ⓐ.
2. Set the new beginning ⓑ and/or end by clicking the new position in
chromatogram graph.

8.1.4 Removing a peak from integration manually

With the introduction of the WAVE integration algorithm, there are now 2 ways to
remove the peak from the integration. First one is present also in a Legacy
Integration algorithm, the second is exclusive for the Wave IA.
1. Use Chromatogram - Baseline - Lock (or icon ⓐ ) or Chromatogram - Peak -
Hide.
2. Click once to mark the start of the interval that should be omitted from integration
and click second time to mark its end ⓑ .

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Fig. 1: Difference between Peak Hide (left) and Baseline Lock (right).

Note the two vertical guidelines marking the beginning and end of the peak. More
than one peak can be removed from integration at once.

8.1.4.1 Baseline - Lock

This tool completely removes all peaks that have their maxima within a set time
interval. This could affect other peaks with maxima outside the specified window,
particularly if they share the same baseline.

8.1.4.2 Peak - Hide (and Show)

By default, the Wave algorithm might automatically ignore some of the minor peaks
identified during integration. However, completely eliminating these peaks could
potentially affect the baseline's trajectory. Therefore, these functions offer a flexible
way to handle unwanted peaks without completely removing them.

8.1.5 Changing the position of a peak separating line

1. Select Chromatogram - Peak - Both or click in the Peak toolbar ⓐ .
2. Set the new position of peak-separating line by clicking in the chromatogram
graph ⓑ .

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3. You can check, modify the position or delete this operation in the Integration
Table ⓒ .

Note the vertical guideline indicating the currently selected peak separator position.

8.1.6 Separating rider peaks by tangent

Rider peaks are small peaks which are not well resolved from a large and
asymmetrical neighbor but sit on its leading or trailing side.

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1. Select the rider peaks you want to separate on the leading side of the mother
peak: use Chromatogram - Baseline - Front Tangent or icon ⓐ .
2. Select the rider peaks you want to separate on the trailing side of the mother
peak: use Chromatogram - Baseline - Tail Tangent or icon ⓐ .
3. You can check, modify the interval or delete this operations in the Integration
Table (Baseline - Front tangent and Baseline - Tail tangent rows) ⓑ .

Note: You can also use the Tangent Slope Ratio and Tangent Area Ratio from
Chromatogram - Separation menu to set a threshold for the separation of rider
peaks based on those two parameters.

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8.1.7 Adding a new peak manually

Caution: Manual addition of a peak should be used as a last resort to finish integration of
individual chromatograms. Since the function is based on absolute time, when
used in template method results might be inaccurate if retention time shift occurs.
1. Select Chromatogram - Peak - Add Positive/Negative (also accessible from
context menu) or click and in the Peak toolbar ⓐ . Holding Ctrl key while
selecting the function will allow you to use it repeatedly.
2. Click in the chromatogram and set the beginning ⓑ and the end of a new peak.

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Note the two vertical guidelines marking the beginning and end of the peak. After
finishing the operation new peak is added ⓒ .

Fig. 2: Add Positive

Fig. 3: Add Negative

8.2 Saving the chromatogram method as a template method

Each chromatogram contains saved copy of the method used for acquisition of
such chromatogram. However, changes done in Chromatogram window (e.g.
Description, Integration Parameters, linked Calibration File...) are not updated in
the original method used for acquisition nor processing. To amend your method

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accordingly, you can create template method from the method in chromatogram,
which is useful after optimizing integration parameters.
1. Open the chromatogram with optimized method.
2. Select the Method - Save as Template… to save the method (including the
changes made by you) from the current chromatogram as a new method, or for
example overwrite (update) your acquisition method.

Note: It is not possible to overwrite any method that is currently in use, for example a
method opened on any Instrument.

8.3 Adding a peak to a group

1. Use menu item Chromatogram - Peak - Peak Groups… to invoke Groups dialog.

2. Either select an existing group from the list or create a new one by inserting a
letter to ID (groups are defined by a single letter) field and click the Add button.
Note: Group Name is based on the calibration file, similarly to the Compound
Name.
3. Click in the chromatogram for the first time to select the start point and second
time to select the end point of the group interval. Peaks with apexes found in the
interval will be added to the new group.

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8.4 Removing a peak from a group

1. Use menu item Chromatogram - Peak - Peak Groups… to invoke Groups dialog.

2. Select an existing group from the list and click Delete.

3. Click in the chromatogram to select the start and again to select the end of the
interval which should be removed from the group.

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8.5 Adding text and lines to a chromatogram

Adding text label
1. Right-click in the chromatogram graph to invoke context menu and select Create
Label - Text.
2. "T" will appear next to the cursor, click wherever you would like to place the label.
Text Label dialog will open.
3. Write the text in the Text field.
4. Select the font by clicking the Font button.
5. Enter the Orientation of the text (0 degrees equals horizontal position).
6. Select the Anchor point for the text.
7. Use Assign to - Workplace, if you want the text to stay in the same location
regardless of the opened chromatogram (labels stored in the desktop file). Or
use Assign to - Active Signal, if you want the text to shift as the chromatogram
signal moves, zooms in and out (labels stored in the chromatogram file). The text
will be displayed only when the respective chromatogram signal is active.
8. Click the OK button to accept the settings.

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9. Click and drag the text if you wish to move it to a different location.
10. Double-click the text to open Text Label dialog to adjust the label settings or to
delete it.

Adding line label

1. Right-click in the chromatogram graph to invoke context menu and select Create
Label - Text.
2. "L" will appear next to the cursor, click and drag to place the line label. Line Label
dialog will open.
3. Select whether you want to add an arrow tip at the beginning, end or at both
ends of the line.
4. Select the color by clicking the Color button.
5. Enter the Line Width.
6. Select the Line Style.
7. Use Assign to - Workplace, if you want the text to stay in the same location
regardless of the opened chromatogram (labels stored in the desktop file). Or
use Assign to - Active Signal, if you want the text to shift as the chromatogram
signal moves, zooms in and out (labels stored in the chromatogram file). The text
will be displayed only when the respective chromatogram signal is active.
8. Click the OK button to accept the settings.

9. Click and drag the line if you wish to move it to a different location. Alternatively
drag one of the ends to change its position.
10. Double-click the line to open Line Label dialog to adjust the label settings or to
delete it.

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9 Calibration
Following chapters contains multiple topics which will guide you through the basic
principles of calibrating in Clarity and also introduces you to advanced solution, for
example using the Bracketing.
Clarity Tips&Tricks videos covering Calibration topics can be found in Clarity
Calibration playlist.

9.1 Creating a new calibration

This chapter covers creating a calibration file. You should have at least one
integrated measured standard to be able to fill in the desired peaks into the newly
created calibration.
1. Open the Calibration window: choose Window - Calibration in the Instrument
window or click .

2. Create a new calibration file: select File - New or click ⓐ .

3. Open the Calibration Options dialog: choose Calibration - Options… or click
ⓑ.

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4. Fill in the units in the Compound Units section ⓒ to suit your analysis
conditions.
5. Set the Mode to Calibrateⓓ .
6. Set the Calibration option to Automatic to add the peaks without modification or
Manual to modify them one by one ⓔ .
7. Open integrated chromatogram of a standard: choose File - Open Standard… or
click on ⓕ in the Calibration window.
8. Add peaks belonging to the compounds of interest from the chromatogram of the
standard to the calibration file.
Note:
Select Calibration - Add All or click on to add all integrated peaks or
the Add Peak / Add Group icons to add specific peaks ⓗ.
Regardless of the set Current Level ⓖ the peaks will be added to the
first free level.

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9. If you selected Automatic calibration:

l Name the peaks identified in the Calibration Summary Table ⓘ by
their retention times by typing the Compound Name for each peak.
No compound name may be used more than once.
l Fill in the Amount ⓙ for each compound into the Calibration
Summary Table.

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10. If you selected Manual calibration: Fill in the Amount, the Compound Name and
set any other parameters related to the peak on the Calibration - Add Peak
window. This window will open once for each one of the peaks processed.

11. Save the calibration file - File - Save or click .

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9.2 Adding a new calibration level

Here we describe how to add concentration levels to the calibration file to obtain the
calibration curve of all compounds. This procedure has to be repeated several
times, once for each calibration level to be added.
1. Open the Calibration window: choose Window - Calibration on the Instrument
window or click icon.

2. Open the calibration file: choose File - Open… or click ⓐ.

3. Open calibration standard: select File - Open Standard… or click ⓑ.
Note: Select a measured and qualitatively evaluated chromatogram where all
peaks are available, if possible.
4. Check that the Automatic option is selected in the first field and the Calibration
option in the second field of the calibration mode settings ⓒ .
5. The calibration level number is in the Current Level field ⓓ set automatically to
the first free level.
6. Add all peaks in the chromatogram of the calibration standard to the calibration
file: select Calibration - Add All or click ⓔ.

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Note: In case more peaks than expected emerge in the calibration, the surplus
peaks can be deleted by selecting them in the Calibration Summary
Table and deleting them using Calibration - Delete Compound or clicking
on ⓕ.
7. Set the amounts of the particular compounds into the Calibration Summary
Table, into the Amount column ⓖ of the respective calibration level.
8. Save the calibration file: choose File - Save or click ⓗ
9. Click any tab below ⓘ and you will be able to see the calibration curve ⓙ with
all the levels added for one specific compound ⓚ .

9.3 Applying a calibration to a chromatogram

If the calibration file was not assigned in the template method, the measured
chromatogram will not have it linked either. Here you will learn how to link a
calibration file to a chromatogram.
1. Switch to the Results tab ⓐ at the bottom part of the Chromatogram window.

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2. Check whether the Calibration File (Peak Table) field ⓑ is set to (None). If that
is the case, then the chromatogram does not have a calibration file linked to it.
3. Also check the Compound Names ⓒ in the Result Table section. This column
must be empty.
4. To link the calibration file to the Chromatogram, click the Set… button ⓓ in the
right section of the Results tab. You will get a list of all calibrations available in
the present project.
5. Select the correct calibration file from the list and click OK. The content of the
Chromatogram window will change.

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6. Check that the Calibration File (Peak Table) field contains the name of the
calibration file. ⓔ
7. The Compound Name column ⓕ in the Result Table, as well as the identified
peaks in the graph ⓖ , will now have the names of the identified peaks from the
calibration file.
8. Check the Calculation field ⓗ to see the type of calculation performed on the
chromatogram.
9. Save the chromatogram: select File - Save or click .

9.4 Setting the calibration in the method

After the acquisition is performed according to a method, the resulting
chromatogram files may be calibrated using a specific calibration. If you need to
measure a large number of similar samples, it would be advisable to define a
calibration file prior to the acquisition.
1. Open the template method from the Instrument window by using the Method -
Method Setup command.
2. Go to the Calculation tab.

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3. Click the Set… button ⓐ to select a calibration file for the method, or create a
new calibration file by clicking the New… button ⓑ .
4. Change the default calibration type in the Calculations field ⓒ .
5. Click OK ⓓ to save the changes to the opened method.
6. You can modify the calibration file after acquisition. For more info go to Apply the
calibration to a Chromatogram.

9.5 Calibrating with manually entered Response Factors

When using a free calibration, the amounts for each component are calculated
using the Response Factor instead of a calibration curve.
1. Create a new calibration file: select File - New or click ⓐ.

2. Open the Calibration Options dialog: choose Calibration - Options… or click .

ⓑ

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3. Check that the Compound Units ⓒ are set correctly, Mode to Calibrate ⓓ and
Calibration option is set to Automatic ⓔ .
4. Open an integrated chromatogram of a standard (containing peaks of
compounds of interest with a known concentration): select File - Open
Standard… or click ⓕ on the Calibration window.
5. Add all peaks in the chromatogram of the calibration standard to the calibration
file. Choose Calibration - Add All or click on ⓖ.

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6. Name the peaks identified in the Calibration Summary Table ⓗ by their

retention times by typing the Compound Name for each peak. No peak name
may be used more than once.
7. Set the Calibration Fit Type to Free Calibration ⓘ for each one of the
compounds in the Calibration Summary Table.
More Info:
Right click on the table and select the option Set Columns... to add the Calibration Fit
Type column to the table. Alternatively, you can click on each compound tab at the
bottom of the Calibration window and set the Calibration Fit Type from there.

8. Type in the Manual Response Factor for each one of the compounds ⓙ .

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Caution: Calibration curve cannot be constructed when amount is set to zero for all levels.
In case calibration curve could not be constructed for one of the compounds, no
results are calculated for all of the compounds (as the total amount could be
wrong). If you do not want to calculate amounts for all identified compounds, you
could use free calibration with zero response factor.

9.6 Recalibrating a calibration

You can modify an existing calibration by reloading peaks within one specific level
using the option Recalibrate.
1. Open the Calibration window: choose Window - Calibration on the Instrument
window or click .

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2. Open the calibration file: choose File - Open… or click ⓐ.

3. Open the calibration standard with which you want to recalibrate: select File -
Open Standard… or click ⓑ .
4. Open the Calibration Options dialog: choose Calibration - Options… or click
ⓒ.

5. Set the Calibration option to Automatic to add the peaks without modification or
to Manual to modify them one by one ⓓ .

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6. Set the Mode to Recalibration ⓔ .

7. Select how and whether the new values will be added in the Calibration Options
dialog.
l Choose Replace or Average option to decide what to do with new
response values ⓕ .
l Recalibration Search Criteria defines how much the original and new
values can differ for the recalibration to be performed ⓖ .
8. Select the Level you wish to recalibrate ⓗ .
9. Add peaks to be recalibrated from the calibration standard to the calibration file
on the Calibration window using Calibration - Add Existing or clicking on ⓘ.
10. If you selected Manual calibration:
l Fill in any parameters related to the peak in the Calibration - Add All
window. This window will open once for each one of the peaks
processed.

11. Save the calibration file: choose File - Save or click on .

9.7 Automatic recalibration using a sequence

Here we describe how to add more data to a calibration point from more than one
calibration standard chromatogram using a sequence.
1. Open the method file: use File - Open Method… on the Instrument window or
click in the Method Setup dialog.
2. Go to the Calculation tab.

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3. Connect the calibration file to the method by using the Set… ⓐ button.
4. Save the method file - click OK ⓑ or select File - Save Method or click .

5. Open the Sequence window: select Analysis - Sequence or click in the

Instrument window.

6. Fill in the Sequence Table as described in the section Run a sequence.

7. For the calibration standards, fill in the Sample Type and Lvl columns ⓒ in the
Sequence Table.
More Info:
The Sample Type column for the calibration standard should be set to the Standard
value, the Lvl column for each standard must have a value between 1 and 20. For a
blank sample, select Blank in the Sample Type column.

8. Save the sequence file: select File - Save or click .ⓓ

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The file is now prepared so that the calibration standards measured according to
their sequence rows will automatically recalibrate the calibration file.

9.8 Creating model calibration to use in calibration cloning

This topic will show you how to prepare model calibration to be used during
calibration cloning. If you have calibration already created from the previous
measurement skip to step 4.
1. In the Calibration window, select New ⓐ calibration and Open ⓑ typical
chromatogram as standard.
2. Use Add All ⓒ to add the integrated peaks to calibration.
3. Fill in the Compound Names ⓓ and the Amounts ⓔ for every level that will be
used.

4. Select the Save As option. In the Save As dialog check the Clear Responses
checkbox and save the calibration under a new name.

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9.9 Calibrating using clone on first recalibration

Option Clone on first recalibration sets the sequence and calibration to the Safe
Calibration Usage mode. This option will create a clone (copy) of calibration defined
in the method upon completing the first row of the sequence. Cloned calibration is
attached to each new chromatogram produced by the given sequence.
1. Open the Method Setup dialog - Calculation tab. Select Method - Calculation
from the Instrument window.

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2. Click on Set... button and select a calibration file ⓐ to be used during cloning at
first recalibration.
Note: This calibration will remain unchanged as newly created clone of the
calibration will be used with new responses.
3. Create a custom name for the calibration files in Calibration Cloning in Sequence
ⓑ as explained in Creating customized file names automatically.
Note: The name of the final calibration file will match just the content of this field -
if you wish to include the name of the template calibration, include the
name in this field again (e.g. "test - %s %L %R").
4. Follow the steps in Creating and running a sequence to create your
sequence based on the example below.
More Info:
l
Set the row/s for the standard/s at the beginning. ⓒ
l Add a row for a blank, if you wish to.
l Set the row/s for the unknown samples.

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5. Click to open the Sequence Options Dialog ⓓ .

6. Select Clone on first recalibration ⓔ and click OK.

7. Run the sequence as explained in Creating and running a sequence.

Note: The measured sequence can be reprocessed using Batch. For more info see the
topic Reprocessing whole sequence while using calibration cloning.

9.10 Calibration adjustments

Following articles will describe how to perform some of the most common
calibration modifications that can improve your calibration. Using this guide you
manage to fit your calibration closer to your analytical application.

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Once you added all chromatograms to your calibration and filled Amount values for
all compounds and all levels, you can start to adjust it. Note that the Amount values
are the values you know, because they originate from the concentration levels of
your calibration solutions. Further adjustments of the calibration are available on
the corresponding Compound Tabs at the bottom of the window. In our case, the
Comp No. 3 ⓐ is edited.

Modifying Response Base

Set the Response Base ⓑ to modify whether the calibration curve will be
calculated using Area or Height of the corresponding peak belonging to the specific
compound. Changing the Response Base can help to create better fitting of the
calibration to not well resolved peaks.

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Modifying Origin
Another option how to improve your calibration is setting of Origin ⓒ and its
incorporation or exclusion in calibration calculations. In Clarity there are three
available setting options, as described on the following images. There is also
demonstrated an effect of the Origin setting on calculated Equation and Correlation
factor ⓓ .

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As you can see from the Correlation factor ⓓ values, changing the Origin setting
from the Curve Passes through Origin to Compute with Origin improved the curve
fit. However, the option Ignore Origin has proved to be the best match for the used
detector.

Modifying Curve Fit Type

Following images demonstrate how to modify Curve Fit Type ⓔ from Linear to
Cubic. Cubic Curve Fit Type is used as an example of non-linear Curve Fit Types.
l Linear calibration curve is commonly used for detectors with linear response,
such as Flame Ionization Detector (FID) or Refractive Index Detector (RID).
l Non-linear calibration curve is typical for detectors such as Electron Capture
Detector (ECD) or Evaporative Light Scattering Detector (ELSD).

When changing Curve Fit Type ⓔ pay also attention to the values of the calculated
Equation and Correlation Factor. Increasing value of the Correlation Factor
indicates better selected Curve Fit Type for the measured data.

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As you can see, changing the Curve Fit Type from Linear to Cubic increased the
Correlation Factor from 0.954 to 0.992.

Excluding of Measured Point from Calibration

Clarity also allows excluding any point from calibration. This is helpful in case that
the specific measurement went wrong. Following images describe how to do that.
Please keep in mind that the excluded point isn’t deleted, the point is still part of the
calibration, however, it is omitted from calculation of calibration curve. To exclude
the selected measurement point from the calibration simply uncheck that
measurement in the Used ⓕ column. The excluded point in the graph of calibration
curve will be changed from cross to empty circle ⓖ and calibration curve Equation
and Correlation Factor ⓗ will be recalculated.

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As you can see, excluding the incorrectly measured calibration point resulted in
more accurate calibration.

9.11 Calibration - Advanced Topics

This chapter contains collection of more advanced SOPs topics covering calibration
usage in Clarity.

9.11.1 Compensating for response drift using bracketing

Bracketing is a direct calibration method used to compensate for the variation in
instrument response with time. Typical use is for detector response deteriorating or
sample containing compounds staining or interacting with the column. Bracketing is
not helpful for random variations. Bracketing may be in place when 2 calibration
curves measured on the same series of standards have a stable trend and good
correlation, but they are not the same.
To use bracketing in sequence, the order of the rows must be standards, then
unknowns, then standards again. Usually, two standards are used; more standards
could be used if the measuring instrument has a non-linear response. Samples are
evaluated by a calibration which is created by averaging the standards before and
after the unknown. As every unknown sample series is demarcated by calibration
standards it uses a single calibration. Calibration will be cloned from the previous
calibration clone whenever an unknown sample or blank follows the calibration
standard. The newly cloned calibration file has all responses cleared - apart from

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the responses from the last series of calibration standards (immediately preceding
the current unknown samples).

1. Open the method that will be used in the sequence: click File - Open Method…
from the Instrument window.
2. Navigate to Calculation tab.
3. Set the template calibration as Calibration File: click Set... ⓐ and select the
calibration. Note that this calibration will remain unchanged, newly created clone
of the calibration will be used with new responses.
4. Set the name of the cloned calibration: set the name in Calibration Cloning In
Sequence ⓑ . You can use predefined parameters (refer to Creating
customized file names automatically).

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5. Click OK and save the modified method.

6. Open Calibration window and the template calibration: click Window -
Calibration from the Instrument window and File - Open... in the Calibration
window, select the template calibration (in this case bracketing_
template.cal).
7. Set Compound Names ⓒ , Retention Time ⓓ , Amounts ⓔ , etc., but no
Responses ⓕ (you can use previously measured standard to get the
Retention Times).
8. Update Calibration Options: Set Recalibration to Averageⓖ and No. of
Points to 2ⓗ (no more points needed as they would not be applied anyway).
9. Save changes and close the calibration.

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10. Open Sequence window and create a new sequence: click Analysis -
Sequence and then icon.
11. Set the sequence according to the following steps: (for more details about
creating the sequence refer to Creating and running a sequence)
l
Set the row/s for the standard/s. ⓘ
l Add a row for a blank, if you wish to.
l Set the row/s for the unknown samples.
l Repeat the row/s for the standard/s.

Note: The sequence must start and end with a row with Standard Sample Type.
l Repeat the previous four steps for every "bracket" of unknown samples you
wish to add.

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12. Set the sequence to operate in the calibration bracketing mode:

l
Click icon to open the Sequence Options dialog. ⓙ
l
Check Calibration Bracketing. ⓚ
l Click OK.

Note: If your sequence is using multiple methods, calibration using bracketing

is still possible to use but make sure that the Calculation tab is exactly the
same for all the methods used in the sequence.

13. Run the sequence (for more details about running the sequence refer to
Creating and running a sequence) .
14. The results shown while the sequence is running are recalculated at the end
of each bracket, when the standard after the unknown sample is acquired.

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The calibration used is an average of the two calibrations, before and after
the unknown.

Note: The measured sequence can be reprocessed using Batch. For more info see the
topic Reprocessing whole sequence while using calibration cloning.

9.11.2 Creating a Multisignal Calibration

This topic describes how to construct a multisignal calibration in Clarity. Below is an

example of creating and constructing a three (concentration) level calibration which
provides calculation parameters for calculating results in two- signal
chromatograms. This procedure should be utilized when different compounds are
detected on each signal. In case all signals detect the same compounds there is no
need to use On Active Signal option, unless you don't want to quantify all of the
compounds on some signals.
Note: For cases there is need to create and construct more than a two-signal calibration,
the applied approach remains the same. It varies from the below procedure
slightly. These aspects are reflected in the respective steps of this topic.
This guide is based on two-signal chromatograms of standards with simulated data
(for demonstration purposes it can be said that first signal detects anions and
second detects cations) on three concentration levels (5 000 ppm, 10 000 ppm and
20 000 ppm) and one sample chromatogram. All chromatograms used in this guide
have been integrated in manner to fit the demonstration purpose.

Prerequisites:
l Integrated chromatograms of standards.

l Integrated chromatogram of sample.

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1. Open the Calibration window: select Window - Calibration in the Instrument

window or click .
2. Create a new calibration file: select File - New or click ⓐ.
3. Open the Calibration Options dialog: select Calibration - Options… or click
ⓑ.
4. Set section Apply on to option On Active Signal field ⓒ .
Note: As mentioned in the beginning. If all peaks in the standard chromatogram
represent the same compound across all signals it is viable to change the
option to On All Signals. In such case there is no difference in working with
multisignal and single signal calibration.

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5. Open calibration standard: select File - Open Standard… or click ⓓ to open

measured and integrated chromatogram with the lowest concentration level
where all peaks are available.
6. Make sure the upper toolbar displays on Active Signal. It is also recommended
to make sure you are currently on the first signal as well (focused red square in
right part of the upper toolbar).
7. Fill the Calibration Summary Table with peaks from the currently selected signal
in chromatogram using the Add All icon ⓔ .
Note: If only some peaks should evaluated it can be done by using Add Peak
on peaks that need to be included in calibration.

8. Rename automatically pre-filled names of peaks ⓕ .

9. Enter values for given standard into the Amount column ⓖ .

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10. Switch to the second signal in chromatogram to make it active ⓗ .

11. Optional: Switch the table filter on using Filter Not Used Compounds icon ⓘ .
With this option enabled, rows with not Used compounds on given signal are
hidden, which makes it easier to navigate Calibration Summary Table.

12. Fill the Calibration Summary Table with peaks from the currently selected
(second) signal in chromatogram using Add All icon. Dialog will be invoked
after clicking Add All icon questioning if an already used chromatogram
should be reused for this calibration. It is necessary to confirm the reuse by
clicking Yes button.
Note: In case of constructing calibration with more than two signals, steps 12 and
14 have to repeated as many times as necessary in order to fill in peaks
from all signals to Calibration Summary Table.

Note:

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This dialog will be invoked multiple times based on number of signals in

calibration for calibration with more than two signals. It is possible to switch
off invoking of the dialog using the checkbox in the bottom of the dialog.

Note: Which signal of chromatogram is active and is being worked with is given
by the Calibration Summary Table title's color and displayed number of
currently active signal.

13. Rename the automatically pre-filled names in the Calibration Summary Table
column.
14. Enter values into Amount column. The first concentration level is finished now. It
is possible to proceed building up to next levels of calibration.
Note: All rows of Amount column have to be filled in.

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15. Open chromatogram of standard of the next (second) concentration level.

16. Fill the next level of Calibration Summary Table with Responses for each signal
following the same steps as for Level 1 (Steps 8-16, renaming the compounds is
omitted as the names carry over from previous levels).
Note:
Add Existing can be used instead of Add All . This command only
adds response for peaks that are preset on first level. This means that extra
peaks (or peaks chosen not to be evaluated) that are present in the second
(and later) standards, but not in the first one will not be added.

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17. Open chromatogram of standard of the next (third) concentration level.

18. Fill the Calibration Summary Table in the same manner as for second level (step
18).

Note: It is possible to review calibration curves for each compound on the

respective tabs of individual compounds. Notice that calibration curve are
displayed only for valid signal (When filtering is enabled tabs of individual
compounds are displayed only on signal where they are used). Signal
selection is located in right upper corner of the Calibration Window.

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19. When calibration is finished do not forget to save it using select File - Save or
click on .

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20. For calculating result in sample open the Chromatogram window select
Window - Chromatogram on the Instrument window or click on and open
chromatogram of sample and link the calibration to chromatogram.
21. Review results on Results Table of each individual signal or review results for all
signals on All Signals Results Table.

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9.11.3 Improving quantification with the standard addition method

Standard addition is a quantification approach (similar to ESTD or ISTD) useful in
case the sample matrix is complex and when it influences responses of analytes.
By spiking samples with a series of increasing amounts of the analytes, standard
addition calibration curves for each sample are obtained from which the
concentrations of unknown samples can be calculated.

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1. Create a new method or open your already prepared method. Go to Method

Setup - Calculation tab.
2. Create New calibration file ⓐ or Set your already created Calibration file ⓑ .

3. Select STDADD in the Calculations drop-down list ⓒ .

4. Create a custom name for the cloned calibration files in Calibration Cloning in
Sequence ⓓ and click OK.
Note: Make sure that each of the measured samples will have a unique
calibration name; use predefined parameters to achieve that.
5. Open the Calibration window by selecting Window - Calibration in the Instrument
window.

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6. Open the Calibration Options dialog. Choose Calibration - Options… or click on
. Select the STDADD in the Display Mode drop-down list and click OK.

7. Create a new sequence with the given order of the lines:

l Sample A
l Sample A with Standard level 1
l Sample A with Standard level 2
l Sample A with Standard level X
l Sample B
l Sample B with Standard level 1
l Sample B with Standard level X
l continue with the given pattern until desired state
8. Set the columns as follows: for Unknown samples set Sample Type column to
Unknown and for Standard Addition samples, set Sample Type column to
Standard and Lvl column to level corresponding to the added amount in given
sample.

Note: In case you want to use a blank sample too, such sample shall be always put in
the sequence before the unknown sample.

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9. Click to open the Sequence Options dialog ⓔ and select Standard Addition
Measurement and click OK.

10. Run the sequence and wait until the sequence is finished.
11. Open the Calibration window: choose Window - Calibration in the Instrument
window or click on .
12. Go to File - Open and open the cloned calibration file for the desired sample.
13. Click on the Compound tab ⓕ to see the calibration curve. Fill in the amounts of
the standard samples.

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14. Open chromatogram of the desired unknown sample. The Result Table now
contains amount of the unknown sample, calculated using Standard Addition.

Note: The measured sequence can be reprocessed using Batch. For more info see the
topic Reprocessing whole sequence while using calibration cloning.

9.11.3.1 How the concentration is calculated

The concentration of an unknown sample is calculated using a calibration curve,
which intersects in the point [0,0].
As shown in the picture below, when not using Blank samples the the concentration
of an unknown sample equals the orange line (0 response corresponds to 0
unknown sample concentration - 0u), whereas the concentration of the UNKNOWN
SAMPLE when using Blank equals the green line (Blank response corresponds to 0
unknown sample concentration - 0b).

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9.11.4 Using a reference peak to improve compound identification

A reference peak is a peak used as a reference for recalculating the retention times
for the rest of the peaks in a chromatogram. This method allows a better compound
identification in those cases where there might be a drift in the retention times in
repeated analyses. It is possible to set multiple reference peaks. For ordinary
peaks, the expected retention times will be adjusted by linear interpolation between
the nearest reference peaks.

1. Open the calibration file: choose File - Open… or click on .

2. Select Refer on the Peak Type column for an easily identifiable compound (i.e.
main compound, ISTD standard, any well resolved peak of the matrix) that you
will use as a reference ⓐ . To apply the reference peak, Used check-box must
be checked ⓑ .

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3. Edit the Left and Right window values to define the range within which the peak
should appear ⓒ . This window may include other peaks if the selected
reference peak meets the Peak Selection criteria.
4. Select the Peak Selection criteria: biggest, nearest, first or last peak ⓓ .
More Info:
Ordinary peaks are identified by the nearest option by default. For reference peaks
the biggest will be set as default. Note that the biggest refers to the selected
Response Base, i.e. if the Area is the Response Base, the detected peak may not be
the highest one. In specific cases selecting First or Last may be advantageous.
To add the Peak Selection column:
l Right click anywhere on the table
l Select Set Up Columns to open the relevant window.
l Select Peak Type on the right and click on Show and then Ok.
5. Repeat steps 3 to 5 to add more reference peaks.

Note: In case of multisignal calibration, where compound used as reference does not
match the selection criteria on some signal(s), create a variant of the compound
only for that signal(s). The name must be different - e.g. Oxalic - UV, Oxalic - RI),
copy the rest of the original row, check the used checkbox only for one variant on
each signal. Now change the Peak Selection criteria value, or if suitable, change
the Peak type to Ordinary, and select other Reference peak on that signal.

6. Save the calibration file: choose File - Save or click .

7. Link the calibration to your chromatogram as explained in Applying a calibration
to a chromatogram.

9.11.5 Normalized Area % Calculation

For Normalized Area % calculation no specific settings are necessary, the
calculation results are always present in the Area% column in the Result table.

9.11.6 Normalized Amount % Calculation

This topic describes how to use Clarity, in order to obtain correct results calculated
according to normalization calibration method. The normalization can be achieved
by two means. First option is applicable to known response factors specific for each
analyte. Second option is to use calibration based on standard sample with known
fraction composition. In the latter case, Clarity automatically calculates response
factors for all analytes that are subsequently applied in evaluation of the unknown
sample. The results are displayed in Amount% column in the Summary Table and
represent percent fraction of each analyte present in the unknown sample.
For both options set the calibration to the NORM Display mode, this ensures that
Clarity checks that all the peaks are used for calculations and 100% Amount really
corresponds to the whole sample.
l Set Display Mode to NORM ⓐ in Calibration Options dialog.

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A) Application of specific Response Factors

l Use procedure explained in the chapter Calibrating with manually entered
Response Factors.
Figure below displays Result Table of a chromatogram with linked calibration that
was created using the above mentioned method. Note different values in columns
Area [%] and Amount% are caused by various values in Manual Response Factor
column.

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B) Application of automatically calculated Response Factors based on

calibration with standard sample with known composition
l Use procedure explained in the chapter Creating a new calibration.
Figure below displays Result Table of a chromatogram with linked calibration that
was created using the above mentioned method. Note different values in columns
Area [%] and Amount% are caused by calculated values in Response Factor
column.

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9.11.7 Using Calculate By to determine the amount of a

compound with no standard available
When no standard of a compound is available and a compound with known
response ratio to the unavailable one is present within the sample (this information
can be found in respective norm etc.) the Calculate By and Correction factor can be
used to determine its amount in the sample.
1. Open the calibration file.
2. The Calculate By and Correction Factor are hidden by default. To display
them right-click the table, select Setup Columns...and in the following dialog
move the respective items from Hide Columns list to Show Columns list.
3. For compound (Chloroform in the example) ⓐ that should be evaulated by
another one, select its Calculate By field ⓑ and pick which compound to use
for the calculation (Trichloroethane in the emxaple).
Note: Only compounds (peaks) already added to the calibration can be
selected.
4. Fill the known response ratio to the Correction Factor column ⓒ .
Note: The Amount filled in the row that will be calculated using calibration curve
of another compound will be ignored.

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5. The resulting amount in Chromatogram Results Table will be calculated
according to the calibration curve of compound selected to Calculate By, and
multiplied by the Correction Factor.
Note: A compound marked as ISTD should neither be used as a compound that
is used to calculate another compound nor as a compound that is
calculated using another compound.

In the example Chloroform is calculated based on the calibration curve of

Trichlorethane, their response ratio is 0.328.

9.11.8 Calibration with ISTD

The use of internal standard (ISTD) helps to compensate for non- reproducible
injected volume or for analyte losses during sample preparation. A known amount
of internal standard compound (which should have similar properties as the
analyte, but should not be present in the samples) is added to the standards and
samples. The determined analyte amounts are then corrected based on the ratio of
the added and detected amounts of the ISTD compound(s).
This chapter provides detailed insights into the differences when creating a
calibration with ISTD compared to a standard calibration, as described in Creating a
new calibration.
1. In the Calibration Options window (accessible via the icon ⓐ in the
Calibration window), change the Display Mode to ISTD ⓑ .
2. Open your first calibration standard and add peaks to the Calibration Summary
Table as usual.
3. Label the peaks by the compound names in the corresponding column ⓒ and
fill in the Amount column ⓓ with the amounts of the present compounds
including ISTD.
4. In the row corresponding to ISTD, change the type of the cell in the Is ISTD
column to ISTD1 ⓔ . The Use ISTD column ⓕ now contains the name of the
selected ISTD compound in all the other rows. In compounds tabs, the axes are
labeled according to the selected ISTD.

Note: You can set up to 10 compounds as ISTDs in the Is ISTD column. When more
ISTDs are present, you can specify which one to use for quantification of which
compound in the Use ISTD column.

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5. Now, the first calibration level is set. Continue as usual to set the remaining
calibration levels using the measured calibration standards (as shown in Adding
a new calibration level). Enter the ISTD amounts according to the mode you plan
to work in.
The created ISTD calibration may now be linked to an already measured
chromatogram for direct results assessment (see Applying calibration to a
chromatogram), and it may be also linked to a method. This causes that the
chromatograms measured using this method will be automatically evaluated using
the pre-selected ISTD calibration.

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6. To link the ISTD calibration to a method, in Method Setup, open the Calculation
tab ⓐ and set the created ISTD calibration file ⓑ . The ISTD parameter ⓒ
should be selected in the Calculations option. Press the OK button to save
the Method and close the dialog.

7. To use the ISTD method in single analysis, set the ISTD1 Amount ⓐ in the
Single Analysis window to the desired value. In the case of more than one ISTD
compound present, set the amounts in the dialog which opens by clicking the
triple dot menu ⓑ .
8. Select the previously created method ⓒ . You can Run Acquisition directly
from the Single Analysis window.

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The sequence analysis setup is analogous to the single analysis. The ISTD2–
ISTD10 amount columns are not shown by default and can be added via the Edit -
Setup columns... dialog.
Note: In the case the amount of internal standard is the same for all standards and
samples, it is possible to enter zero instead of the amount (which may not be
known). In such case, the correction will be based on the ratio of the ISTD peak
response in the standards and unknowns. Note that the ISTD amounts must be
entered or set to zero both in Calibration and in the Sample Header. A mismatch
will be detected and reported as error.

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9 Batch Processing
This chapter focuses on processing more chromatograms using Batch dialog.
There are 3 main ways of workflow Reprocessing whole sequence, Reprocessing
by Method and Post Run options, all will be explained in more detail in this chapter.
Clarity Tips&Tricks videos covering Batch topics can be found in Clarity Batch
playlist.

9.12 Reprocessing whole sequence

Reprocessing whole sequence can be convenient if performing reintegration,
recalibration, or changing types of samples is needed. It can also be used with
calibration cloning, more in the topic Complete processing with calibration cloning.
Steps below described process where sequeunce is already measured by template
method with optimized integration parameters, for more see Save Method as a
Template.
1. Measure the sequence with no post run options set and/or no Levels for
standards filled in (Typically, you want to perform the
recalibration/export/print of the results after reviewing the chromatograms).
2. Review the chromatograms: check the integration, etc.
3. Go to the measured sequence, set Levelsⓐ for calibration standards and
enable Post Run options you wish to perform, e.g., Print To PDF ⓒ . It is also
possible to uncheck (check) the Run checkbox at rows you don’t want to
reprocess.
Note: To print or export the data the chromatogram has to be opened in the
Chromatogram window - this is achieved by checkbox in the Open
ⓑ column on a given row.

4. Open the Batch dialog by using Analysis - Batch in the Instrument window.
5. Switch File Type to Sequence Files ⓓ .
6. Select the Sequence you wish to reprocess.
7. Check the Complete Processing ⓔ checkbox.
8. To preserve manually updated integration (this mainly considers small
individual adjustments where optimized parameters weren't satisfactory)
select the Preserve ⓕ in the Integrationpart of Options section.
9. To perform recalibration based on updated integration select Update ⓖ in

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the Calibration part of Options section.
10. Proceed ⓗ with the batch processing.

The recalibration will be performed and Post Run options defined in the sequence
will be performed.

Caution: The operations during Batch reprocessing are done row after row, injection after
injection. In some situations it is necessary to perform the Complete Processing in
two steps - first just the recalibrations, second the post-run actions (either using
the Complete Processing again with the Integration a Calibration settings in the
Options section to Preserve, or through running the post- process on selected
chromatograms only through procedure described in Performing Post Run
Options from Batch dialog section). For example, if the sequence is using
calibration bracketing the unknowns are measured before second standards set
and if the unknowns were reported during the recalibration step, the responses
from the second standards set would be missing in the report.

9.13 Reprocessing whole sequence while using calibration

cloning
If you are using any kind of the calibration cloning in the sequence the reprocessing
whole sequence is similar to regular reprocessing described in the previous topic.

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Please refer to the Calibrating using clone on first recalibration, Compensating for
response drift using bracketing or Improving quantification with the standard
addition method topics to learn more about Calibration Cloning in Clarity.
The difference from the standard Reprocessing procedure described in
Reprocessing whole sequence topic is shown below.
l In the Batch dialog you have additional option for calibration behavior, the
meanings of options are:
l If you select Update ⓐ in Calibration part of Options section the
calibration(s) that are currently linked to measured chromatogram(s) will
be recalibrated (new cloning is NOT performed).
l If you select Clone New ⓑ in Calibration part of Options section new
calibration(s) will be created as if the sequence was run again (new clone
(s) are created and linked to chromatograms).

9.14 Reprocessing by selected method

Reprocessing by method is suitable for applying Integration parameters to
previously measured chromatograms after these parameters were saved to the
method by Save Method as a Template. You can also changed the link to the
calibration file without the calibration being reprocessed.
Note: If the Sequence file is selected to be reprocessed by method, all currently linked
chromatograms will be reprocessed. No recalibration is carried out, when
Calibration - Update is selected only links to calibration are changed without any
changes to the calibration file itself.
1. Prepare your method with desired integration and linked calibration.
2. Open Batch dialog by menu Analysis - Batch... from the Instrument window.
3. Select chromatograms you want to reprocess (Alternatively, select sequence(s),
depending on your File Type).
4. Select Reprocess by Method ⓐ and define your created method.
5. Select Update ⓑ Integration in case you want to change integration parameters
as set in the defined method.
6. Click on Proceed ⓒ .

Note: Reprocess by Method can be combined with Post Run Options if you are sure that
changes in chromatograms do not have to be reviewed before exporting/printing.

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Now your chromatograms are reprocessed, with linked calibration file and
amended integration parameters from the used method.

9.15 Performing Post Run Options from Batch dialog

This procedure is useful if you need to Print or Export more chromatograms at
once, e.g. after all of them were reviewed and signed.
1. Navigate to Batch dialog by clicking Analysis - Batch in Instrument window.
2. Select chromatogram(s)/sequence(s) that you want to print reports for (when
sequence file is selected, all chromatograms that are currently linked in it will be
reported). Which files are displayed is based on File Type drop-down menu.
3. Select Open in Chromatogram Window to be able to select Print Results and/or
Print Results to PDF and/or the Export Data (or select any other option).
4. Select report style you would like to use by clicking button.
5. (Optional) change Open with Calibration to Stored, this will ensure that data will
be printed in the state they were saved in last time.
Note: By default chromatograms are opened with Linked calibration. If the
calibration was changed after saving chromatograms the results might be
influenced.
6. Click Proceed.

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Note: It is also possible to process data before printing them by using Complete
Processing or Reprocess by Method options. When Complete Processing is
selected Post Run options are governed by settings in reprocessed sequence. For
more info see chapter regarding Batch dialog for more info.

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10 Results and Calculations

Advanced topics describing how to use User Columns to calculate custom results,
etc.

10.1 User Columns

This article describes how to append a new column with user-defined calculation to
the Chromatogram - Result Table. For more details about User Columns refer to
Reference Guide Manual.
Note that majority of calculations require chromatogram to be calibrated. Without it
the necessary values are not available.
Caution: User Columns are stored in .DSK files. If the station is used by more users and
User Columns are needed it is recommended to set shared .DSK file as described
in chapter "Sharing settings among users".
1. Open a chromatogram you want to work with and switch to Results tab.
2. Right click on the Result Table and select User Columns - Add... ⓐ , the Add
User Column dialog will be opened.

3. Fill in the Title ⓑ of the new column. In our case Ratio Area/ISTD.
4. Check/Uncheck Calculate Total ⓒ (depends on whether sum of calculated
values has a meaning).
5. Fill in Expression ⓓ line , which presents the user's defined calculation. In our
case:

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l In Columns: ⓔ list double-click Area.
l In Opers: ⓕ list double-click /.
lIn Columns:list select Area, then click on Special Values ⓖ , select
Compound ⓗ , choose ISTD ⓘ and click OK.
6. Fill in appropriate Units ⓙ based on the formula.
7. Click OK ⓚ in the Add User Column dialog.
Note: It is possible to fill Expression by typing if you know the correct syntax.

8. New User Column is added to the Result Table ⓛ .

Note: You can edit existing User Columns by right-clicking into them and selecting User
Columns - Edit Selected....

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10.2 User Variables

This article describes how to set Analysis and Method User Variables which can be
subsequently used in User Columns calculations. Analysis User Variables can be
defined in Single Analysis or Sequence window. Method User Variables can be
defined in Method Setup window.

A) Setting of Analysis User Variables in Single Analysis window

1. In Single Analysis dialog navigate to the User Variables tab ⓐ .
2. Define Name of the variable ⓑ . If the field is left empty, default name
AnalysisUserVar1-AnalysisUserVar3 will be used.
3. Define numerical Value of the variable ⓒ .

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B) Setting of Analysis User Variables in Sequence window

1. In Sequence window the AnalysisUserVar1 - AnalysisUserVar3 columns are
hidden by default.
2. To display them right-click on the Seqeunce Table and use Setup Columns...
command.
3. Select the variable in the Hide Columns list ⓓ , fill its name ⓔ and click Show
ⓕ (item will be move to the Show Columns list ⓖ ).
4. Repeat the previous step if more variables are needed then click OK ⓗ .

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5. Defined Custom Name of the variable is used directly in the column header ⓘ .
Fill in the values for each row (different values can be used).

C) Setting of Method User Variables in Method Setup window

1. In the Method Setup dialog navigate to Advanced tab
2. Define Name, numerical and Value of the variables that should be used ⓙ .
Default name MethodUserVar1- MethodUserVar3 is used when the Name is
empty.

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D) Setting of User Columns with User Variables

Analysis and Method User Variables are also editable directly from Chromatogram
window on Results tab in User Variables section (it is collapsed by default and must
be expanded by clicking the arrow symbol).
Variables can be modified in the same manner as in the previous cases.

Note: To use variables in custom calculations add User Column as described in chapter
"User Columns" and while formulating the Expression select the desired variable
from Variables list ⓚ .

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10.3 Signal to Noise Ratio Calculation

This article describes how to calculate Signal to Noise Ratio using User Columns
calculations with Variables.

10.3.1 Noise Parameter Evaluation

At first Noise value has to be evaluated. This value is subsequently used to
calculate the Signal to Noise Ratio.
1. Open measured chromatogram in the Chromatogram window
2. Use Chromatogram - Noise & Drift - Noise Evaluation ⓐ and select the interval
for noise calculation. The same result can be obtained from the Integration Table
after selecting the Evaluation - Noise operation and inputting the desired interval
manually.
3. The value of the evaluated Noise Parameter is shown in the Result Table header
ⓑ.
4. For the same chromatogram such value is stored as a Noise variable in the Edit
User Columns - Variables ⓔ .

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10.3.2 Calculating Signal to Noise Ratio

Signal to Noise Ratio is important parameter used for method validation. Most
commonly used generic formula for Signal to Noise = 2*Peak Height/Noise.
For such calculation, two possible approaches exist:
l The Noise is determined from the same chromatogram within area with no
peaks. The Noise variable ⓔ can be used directly in the formula entered in the
Expression ⓒ edit box. In that case the resulting formula will be for example 2*
[Height]/ [Noise], where both parameters are determined from the same
chromatogram.
l The Noise is determined from other chromatograms (e.g., by measuring blanks
and evaluating the Noise in the area of expected peak). In the Edit User Column
dialog in the Expression ⓒ edit box use the [Height] ⓓ from the Columns
section for peak height and enter the calculated Noise value as a constant. The
resulting formula will be then e.g. 2*[Height]/0.1080, where the number 0.1080 is
the calculated Noise parameter. Alternatively, the calculated Noise parameter
could be stored as a Method User Variable or as an Analysis User Variable ⓕ to

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simplify changes of the value - this variable can be then used instead of entering
the numerical value in the Expression edit box.

Note: In the Expression edit box, variables are treated as numbers, therefore operators
and numbers can be used to modify the formula. The resulting formula can be e. g.
2* [Height]/ [Noise] or 2* [Height]/ [UserVariableNoise] (where the
[UserVariableNoise] represents user variable to which the Noise value
determined from chromatogram blank is stored) or 2*[Height]/0.1080 (where the
0.1080 represents the actual Noise value determined from chromatogram blank).

Note: Setting the Analysis User Variable or the Method User Variable is described in the
section User Variables on pg. 142.

10.4 How to calculate Relative Retention Time

This chapter describes how to calculate Relative Retention Time (RRT). In Clarity,
there are basically two ways how to achieve that. In the first one, there is peak in the
chromatogram that you want to use for the calculation. In the second approach, you
fill in the time for an Unretained Peak and then use it for the calculations.

10.4.1 Relative Retention Time calculation based on an existing

peak
1. Open a chromatogram you want to work with and switch to Results tab.
2. Add a User Column as described in chapter "User Columns".
3. Fill the Title for the new column - e.g., RRT ① .
4. Uncheck Calculate Total ② .
5. Enter "[Reten. Time]/[malic$Reten. Time]" formula to the Expression field ③ ,
where "malic" represents your compound which should be used for calculation of
RRT. You can either use items from the Columns: list or type them manually.

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Note: To insert [malic$Reten. Time] select Reten. Time in Columns: list, click Special
Values ④ , in the drop-down list select Compound ⑤ , and in the following dialog,
select the compound ⑥ you want to use for calculation of RRT (the list is based
on the used calibration file).

6. Close the Add User Column dialog using OK

7. A new RRT column ⑦ is displayed in the Result Table.

Note: You can do a quick check that the calculation is correct: look at the malic
compound, the RRT shoud be 1.

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10.4.2 Relative Retention Time based on the Unretained Peak

variable
1. Open the chromatogram you want to work with and switch to the Performance
tab.
2. Fill in the Unretained Peak Time as you need ① .

3. Go to the Results tab.

4. Add a User Column as described in chapter "User Columns".
5. Fill the Title for the new column - e.g., RRT ② .
6. Uncheck Calculate Total ③ .
7. Enter "[Reten. Time]/[Unretained Peak Time]" formula to the Expression field
④ . You can either use items from the Columns: and Variables: lists or type them
manually.

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8. Close the Add User Column dialog using OK.

9. A new RRT column ⑤ is displayed in the Result Table.

10.5 How to calculate Peak to Valley Ratio

This chapter describes how to calculate Peak to Valley, which is a ratio of signal
height in peak apex and signal height in the end of peak. This ratio is used for e.g.,
impurity determination.
1. Open a chromatogram you want to work with and switch to Results tab.
2. Add a User Column as described in chapter "User Columns".
3. Fill the Title for the new column - e.g. P/V Ratio ① .

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4. Uncheck Calculate Total ② .

5. Enter "[Height]/([End Value (Signal)]-[End Value])" formula to the Expression
field ③ . You can either use items from Columns: list or type it manually.
6. Close the dialog by clicking OK.

7. New P/V Ratio column ④ is displayed in the Result Table.

Note: Value is only valid for peaks, where peak end is not on the baseline.

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10.6 How to handle not-found compounds in your

calculations
If any compound is missing from a chromatogram, its amount is not calculated. In
any equations within User Columns, where this amount would be used, the
calculations would produce ??? (invalid result). In such cases, the iferr0 function
can replace the missing value with 0 (analogically, the iferr1 function replaces the
missing value with 1). This functionality can be used in situations, when a
substance is present in multiple chromatogram peaks, possibly even in different
ratios. User Columns can be used to determine its total content. The Expression
(equation) would then contain the Amounts of compounds in the chromatogram.
However, some of the compounds may not be present in the evaluated
chromatogram. The following case scenario shows how the iferr0 function can be
used. The goal is to calculate the content of Vitamin E in different Tocopherols.
1. Open a chromatogram you want to work with and switch to Results tab.
2. Add a User Column as described in chapter "User Columns".
3. Fill the Title for the new column - e.g. Vitamin E ① .
4. Uncheck Calculate Total ② .
5. Enter the formula for calculating the vitamin E content, e.g., " ([α-
Tocopherol$Amount]+0.5* [β- Tocopherol$Amount]+0.25* [γ-
Tocopherol$Amount]+0.01*[δ-Tocopherol$Amount])/10" to the Expression field.

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You can either use items from the Columns: list with Special Values or type it
manually.
6. Apply the iferr0 function on the items that may be missing from the result table.
The resulting function will look like the following: (iferr0 ([α-
Tocopherol$Amount])+0.5*iferr0 ([β- Tocopherol$Amount])+0.25*iferr0 ([γ-
Tocopherol$Amount])+0.01*iferr0([δ-Tocopherol$Amount]))/10 ③ .
7. Close the dialog by clicking OK.

8. The new Vitamin E column ④ is displayed in the Result Table.

9. In the case that any of the compounds is not found in the chromatogram (such as
here, in the case of α- Tocopherol), the Amount is not calculated. The iferr0
function replaces the not-found Amount with zero in further calculations.

Note that the All Peaks in Calibration ⑤ option is selected. Otherwise, the missing
compound would not be present in the Result Table, and the calculation would not
be possible.

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10.7 How to Display Older Results when Linked Calibration

is Modified
Clarity does not store any results in the chromatogram, the result table is always
calculated from the actual state of the calibration file referenced in the Calibration
Table (Peak Table), i.e. Linked calibration. Any changes in this calibration will be
immediately reflected in the displayed results. Each time a chromatogram is saved
the current state of the linked calibration is stored (i.e. Stored calibration) in the
chromatogram history (just values needed to calculate the results, not a complete
calibration). Chromatogram opened with a version from history (i.e. opened with
Stored calibration) will display results as they were at that time.
In case the calibration file is reused for some time, opening the chromatogram with
linked calibration will show changed results due to changes in the linked calibration.
To avoid this, two approaches are possible:
1. Make a copy of the calibration file so each series of measured chromatograms
will be linked to a separate calibration file. This has advantage in case some
amendments to the calibration will be necessary later, as the amendments will
affect only the related chromatograms. Such procedure could be automated
from sequence. For more information regarding this procedure, see the chapter
"Calibrating using clone on first recalibration" on pg. 96..

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2. Using the Open with stored calibration option. Such option is accessible from
multiple dialogs, depending on whether Single Analysis or Sequence is
measured (automated approach) or this option can be selected upon opening
the chromatogram.
l In the Single Analysis dialog - Post Run Settings tab select Open with
stored calibration option.

l In the Sequence window select checkbox in the Stored Calib.

column. By default, Stored Calib. column is hidden. To show it, right
mouse click in the sequence table and choose Setup Columns....
From the Setup Columns dialog, choose Stored Calib. from the left
list and click on the Show button - it will be added to the show list.
Once you click the OK button, you will return to the Sequence
window and the new Stored Calib. column will be added.

l In the Chromatogram window select Open with stored calibration

option. This will open the chromatogram with the most recent point

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from history and show the results according to the stored calibration.
Any changes in the linked calibration will not affect those results. To
open the chromatogram with the stored calibration this way it is
necessary to re- open the chromatogram using the Open
Chromatogram dialog - re-opening the Chromatogram window is not
sufficient.
Note: This setting is only applied and saved to the currently opened
chromatogram. It will not be transferred to the next (different)
opened chromatogram.

10.8 Calculating percentage content of a compound in a

solid sample
This is a standard procedure used across various chromatography applications - a
known amount of a sample is dissolved in a known volume of a solvent and the goal
is to determine the percentage content of the compound in the sample.
1. Open your calibration/create a new one in the Calibration window.
2. Click the icon to open Calibration Options dialog ① .
3. Specify used unit for the amount in Compound Units field ② . Confirm changes
by clicking OK button.
Note: Fill the unit used for the total amount of sample. In our specific case
sample was weighted and mg is used. Set units are used in the
Chromatogram window for further calculations.

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4. Fill corresponding Amount for each compound as concentration ③ .

Note: That means amount divided by the volume of solvent used to prepare the
standard solution. In our example 400 mg of vanilin was dissolved in 100
ml, thus the Response from the standard chromatogram corresponds to 4
mg/ml which is the value entered in the Amount field in the calibration.
5. Save the calibration and open Chromatogram window ④ .

6. Open chromatogram(s), assign each chromatogram prepared calibration using

the Set... button ⑤ .
7. Fill the amount of the sample that had been used ⑥ . Amount refers to the mass
of the sample used. Units are automatically copied from the Calibration Options
(see step 3). Amount replaces the Total value in the Amount column of the
Result Table. In our example: 325 mg of sample had been used.
8. Fill the dilution that had been used ⑦ . Dilution refers to the solvent volume that
has been used to dilute the sample. Dilution multiplies the values in the Amount
column of the Result Table. In our example: 325 mg of sample had been diluted
by 100 ml of solvent.
9. Column Amount% in the Result Table now displays the percentage amount of
the compound in the sample ⑧ .

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Note: It is possible to automatize this process. Calibration can be linked to the used
method so it is automatically linked. Amount and Dilution can be pre- filled in
Single Analysis or Sequence windows. Beware that columns in Sequence have
slightly different names - Sample Amount and Sample Dilut.

10.9 Comparing the results from several chromatograms

The default maximum number of chromatograms in Overlay is set to 20. In case
summary report should include more chromatograms, this limit can be changed in
the User Options window, which can be invoked from the Instrument window by
using Setting - User Options....

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1. Open the chromatograms using File - Open Chromatogram.... In Open

Chromatogram dialog select desired chromatograms and click Open in Overlay.
Note: You can also use File - Open Chromatograms From Sequence...
command which opens all chromatograms from sequence including
Standards.
2. Click on the Summary tab in the lower part of the window to display the
Summary Table. In the rows you can see chromatograms and signals with
measured values and in the columns there are identified peaks from all
calibrated chromatograms.
Caution: Summary Table is based on calibration meaning only calibrated peaks
will be present in it.

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3. Right click on the Summary Table, if you want to change the visualization of the
table or add a custom column, etc.
4. To see all signals, select the Show All Signals checkbox in the Summary Table
Options dialog accessible from the pop- up menu of the Summary Table. By
default, only signals containing calibrated peaks are visible in the Summary
Table.

Note: It is also possible to compare parameters from different chromatograms and

check if they fall within set limits by using the SST Extension.

10.10 Confirming the identity of a compound by using the

signal ratio
The identity of a compound can be confirmed by using a dual wavelength detector
in conjunction with the Virtual Detector and checking if the signals ratio is constant
with the following procedure. Prerequisite to this is a know signal ratio for used
wavelengths. With correct comparison formula the Virtual Detector signal should

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result in flat line when the peak is pure compound, impurities with different signal
ratio would be represented as response change on the Virtual Detector signal.
1. Add the Virtual Detector as well as your dual wavelength detector to the
instrument, if not already present, based on chapter Adding a new device.
2. Open the Method Setup dialog and navigate to Acquisition tab.
3. Select VD: Channel 1 in the Select Detector drop-down list ⓐ .
4. On the Argument settings tab, tick the Argument X checkbox, select an Ext.
Source ⓑ , then click on the Settings button ⓒ , select the appropriate detector
Channel ⓓ and click OK .
5. Repeat the same steps for Argument Y and select the second channel from the
detector.
6. If want to use the same signal ratio for entire analysis you can fill in the Resulting
Formula field ⓔ with the proper formula. If you need multiple formulas for
different times skip this step and continue with the next one.

7. To set multiple formulas for different time intervals navigate to the Advanced
settings, check the Use Advanced Settings ⓕ checkbox and fill the time table as
needed.

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8. On the Detector settings tab, set the Time to 0 ⓖ to avoid distortion and fill
Sampling Rate ⓗ equal to the actual detector sample rate.

Method prepared this way can be used to check compound identity as mentioned in
the beginning of this chapter.

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User Guide 11 Data Reports

11 Data Reports
Following chapters describe how to create a report, adjust it and print.

11.1 Setting up a report style for printing

It is possible to select what information and how you want to have printed in the
report. You can create different report styles and store them in different *.STY files.
To see an example on how to set up a style to obtain a specific layout see chapter
Creating a report (example).
1. From the Instrument, Calibration, Chromatogram or Sequence windows, select
File - Report Setup. From the Method Setup window click the Report Setup
button.
2. Click the New button if you wish to create a new report style or click the Open
button ⓐ to open existing report style. Name of currently opened style is
included in the window header.
3. Select the tab corresponding to the section you wish to modify ⓑ .
4. Click and drag the tabs to a new position if you wish to change the order in which
they will be printed in the report. Tabs can also be moved via context menu
which is invoked after right-clicking on them. The first two (Page Setup, Lab.
Header) and last two (Audit & Signatures, Lab. Footer) tabs have fixed position.
5. Select options you would like to include in that section. ⓒ
6. Click Preview ⓓ to see the result preview and repeat steps 3.-5. if you wish to
modify anything.
7. Click Save As to save the report style under a new name or OK to accept the
changes to the current style. ⓐ

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11.2 Printing or previewing a report

The report may include information about methods, calibrations, chromatograms
etc. It is possible to setup what information you would like to include in the report as
explained in Setting up a report style.
Caution: While setting reports it is necessary to pay attention to several crucial settings
bellow:
l The information on the report will vary depending on which window we open it
from, even if we use the same report style.
For example, the Chromatogram tab in the Chromatogram Report Setup
refers to the chromatograms opened in that specific window. Same tab in
the Calibration Report Setup refers to the calibration standard opened in
the Calibration window if any. In the Instrument window it will refer to the
chromatograms produced after the last run or analysis.
l Only opened chromatograms will be printed. For this reason when setting up
automatic printing from Single Analysis, Sequence, Batch windows etc. Open
in Chromatogram Window option must always be used as well.
l If you set up the report to be printed automatically it is always necessary to
specify Report Style to be used.

Note: It is also possible to report multiple already measured chromatograms at once in

Batch dialog. See Post Run Options from Batch topic for more info.
For more info regarding reports see the Clarity Reference Guide.

To Print a Report:
1. Select File - Print in the Instrument, Calibration, Chromatogram or Sequence
windows. In Method Setup click Report Setup icon and in the following dialog
click Print....

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2. Print dialog will open for you to setup your printing options and confirm the
printout.

To Print to PDF:
1. Select File - Print to PDF in the Instrument, Calibration, Chromatogram or
Sequence windows. In Method Setup click Report Setup icon and in the
following dialog click Print to PDF.
2. Print to PDF dialog will open for you to enter file name confirm the saving of the
file.

To display Print Preview:

1. This feature is useful while preparing your own report style to check whether the
outcome is as needed.
2. Select File - Print Preview in the Instrument, Calibration, Chromatogram or
Sequence windows. In Method Setup click Report Setup icon and in the
following dialog click Preview....
3. Print Preview dialog will open. From there you can browse or print the report.

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Automatic report generating after analysis is finished:

By default generated reports are placed next to the original files, to change it use
Setting - User Options in the Instrument window. Navigate to Directories tab and
specify your custom path.
Single Analysis
1. Navigate to Single Analysis - Post Run Settings tab.
2. Check options Open in Chromatogram Window, Print Results and/or Print
Results to PDF.
3. Select Report Style by clicking button.
4. It is also possible automatically export data, to do so check Export Data option.
What should be exported can be set by using Setting - Export Data in the
Instrument window.

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Sequence
1. Procedure is similar to the single analysis. In Sequence window some of the
required columns are hidden by default, to display them right-click the sequence
table and use Setup Columns in the following dialog move desired columns to
the Show Columns list.
2. Check checkboxes in columns Open, Print and/or Print to PDF on rows where
report should be generated.
3. Select Report Style for each row where report is generated. It is possible to
modify specif report style by selecting its cell and clicking .
4. It is also possible automatically export data, to do so check Export Data option.
What should be exported can be set by using Setting - Export Data in the
Instrument window.

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11.3 Creating a report style (example)

This is an example on how to setup a new report style to obtain the results shown in
the picture. Beware that tables are printed as on screen, if e.g., calibration table is
to wide to fit on one page you can adjust the column width in Calibration window.

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1. Open the chromatograms PERS01 and PERS02 in overlay (located in

C:\CLARITY\DATAFILES\DEMO1\DATA).
2. Select the graph area you want to print by clicking and dragging the cursor in the
chromatogram graph.
3. Create a new report style.
l Select the File - Report Setup.
l Click on the New button ⓐ to create a new report style.
l Click on the Save As... button ⓑ and save the style under the name
(myReport in this example).
4. Click and drag the tabs ⓒ to set them in desired order. This will be the order the
sections will have in the report.
5. Set the Margins as needed.

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6. Set the Lab Header.

l Click the Lab Header tab ⓓ .
l Check the checkboxes Print, On First Page Only and Border.
l Check the Image on the Left checkbox and click on the Options... button
to select the logo.
l Click in each line in the text box and write the you want to have in the
header.
l Click in the first line of text and then on the Font icon (icon with "A") and
select Bold as a Font Style.

7. Set the Report Header.

l Click the Report Header tab ⓔ .
l Check the options Print and Chromatogram Info.

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8. Set the Chromatogram section. Only the format of printed graphs is set here,
result tables are printed based on Results tab, see next step.
l Click the Chromatogram tab ⓕ .
l Check the options Print and Fixed Height and set the height to 110 mm.
l Select the options Signals - All and Print range - As On Screen.

9. Set the Results section.

l Click the Results tab ⓖ .
l Check the options Print and Result Table.
l Select the option Signals - All.

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10. Set the Method section.

l Click the Results tab. ⓗ
l Check the options Print, On New Page, Info Header, Instrument
Parameters and Acquisition Parameters.
l Select the option Signals - All

11. Set the Calibration section.

l Click the Calibration tab ⓘ .
l Check the options Print, Info, Parameters and Summary.

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12. You can preview your report by clicking Preview.... For more info see Printing or
previewing a report.
13. Click the OK to save the report style.

11.4 Printing the summary table

1. Setup Summary table in Chromatogram window. For information on how to
create Summary Table, see the chapter "Comparing the results from several
chromatograms" on pg. 159.
2. Right-click in the Summary Table, if you want to change the visualization of the
table, add a custom column, etc.
3. Open the Report Setup dialog and check the Summary Table checkbox in the
Results tab.
4. It is also recommended selecting Word Wrap Long Texts and Force Inverted
(table will be printed with inverted layout ignoring the on-screen layout which is
more suitable for reports) options. Print User Column Formulas can be used
when custom columns are included in the table.

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5. The results for all opened chromatograms will be printed.

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User Guide 12 File Management

12 File Management
How to set project directories, create new projects, preset file names of measured
chromatograms based on variables, store files into subfolders etc.

12.1 Setting up project directories

It is possible to set different directories for projects from each instrument and to set
Audit Trail directory. It is useful while working with shared disk and it is needed to
access measured data from another PC using Clarity Offline.
To setup custom project directories do following:
1. Open Main Clarity window.
2. Open the Instrument Directories for Projects dialog using the System -
Directories... command or the icon.

3. Set the desired directory e.g., U:\Shared.

4. If needed change the Audit Trail directory as well.
5. When saving the changes, the following dialog may appear. Confirming it will
create the necessary subfolder structure in your target location. COMMON is
filled by default files that are necessary for functioning.

Caution: Be aware that when updating Clarity the COMMON files outside of the installation
directory must be updated manually.

12.2 Creating a new project

Creating a new project ensures that the measured data will be later easily found.
The project itself is a directory in Clarity's DATAFILES subfolder or selected
directory where all relevant files are saved (methods, calibrations, sequences,
chromatograms).

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1. To create new project navigate to the Project Setup dialog by selecting
Instrument - Project... in the Instrument window.

Note: You can also open a project through the Login Dialog opened from the Main
Clarity window by selecting the New Project option and clicking OK.

2. In the Project Setup dialog click the New button ⓐ to create a new project.

3. Set the name of the new project ⓑ and click OK ⓒ .

Note: Entered project name must not contain invalid characters, i. e. \ /:*?"< >|.

4. Fill in the project description in the Description field ⓓ and click OK ⓔ .

Note: The change of the project will require you to restart the Instrument. If
there are any unsaved files opened, you will be prompted to save them.
The newly created project does not include any files (for example method,
calibration etc.).

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12.3 Creating customized file names automatically

You can create customized file names automatically by appending variables to
them.
File names can be created in the Single Analysis window, in the Sequence window
and on the Method Setup - Calculation tab.
1. Click on the respective icons , , in the Instrument window to open the
Single Analysis, the Sequence or the Method Setup - Calculation window.
2. Click on to open the variable list. ⓐ
3. Select the variable you want to include in the file name. ⓑ
4. Repeat the previous two steps to add more variables.
5. Insert any allowed characters between the variables to create your file name. ⓒ
More Info:
l Variables are preceded by the "%" character and they are substituted by their
value upon file creation. For example "%g-%Q-%D" will create a file name
with the name of the Analyst, the Sample and the date: " Administrator-
Ethanol-24_02_2023.prm".
l To prevent an Unresolved File Name error you can append the Sample Serial
Number "%n" or the date and time "%R".

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12.4 Storing files into project subfolders

It is possible to include the name of a subfolder in the File name to store
chromatograms into project’s subfolder. If the subfolder doesn't exist, it will be
created when the chromatogram is stored. The directory can be set using the "\"
character. Any string of the variables or characters in front of the "\" character is
considered as the subfolder name. Any string of variables or characters after the "\"
character is used as the file name.
Subfolders created this way are present in DATA and CALIB subfolders of used
project.
Here we provide an example on how to store chromatograms from one sequence
into subfolder named after it.
1. Login to Instrument with DEMO1 project.
2. Open the Sequence window.
3. Open ETHANOL IN BLOOD.SEQ.

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4. Set the File Name of the first row to %s\%q_%Q_%R. (To see detailed
description on how to create the name using variables see chapter "Creating
customized file names automatically" on page 179.)
5. Right click on the File Name column and select Fill down to apply the name to all
rows.

6. The Chromatogram file with a name of SAMPLEID_SAMPLE_DATE-AND-TIME

will be stored in Demo1\Data\Ethanol in blood folder for unknown samples and in
Demo1\Calib\Ethanol in blood folder for standards and blank.

l To create subfolder for each month use the %m or %B variables and for
each day use the %a or %A variables.
l Same procedure can be also used in Single Analysis window.

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User Guide 13 Import and Export Data

13 Import and Export Data

Clarity allows to import or export chromatograms from/to various formats. Following
chapters describe you how to, for example, set exporting chromatograms to a
LIMS.

13.1 Importing a chromatogram into Clarity

It is possible to import chromatograms from other chromatography software.
Supported formats are : AIA (*.CDF suffix), EZChrom ASCII (*.ASC suffix), Text
format (*.TXT), Comma Separated Values format (*.CSV) or Multi-detector format
(*.CHR). The particular procedure depends on type of file you want to import.
1. From the Chromatogram window open the Open Files To Import dialog by
selecting File - Import Chromatogram….
2. You can select the File Type which you want to import ⓐ . By default you can
see all supported formats.
3. Select the file(s) you want to import ⓑ and click on the Open button.

4. Set the parameters as needed in the subsequent dialogs depending on the file
format.
5. For all file formats you can select imported file name and which method to apply
ⓒ . This will apply integration, calibration etc.
l Import AIA File - when importing AIA file (*.CDF suffix).
l You have option to inspect data from the source file and override some of
them ⓓ e.g, Detector Unit.
l Import Text File - when importing Text, Multidetector or EZChrom ASCII file
(*.TXT, *.CHR, *.ASC and *.CSV suffixes).
l You can set information regarding given sample ⓔ like Dilution or
Injection Volume etc. You can also set information regarding source file

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format ⓕ .
Note: File format related settings is typically detected automatically
and there is no need to change it.
l Save As - when importing *.RAW file, as there is no need to set other
parameters.

13.2 Exporting a chromatogram from Clarity to a different

chromatography data station
It is possible to export chromatograms to other formats used by chromatography
data stations. The supported formats are : AIA ( *.CDF suffix), EZChrom ASCII (
*.ASC suffix), Text format ( *.TXT), or Multi-detector format (*.CHR).
1. Open the Chromatogram window by selecting Window - Chromatogram on the
Instrument window or click on .
2. Open the chromatogram you want to export, then open the Export
Chromatogram dialog by selecting File - Export - Export Chromatogram….
3. Select the export format ⓐ . Notes:
Note: For PDA export of 3D data only the EZChrom ASCII format is supported.
4. Select the signals to be exported ⓑ .
Note: You can choose individual signals, All Detectors, 3D Data or All Detectors
+ 3D Data (3D Data variants in EZChrom ASCII only).
5. Select the field separator character ⓒ .

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6. Select the decimal separator character ⓓ .

7. Open the Export Chromatogram As dialog clicking on . Enter the name and
location of the file into which you wish to export the chromatogram ⓔ or fill in the
file name.
8. Select the character encoding for the exported file (ANSI or Unicode (UTF-8))
ⓕ .
9. Click OK to finish the export.

13.3 Exporting data from Clarity

It is possible to export selected parts of the results into external files. All of this can
be achieved automatically from Sequence or Single Analysis window by selecting
Export Data in Postrun Options or manually from the Chromatogram window.
1. Open Export Data dialog from Instrument window by using Setting - Export
Data...
2. Select which data you want to include in the exported files in the Export Content
group ① . Detailed description of these fields can be found in the Reference
Guide.
3. Select whether you want the tables exported with headers and/or in the full
format ② .
4. Select whether the exported chromatogram data will contain time column or not.
If you intend to perform bunching for the exported data specify the time period for
the bunching ③ .
Note: The mean value for selected Time step period is calculated as a sum of
the highest YMax and lowest YMin signal curve value found within each
Time Step period divided by two - (YMax+YMin)/2.
5. Select the character encoding to be used (ANSI or Unicode (UTF-8)) ④ .
6. Select the appropriate text formatting for the export ⑤ .
7. Select the format or formats to which the data will be exported. You can choose
any number of export types at the same time ⑥ .
8. Select whether the exported data should be appended into an existing file ⑦ (in
this case file name ⑧ must be filled in) or exported as a new file (leave the file
name empty as shown bellow).

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l This setting will be used for automated data export from Sequence or Single
Analysis.
l To manually export data you can invoke the same dialog from Chromatogram
window by using File - Export - Export Data... command or icon. In this case
dialog also includes Export button which can be used the export data from
currently opened chromatogram.

13.4 Exporting data for LIMS

Following chapter describes how to export data from Clarity to be used for LIMS.
Each LIMS requires a different approach in importing external data, therefore it may
be necessary to adjust your LIMS to be able to correctly process imported data from
Clarity.

Export settings
1. Open Clarity Instrument window and select - Setting - Export Data....
2. In the Export Data dialog set the required Export Content ⓐ .
Note: While exporting Result Table it is recommended to check In Fixed Format.
Otherwise the content will change according to changes on screen.
Beware that In Fixed Format is only applied to the In Result Table.
3. Select desired file formatting in Text Format section.
4. Select Export to - Text File ⓑ and choose preferred suffix.
5. Select Full Format option ⓒ . This will precede each result table row with a file
name, date and time, thus allowing easy sorting after import.

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6. Set File Name ⓓ and check Append option, in this way all results will be
exported to a single file which can then be simply imported directly to your LIMS.
Alternatively, leave the field empty in which case each export will be performed
to a separate file. Exported files will have automatically generated file name from
the chromatogram name.

l By default, files are exported to the same directory as the original

chromatogram.
l To export to a single directory, specify it in the User Options - Directories tab
ⓔ , accessible from the Instrument window by Setting - User Options...
command.

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Locations to Export from

Three most common locations in exporting data to LIMS are:

Single Analysis
l In the Post Run Settings tab, of the Single Analysis dialog, select
Export Data ⓕ .
Note: Export of data will be performed automatically after a single
analysis is finished.

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Sequence
l In the Sequence window, select checkbox in the Export Data ⓖ
column for row(s) to be exported.
Note: Export of data will be performed automatically after the row
has been measured.

More Info:
l By default, Export Data column is hidden. Right mouse click in
the sequence table and choose Setup Columns... to show it.
l In the Setup Columns dialog, choose Export Data from the left
list and click on the Show button - it will be added to the show list.
Once you click on the OK button, you will return to the Sequence
window and new Export Data column will be present.

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Batch
l Export multiple chromatograms at once using the Batch dialog,
accessible from the Instrument window by Analysis - Batch...
command.
l Select chromatograms to be exported and check the option to Export
Dataⓗ .
l Clarity is able to start external program with a parameter ⓘ . Specify
a program to run using the and specify a command line parameter
- typically the file name of the exported text file %e. Once ready to
export the data, click the Proceed button.

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13.5 Exporting sequence

It is possible to export sequence to other more common formats. Supported formats
are Excel Table (*.XLSX and *.XLS suffixes) or Text format (*.TXT).
1. Open the sequence you want to export, then use the File - Export… command to
open the Export Sequence Table To dialog.
2. Select the appropriate folder for saving the exported sequence ⓐ .
3. Fill in the name under which the exported sequence will be saved ⓑ .
4. Choose the format in which you want to export ⓒ . For Text format, the ANSI or
Unicode encoding are available.
5. Press the OK button to perform the export ⓓ .

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13.6 Importing sequence

It is possible to import sequence that has been stored in a text file. Values have to
be in delimited format and separated by an arbitrary delimiter.
Import of the sequence is one of the functions that enables an interconnection
between Clarity and LIMS systems.
1. Open an Import dialog (File - Import…) from the Sequence window.
2. Choose the file which you want to import ⓐ . Supported formats are : .TXT,
.CSV and .PRN
3. Select the character used as field delimiter ⓑ . Possible options are <TAB>,
<SPACE>, <COMMA> or <SEMICOLON>.
4. Select the character used as decimal delimiter ⓒ . Options for the decimal
delimiter are <Window's Locale> (the station will use the setting specified in the
local settings of MS Windows), <COMMA>, <DOT> or <SEMICOLON>.
5. If the text file to be imported contains column descriptions in the first row, use
First Row Is Header ⓓ checkbox. This row is used for mapping in the Import
Sequence Step 2 dialog.
6. Preview of the first five rows of the imported sequence table is displayed in the
bottom part of the dialog ⓔ .
7. Click Next to continue ⓕ .

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8. Set the mapping so that the columns used in Clarity (Sequence Column) will
correspond to the columns from the imported file (Imported Column) ⓖ .
Columns that are highlighted in bold letters are required. When the imported
table contains column headers (the First Row is Header checkbox from the
Import Sequence Step 1 dialog has been checked), Clarity will attempt to
automatically map the columns according to their names. Manual mapping will
override the default name mapping. Clarity will store these names for future
imports .
9. Select whether you want to save imported sequence as a new file or just append
it to currently opened one ⓗ .
10. Three checkboxes allows you to do following ⓘ :
l Original file will be erased after successful import.
l Settings of this dialog will be saved for future imports.
l Sequence Option will be shown immediately after finishing import.
11. Press the Finish button to accomplish import and close the dialog ⓙ .

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13.7 Exporting a chromatogram as a picture

You can export a chromatogram as a picture to the clipboard or as a file to a folder
of your choice. The picture will include the labels and lines included in the
chromatogram.
1. Open the Chromatogram window by selecting Window - Chromatogram from the
Instrument window or click on .
2. Open the chromatogram you want to export.
3. Select File - Export - Export as picture to clipboard and paste the picture to MS
Word, MS Powerpoint, Open Office Writer or any other suitable application of
your choice.
or
4. Select File - Export - Export as picture to file... and then select the folder where
you would like to save the file in Enhanced Metafile Format.

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User Guide 14 Mathematical Operations

14 Mathematical Operations
This functionality was implemented into Clarity to give users a tool to manipulate
already measured data without modifying original raw data. Mathematical
operations present a very convenient approach to perform various actions such as
extraction of a selected signal(s) from multiple signal chromatogram or subtraction
of various chromatograms from each other. You can display three examples of
applications of Mathematical Operation in following chapters. Many other
applications may be developed by Clarity users on their own.

14.1 Extract chromatogram's signal using Mathematical

Operations
You can save a particular signal from a chromatogram that contains several of
them. This results in a stand-alone chromatogram file containing only the individual
signal of choice, not all of the signals from the original chromatogram which might
be confusing when working with a larger number of signals.
1. Open your a multi-signal chromatogram that you want to work with.
2. In Chromatogram window select Chromatogram - Overlay - Mathematics to
open Mathematical Operations dialog.
3. From the drop-down menu ⓐ in the Operand A section select the desired signal
of chromatogram you want to save separately. Select the Copy operation ⓑ ,
check Save As Chromatogram ⓒ , fill a name of the new chromatogram ⓓ and
click OK to save the signal as standalone chromatogram.

14.2 Subtraction of various chromatograms using

Mathematical Operations
If you would like to use one of your chromatograms as a baseline for another
chromatogram(s) there is a way to subtract the desired chromatogram from any

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other chromatogram. It is possible to set Subtraction Chromatogram directly in
Chromatogram window on Measurement Conditions, however, if you want to have
both original and subtracted chromatograms as individual files you can use
Mathematical Operations.
1. Open your chromatograms that you want to work with in Overlay.
2. In Chromatogram window select Chromatogram - Overlay - Mathematics to
open Mathematical Operations dialog.
3. Select operation A - B ⓐ . From the drop-down menu in the Operand A section,
select the chromatogram you want to subtract from ⓑ .
4. From the drop-down menu in the Operand B section, select the chromatogram
you want to subtract ⓒ .
5. Check span Save As Chromatogram ⓓ , fill a name ⓔ and click OK to save the
new subtracted chromatogram.

14.3 Copying of chromatogram using Mathematical

Operations
Following chapter describes how to copy a modified chromatogram into a new one
without changing the original chromatogram. For example we set up new Offset of
Y-axis and this modification is about to saved in new chromatogram and want to
keeping the original chromatogram unchanged.
1. Open your chromatogram that you want to work with.
2. In Chromatogram window click Display - Properties to open Graph Properties
and go to Signals tab.
3. Into Field Y Offset ⓐ write down value of desired offset in mV, in this example
we choose 333 mV, and click OK button.

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4. Select Chromatogram - Overlay - Mathematics... and the Mathematical

Operations window will open.
5. Select Copy option ⓑ . Check Save as Chromatogram ⓒ , name the new
chromatogram ⓓ and click the OK button.

6. Both chromatograms will be displayed in overlay mode.

7. Restore the original chromatogram by navigating to Graph Properties - Signals
as in step 2.
8. Select the original chromatogram ⓔ , click Original button ⓕ and close the
dialog by clicking OK.

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9. Both chromatograms will be displayed in overlay mode as shown in the next

image.

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User Guide 15 Archive and Restore

15 Archive and Restore

Clarity allows you to archive your PROJECTS (methods, sequences, measured
chromatograms) and also the COMMON folder in which the print styles are stored.

15.1 Archiving a project (Creating an Archive)

It is strongly recommended to archive the whole project folder after being shelved,
but it is also possible to archive specific files only. An archive can be made by
simply copying the files or by compressing them into one file (*.DGZ format).
1. Open the Backup dialog by selecting Instrument- Archive... on the Instrument
window.
2. Select Projects in the File Type ⓐ option to archive a complete project directory.
3. Select the project or projects you wish to back up from the list. The Select All
Files button ⓐ will select all projects.
4. Choose from the following options ⓑ :
l Uncheck the Without Compressing option to archive all files into one
compressed file.
l Check the Move to Archive option to have the original files erased
after backing them up.
l Check the Including Common option to also back up the COMMON
subdirectory.
5. Choose the output directory and name for the archive ⓒ . Compressed files will
have the .DGZ extension.
Caution: If you archive data in compressed format with a previously used name,
you can possibly override the former archive and loose all data.
6. Click the Archive button ⓓ to back up the project or the OK button ⓔ , if you do
not need to back up any more files.

Note: Clicking OK will archive current selection.

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User Guide 15 Archive and Restore

15.2 Restoring a project from an archive

1. Open the Backup dialog by selecting Instrument - Restore... in the
Instrument window.
2. Choose the source directory and select the source file ⓒ . Compressed files will
have the .DGZ extension.
3. Select Projects in the File Type ⓐ option to restore a complete project
directory.
4. Choose from the following options ⓑ :
l Uncheck the Without Compressing option to restore all files from a
compressed format.
l Check the Move from Archive option to have the archived files
erased after restoring them.
l Check the Including Common option to also restore the COMMON
subdirectory.
5. Select the project or projects you wish to restore from the list. The Select All
Files button ⓐ will select all projects.
6. Click the Restore button ⓓ to restore the project or the OK button ⓔ if you do
not need to restore any more files.

Note: Clicking OK will restore current selection.

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15.3 Archiving specific files (Creating an Archive)

It is strongly recommended to archive the whole project folder after being shelved
but it is also possible to archive specific files only. An archive can be made by
simply copying the files or by compressing them into one file (*.DGZ format).
1. Open the Backup dialog by choosing Instrument - Archive... in the Instrument
window.
2. Select the File Type ⓐ option according to the files you wish to archive.
3. Select the files you wish to back up from the list. The Select All Files button ⓐ
will select them all.
4. Choose from the following options ⓑ :
l Uncheck the Without Compressing option to archive all files into one
compressed file.
l Check the Move to Archive option to have the original files erased
after backing them up.
l Check the Calibration Standards option when archiving
chromatograms. The chromatogram files from the CALIB
subdirectory (instead of the DATA subdirectory) should be listed.
l Check the From Common option to display the system files from the
COMMON directory.
5. Choose the output directory and name for the archive ⓒ . Compressed files will
have the .DGZ extension.
6. Click the Archive button ⓓ to back up the file or the OK button ⓔ if you do
not need to back up any more files.

Note: Clicking OK will archive current selection.

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User Guide 15 Archive and Restore

15.4 Restoring a file from an archive

1. Open the Backup dialog by choosing Instrument - Restore... on the Instrument
window.
2. Choose the source directory and select the source file ⓒ .
3. Select the File Type ⓐ option according to the files you wish to restore.
4. Choose from the following options ⓑ :
l Uncheck the Without Compressing option to restore files from a
compressed format.
l Check the Move from Archive option to have the archive files erased
after restoring them.
l Check the Calibration Standards option when restoring
chromatograms to the CALIB subdirectory (instead of the DATA
subdirectory).
5. Select the files you wish to restore from the list. The Select All Files button ⓐ
will select them all.
6. Click the Restore button ⓓ to restore the files or the OK button ⓔ if you do not
need to restore any more files.

Note: Clicking OK will restore current selection.

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User Guide 16 Managing the Chromatography Station

16 Managing the Chromatography

Station
Following chapters contains extended information how to set restrict access to
various parts of Clarity to certain users or set up communication with a mobile
application.

16.1 Enabling instruments to be used by Clarity2Go

application
Clarity enables to send specific parameters over the internet to be monitored via
Clarity2Go application. In this way you can monitor your analyses while outside the
laboratory. Note that both PC with Clarity and smartphone must be connected to
internet. For more information regarding Clarity2Go installation refer to
www.dataapex.com/product/clarity2go.
The whole solution consists of three independent parts:
l Clarity station (at your side) - sends information about state and running
analyses to the server.
l Server (at DataApex's side) - dispatches the information from Clarity
stations to Clarity2Go clients.
l Client (at your side) - device (smartphone or tablet) with installed
Clarity2Go application processes information from the server.
DataApex is providing a free public server for this use.

How to set up Clarity:

1. In the Clarity main window, go to System menu and click on the command
Clarity2Go....
2. In the opened Clarity2Go Configuration dialog, check the checkbox of
Instrument 1 to 4, depending on the instruments you want to monitor. Every
checked Instrument will get its unique Instrument ID.
3. Click the OK button to save the configuration and continue with steps described
in How to set up Clarity2Go section or refer to Advanced options bellow.

Fig. 4: Clarity2Go Configuration - Basic

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User Guide 16 Managing the Chromatography Station
Options described below are optional and are not obligatory for correct
functionality. They are revealed by clicking the Advanced button.
l Unregister All Instruments - disables the monitoring in the Clarity2Go
application. Instruments that have been registered will no longer be available
for monitoring. If you will later change your mind, you will have to generate
new Instrument ID.
l Web Server Address - do not change this field. It defines the address of
Clarity2Go web server. Address other than default will result in the
monitoring to be not functional! Press the Default button to set functional web
address of the server.
l Proxy Server Address - consult with your local administrator if a proxy server
is applied in your local network and then provide the proxy server address.
l Protect by Password - provided password will be valid for all Instruments.
The same password needs to be provided in the Clarity2Go application to
unlock the monitoring.
l Click the OK button to save the configuration and continue with steps
described in How to set up Clarity2Go.

Fig. 5: Clarity2Go Configuration - Advanced

How to set up Clarity2Go:

Once you have configured instrument (s) in Clarity, it's time to monitor those
instruments using Clarity2Go application. This part assumes that you have
Clarity2Go for Android application installed and running.
1. Make sure that you are not in the Clarity Demo mode, indicated by a gray stripe
at the bottom of the application with the inscription DEMO mode. Tap on the
TURN OFF DEMO.
Note: Clarity Demo mode does not allow to add instruments.

Fig. 6: Clarity Demo mode gray stripe

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User Guide 16 Managing the Chromatography Station
2. In the Settings, tap on Demo - Switch to demo mode which turns the Clarity
Demo mode OFF.
3. Return back. In case you are configuring Clarity2Go for the first time, you will
see that there is no instrument.

Fig. 7: No Instrument screen

4. Tap on the blue "plus" button at the bottom right corner to add a new instrument.
5. Enter Instrument ID that has been generated by Clarity and enter password
(only if you have set it up in Clarity). Tap on the OK button to start monitoring
this instrument.

Fig. 8: New Instrument screen

6. The newly configured instrument will be added to the list of instruments that are
being monitored.
Note: You can invoke the application menu by tapping on the 3 horizontal lines -
the menu contains Settings, built-in Help and About options.

16.2 Locking/Auto Locking a Clarity Instrument

You may lock a Clarity Instrument protected by password if you want to prevent
unauthorized access to it, for example, when an analysis is running.

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Manual Lock
l Instrument can be manually locked either from Instrument window by clicking
Instrument - Lock Instrument_Name.
or
l From the Main Station window by clicking Instruments - Lock Instrument_Name.

Auto Lock
It is possible to set the automatic lock function so that all opened instruments will be
locked after a period of inactivity.
1. Open the User Accounts window by clicking on or choose System - User
Accounts.
2. Check the Auto Lock function ⓐ .
3. Set the period of inactivity in minutes after which all opened Instruments will be
locked ⓑ .

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Caution: When an Instrument is Auto Locked, all eventual unsaved changes in modal
dialogs (Method Setup, Single Analysis, Report Setup, etc) are discarded and
those dialogs are closed.

16.3 Unlocking a Clarity Instrument

1. Select Instruments - Unlock Instrument 1 from the Main Clarity window or
click on the Instrument image.
2. Enter the password and click OK.

Unlocking Instrument after entering wrong password three or more

times:
If you enter the wrong password three times or more, then a message will appear
asking you to restart the program.

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User Guide 16 Managing the Chromatography Station
1. Unlock the Instrument using credentials for a user with administrator rights
over the locked Instrument according to chapter Taking control over locked
instrument.
2. Restart Clarity. Instrument can again be opened by the previous user.

16.4 Taking control over Clarity Instrument

You may take control of Instrument where different user is already logged. To be
able to do that the option Take Control of Locked Instrument has to be enabled in
the User Accounts settings for the user who wants to take over.

Setting up the User Right

1. Open the User Accounts window by clicking on or choosing System - User
Accounts.
2. Check the Take Control of Locked Instrument in User Access Rights ⓐ part of
the dialog for users who should be able to do so.

Note: It is recommended to set one common Desktop File for all users with this option
enabled. Otherwise desktop of the first logged user will be used for all users that
take control over the Instrument, until the Instrument is closed again.

Note: It is also recommended to set the same Edit... rights for users that plan to take
over Instruments as different rights may limit the options of second user.

Note: It is possible to set the Auto Lock function so that all opened instruments will be
locked after a period of inactivity.

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User Guide 16 Managing the Chromatography Station

Taking control of Locked Instrument

Steps are similar to the standard logging to instrument.
1. Select Instruments - Unlock Instrument 1 from the Main Clarity window or
click on the Instrument image ⓑ .
2. Choose your User Name ⓒ .
3. Enter the password and click OK.

Caution: All unsaved changes in files made by the previous user will be discarded.

Note: It is possible to take control of locked Instrument using the Command line
parameters. Always include the user (user=…) and password (p=…) parameters
for each command, because the instrument is kept locked.

16.5 Monitoring Events and Operations in Clarity

The Audit Trail can be used for finding out who did what and when, including file
operations, changes to settings, events that take place during data acquisition and
system messages. Therefore this is an essential tool for troubleshooting and
managing Clarity.
To access the Station Audit Trail:
1. Select Window - Station Audit Trail from the Instrument, Chromatogram,
Calibration, Sequence or Data Acquisition windows. Alternatively click icon in
the Main Station window.

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User Guide 16 Managing the Chromatography Station

2. Click on the Session tab ⓐ if you would like to see the log from the time Clarity
was started or on the Daily Audit Trial tab for the present day events.
Note: The Daily Station Audit Trail is stored in one separate file every day the
station is running. These files can be opened by using the command File -
Open Audit Trail (Append).
3. Click on the Instruments or System icons ⓑ to filter out events and operations
based on instrument where they occurred.
4. Inspect the Description column to find out about operations and events that have
taken place ⓒ .

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5. Click on the Properties icon ⓓ to set up which events and operations should
be recorded in the Session or Daily Audit Trail.

To access the file-specific Local Audit Trail (Chromatogram, Calibration, Sequence

and Method):
1. Select Window - Chromatogram, Calibration or Sequence Audit Trail from the
corresponding window or click on the Audit Trail icon in the Method Setup
window to open corresponding Audit Trail.
Note: The Local Audit Trails are included in the Chromatogram, Calibration,
Sequence and Method files and contain the whole file history.

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16.6 Controlling Clarity from an external application

It is possible to send commands to Clarity using Windows command line
parameters and also to read its status through Windows Dynamic Data Exchange
(DDE).
l For more information on the commands go to our List of commands in the
Clarity Reference Guide.
l You can also find the list of variables which will give you information on
Clarity status on our DDE datasheet.

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User Guide 17 Clarity in Network

17 Clarity in Network
Clarity might be used in network and following chapters describe different
approaches of such usage.

17.1 Clarity in network overview

Clarity is not a client-server (C/S) solution, nonetheless it can be configured for use
in multi-user and multi-instrument networked environment.

What does the solution Clarity in network offer?

l Instrument control, real-time signal monitoring and run control is possible
only trough the local Clarity station, i.e. Clarity must be connected to
respective chromatography instrument. Each Clarity needs to be set locally
(including .cfg and .psw).
l Using the System - Directories, the location of the Clarity data/projects can
be set anywhere within the network (typically on a shared server back upped
drive). The data can be then accessed from any Clarity station on the
network, including the Clarity Offline stations intended for evaluation of data
from another computers.
l Clarity Offline allows users to prepare methods and evaluate acquired data.
l With Clarity Offline users are able to work with acquired data on additional
computers in the laboratory or at home.
l File access conflicts may occur when accessing the same file (e.g. method)
from different Clarity stations.

What does the solution Clarity in network not offer?

l Central management of users.
l Central management of documents such as chromatograms, calibrations
and methods.
l Direct control of acquisition, i.e. run/stop/abort from other Clarity stations.
l Direct control of instruments from other Clarity stations.
l Watch real time signal being acquired by detectors from other Clarity
stations.

17.2 Multiple Clarity stations in a network

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User Guide 17 Clarity in Network

More Info:
l
Note that it is possible to have more than one Clarity ⓑ in the network.
l
Shared Network Disk ⓒ can be on the same PC as well and not as a separate unit as
seen in the picture above.

Clarity in network is a solution that consists of at least one Clarity, at least one
Clarity Offline and a reliable computer network as the most basic setup.
Simplified scheme of the possible configuration is displayed in the diagram above.
LC and GC instruments ⓐ are controlled via Clarity ⓑ . Chromatograms,
calibrations and methods are all saved (using directory configuration) on a shared
network disk ⓒ . Clarity Offline ⓓ could then be used for evaluation of acquired
chromatograms and preparation of methods which are saved (using directory
configuration) on the shared network disk. Clarity ⓑ is able to send those prepared
methods to corresponding instruments.
Note that this shared network disk is accessible to all computers within this
computer network therefore a much wider configuration can be implemented than
the one described above.
Following step-by-step guide will help you configure the Clarity in network solution.

Procedure A - Firstly we will configure Clarity ⓑ which will acquire

data and save them to the shared network disk.
1. In the main Clarity window, go to System - Directories or use the icon .
2. Instrument directories for Projects dialog will open.
3. Choose Instrument that will share all the created files; chromatograms,
calibrations, methods, sequences, reports etc..
4. Use the ⓔ to browse for shared network disk. Once you locate it, click OK.
Path to the shared network disk is now filled in the corresponding Instrument.
5. In case you want all Instruments to have the same directory, check the option All
As Instrument 1 ⓕ . This will copy the directory path for the rest of the
instruments as it is set for Instrument 1.

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6. To save the configuration click the OK button.

7. Configuring the directory for the first time will result in the following message.
Click Yes to allow the creation of necessary structure. Upon clicking Yes,
COMMON and PROJECTS folders are created with default documents
necessary for correct functionality.

8. When you try to login for the first time with the new directory configuration, you
will be asked to create a new project.

9. Fill project name and click OK.

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Anything created/measured within this project is saved on the shared

network disk and therefore is accessible to other Clarity stations.

Procedure B - Secondly we will configure Clarity Offline ⓓ which will

be used for data evaluation from shared network disk.
We need to configure directory from which Clarity Offline will open chromatograms,
calibrations and methods saved on the shared network disk.
1. Configure the directory according to step 1-6, described above.
2. When you login, select the appropriate project (the one you filled in step 9) using
the drop-down box ⓖ and click OK.

If you have followed the steps correctly, your Clarity in network is configured. If you
are not sure, you can test it by measuring some chromatogram and evaluate it on
Clarity Offline. Once you see measured chromatogram in the Data directory you
know it has been configured correctly.

17.2.1 Migrating Clarity Project into a Network

This step by step guide will help you to move your Clarity project with measured
chromatograms, calibrations, prepared methods and other files into a shared
network disk or a shared server back upped drive.
This guide assumes that you have already set up directory for Clarity in network
therefore you have all the necessary structure prepared - if not, refer to Procedure
A described in the chapter "Multiple Clarity stations in a network" on pg. 214.

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Principle behind migrating Clarity project into a different location is straightforward.
It is necessary to move the whole project directory (e.g. WORK1) as well as the
project file itself (e.g. WORK1.PRJ).
More Info:
l Note that it is possible to move the project directory and the project file also using File
Explorer when Clarity is turned off.

1. Switch Directories back to the previous (default) location, so you can see
previously used projects.
2. Log to the project you don't want to migrate, e.g. one of the demo projects.
3. In the Instrument window, go to menu File - Archive....
4. Backup dialog opens on the Create Archive tab ⓐ .
5. Because we want to migrate whole project, change File Type using the drop
down list ⓑ to Projects.
6. Section File List now contains all projects in Clarity. Click the project to be
migrated (e.g. WORK1) ⓒ .
7. As a Target select the destination of the shared network disk using the at ⓓ .
8. Check the options Without Compressing and Move to Archive ⓔ .
9. Check also Including Common, if you use customized report style, template
sequence and other files stored in Common folder ⓕ (you will be prompted to
confirm overwriting the default files created during Procedure A).
10. When everything is set as described above, you can click the Archive ⓖ button
which migrates project WORK1 to the D:\SHARED\.

11. Now change the directories back to the network shared drive.
12. Login to the Instrument which has set directory in the network. Notice that in your
Clarity Login Dialog the Select Project drop down list offers your migrated project
(WORK1) and project created after setting the new directory only.

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13. Your Clarity project has been successfully migrated and you can start working.

17.3 Using remote desktop to control Clarity

This step by step guide will help you to connect remotely to a PC with Clarity ⓒ
installed from your home or office ⓐ . It will allow you to connect remotely to that
PC and take control over the whole computer and thus control Clarity and
connected instruments. The connection is realized over the internet or a local
computer network. Connection over the local computer network is more secure
since the transferred data never enter the internet.
Requirements:
l ⓐ PC needs to have Remote Desktop Connection installed
l ⓑ Internet connection or a reliable computer network
l ⓒ PC with Clarity needs to have Remote Desktop Connection installed
More Info:
l Remote Desktop Connection is a standard application installed in Windows operating
systems.

This description is for setting up a remote connection in Windows 11.

Dialogs may vary depending upon the Windows version used.
1. To allow remote connections on the PC with Clarity ⓒ you want to connect
follow the steps below:
l Go to the Control Panel - System and Security - System - Allow
Remote Access.
l If you're prompted for an administrator password or confirmation,
type the password or provide confirmation.

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l Under Remote Desktop, select one of the three options.
l Click Select Users.
l In the Remote Desktop Users dialog box, click Add.
l In the Select Users or Groups dialog box, do the following:
l To specify the search location, click Locations and then
select the location you want to search.
l In Enter the object names to select, type the name of the
user that you want to add and then click Check Names.
This will check whether the user exists. If not, it will trigger
a not found dialog. Check the name once again. Note that
this user must have a profile on this computer. If the user
name is correct, click OK.
l The name will be displayed in the list of users in the
Remote Desktop Users dialog box. Click OK and then
click OK again.
l In case Remote Desktop options are grayed out your computer is
probably in a domain and due to domain policies you may not be able
to change the settings. Contact your network administrator to resolve
the situation.

2. Look up the name of the remote computer ⓒ . You will to provide this
information in step 5.
l Go to System - About.
l There is the Device Name, which is the info you need.
l Alternatively your network administrator might also be able to give you the
name of the computer.
3. Set a password for your user account on PC with Clarity ⓒ . Your user account
must be password protected before you can use Remote Desktop to connect to

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another computer. Password protection is now default setting in Windows, so
you may have that already set up.
l Go to the User Accounts - Sign In Options.
4. To allow Remote Desktop connections through a Windows Firewall on the
remote PC ⓒ follow the steps below:
If you're having trouble connecting, Remote Desktop connections might be
getting blocked by the firewall. Here's how to change that setting on a PC. If
you're using another firewall, make sure the port for Remote Desktop
(usually 3389) is open.
l Go to the Control Panel.
l Click System and Security.
l Click Allow an app through Windows Firewall under Windows Defender
Firewall section.
l Click Change settings and then check the box next to Remote Desktop.
l Click OK to save the changes.
5. Start Remote Desktop from the computer you want to work from ⓐ .
l Open Remote Desktop Connection.
l In the Computer box, type the name of the computer that you want to connect
to, and then click Connect. (You can also type the IP address instead of the
computer name.)
l Note that the remote PC cannot be in sleep mode or hibernating.

More Info:
l This text has been taken from the How- to: "Connect to another computer using
Remote Desktop Connection" created by Microsoft Windows.

Once you successfully connect to the remote PC you can work as if you were sitting
in the lab and working with Clarity. The remote desktop will be presented in the
normal window. To terminate the session, close the window.
This solution then enables you to:
l Control instruments that are directly connected to Clarity.
l Monitor data acquisition.
l Evaluate chromatograms in Clarity.
l Work on other projects and leave the remote session open and check once
in a while if everything is running smoothly.

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Possible situations that may arise using the Remote Desktop Connection:
l If you remotely connect to a PC where you are currently logged in, you will be
automatically put through and you can start working.
l However, if you try to connect to a PC when there is logged in someone else,
e.g. another analyst, he will be asked if he allows the remote connection to
put through. If he declines the remote connection you will not be able to
connect.
l PC that you are connecting to must be turned on, it is not possible to connect
to a PC that is off or in sleep mode.

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18 Utilities
Clarity installation contains various utilities for validating the installation or
predefining various Clarity profiles which helps you in using more configurations of
laboratory instruments.

18.1 Checking that the software has been installed correctly

(Installation Qualification - IQ)
The Installation Qualification (IQ) is a procedure confirming that the software has
been installed successfully and that correct versions of files are present.
1. Install the Clarity station according to the instructions of the Installation Wizard.
2. After the installation has been completed, you can open IQ by searching for
IQ Report in the search field of the Start menu. Alternatively you can start IQ by
using C:\CLARITY\BIN\IQ.EXE.
3. If the installation has been correctly performed, the status should read:
"Installation Qualification Test: Passed".
4. If the Installation Qualification fails, it is recommended to uninstall and then re-
install Clarity. If it fails again, contact DataApex support.
Note: You can use Show files list to display list of all validated files and search
for the ones that are causing issues.
5. The Installation Qualification report can then be printed, copied to the Windows
Clipboard or sent as an email.

Caution: Some driver packages have standalone IQ that must be performed separately by
clicking here in given section. Clarity IQ is NOT valid unless IQ of all components
passed and reports are stored together.

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Note: The most common reason for a "Failed" result is the installation of an updated
version over an existing installation of Clarity. This itself does not produce any
errors but since some of the files are preserved from the original installation, the
checksums will not match.

18.2 Editing Clarity profiles for different analyses using the

Launch Manager
Launch Manager is a utility that allows you to start the Chromatography Station with
specific setting. The collection of these settings is saved as a Profile in Launch
Manager. You can select specific configuration, desktop file containing custom
calculations and which instrument and project specifc user will be asked to log in.
1. Start the Launch Manager either from the Windows Start menu or using
C:\CLARITY\BIN\LAUNCHMANAGER.EXE.
2. Click on the Edit Profiles button to create or modify the profiles.

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3. Select a profile ⓐ to modify it or click on the New button to create a new profile
ⓑ.
4. If you created a new profile, fill its name. For easier orientation it is
recommended to fill in the Description which eases the distinguishing of different
profiles.
5. Select the configuration file that will be loaded after the start of Clarity ⓒ .
Note: The list of configuration files is retrieved from the installation directory
(configuration files are located in C:\CLARITY\CFG by default). Clicking
on button opens menu for managing the configuration files, see
Creating a duplicate configuration using the Launch Manager for one
example of usage.
6. If you select the <Last Used> option, Clarity will start with the last configuration it
was opened with or if Clarity is running, the present configuration will be
preserved.
7. For each Instrument, choose if it should be opened at the Clarity start by Open
Instrument checkbox. Select the User, Desktop, Project, Method and Sequence
files that will be loaded when opening instruments.
Note: In the desktop file, all layout setting is saved (the width of the table
columns, the custom toolbars), but also custom calculations created in
User Columns.

Note: If <From Project> is selected, the Method and Sequence that were last
opened in selected Project will be used.
8. You can use Refresh Files button ⓔ to reload all the files displayed in the Edit
Profiles dialog.
9. Once the profile is configured, Close the Edit Profiles dialog and Launch the
profile either by double clicking on the profile or by selecting a profile and clicking
on the Launch.

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Note: You can use Create Shortcut ⓕ to place shortcut on the desktop which
can be directly used to launch given profile.

18.3 Creating a duplicate configuration using the Launch

Manager
This topic describes how to create a duplicate configuration using the Launch
Manager. This becomes especially handy when you have system with two
detectors (e.g., RI + DAD) but you don't need to run them together every time.
1. If you don't have any configuration yet, start Clarity and configure your device(s)
according to the chapter "Adding a new device" and close Clarity. Otherwise
start with the next step.
Note: In this example we start with LC system with both DAD and RI detectors
configured.

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2. Open Launch Manager either from the Windows Start menu or by using
C:\CLARITY\BIN\LAUNCHMANAGER.EXE.
3. In the Select Clarity Profile dialog click Edit Profiles....
4. In the Edit Profiles dialog, click the New button ⓐ to create a new profile and
name your profile (e.g. RI + DAD). Click OK to save the profile. Newly created
profile is displayed in the small table on left ⓑ .
5. From the drop-down list ⓒ , select CLARITY.CFG, click the button, from the
selection choose Duplicate and in the following dialog name your configuration
(e.g. ri+dad.cfg).
Note: This step will create a duplicate configuration (.cfg file) based on the
current Clarity setup (as described in step 1.). It prevents Clarity from
overwriting a default configuration.

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6. Create a new profile (DAD) with a different configuration (duplicated ri+dad.cfg

named as dad.cfg), similarly to steps 4.-5. Once done, your profile should look
similar to the image below.

7. Close this dialog to return to the main Launch Manager window.

8. In the Launch Manager window select the DAD profile ⓓ which has not been
configured but simply duplicated and click on the Launch ⓔ button.

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9. Clarity has launched with the selected profile, open System Configuration. Since
the configuration has been duplicated from the initial configuration, both
detectors are present. Remove the RI detector from instrument and save the
configuration by click OK in the System Configuration window.
Note: This step may differ based on used control modules. In our case simply
drag the RI module from right side to the left one. In other modules e.g.,
when using ICF you have to invoked the control module setup and
change it there.

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10. Launch each profile using the Launch Manager to make sure that correct
configuration is loaded. Make necessary changes to the configuration if needed.

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19 Extensions
Chapters describing topics related to specific Extensions.

19.1 GPC operations

Following chapters describe specific procedures concerning GPC.

19.1.1 Creating a GPC calibration

To be able to create a GPC calibration, you need to have a measured and
integrated GPC chromatogram of a standard sample and the instrument type of
Clarity must be set to GPC. The GPC mode can be toggled on/off by selecting the
Setting - GPC Mode in the Instrument window.
1. Open the Calibration window: select Window - GPC Calibration in the Instrument
window or click on .
2. Create a new calibration file: select File - New or click on ⓐ.
3. Following dialog GPC Calibration Options will show up. Here you can setup
various options and Calibration Types.

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Caution: Once selected, the Calibration Type can't be changed later. More on GPC
Calibration Options can be found in the GPC Extension manual, accessible on
www.dataapex.com.
4. Click OK to save the calibration. To fill calibration name open the File - Save As
dialog window.
5. Open integrated chromatogram of a standard: select File - Open Standard… or
click on ⓑ in the Calibration window.
6. Add peaks in the chromatogram of the calibration standard to the calibration file:
select Calibration - Add All or click on ⓒ (if you have multiple peaks in your
chromatogram) or select Calibration - Add Narrow Peak or click on ⓓ to add
desired peak from your standard.

Note: If you have multiple chromatograms of standards, you can repeat these steps to
add the desired peaks: open the standard and click Add Narrow Peak, then open
another standard and click Add Narrow Peak, repeat for all standards. The
number in field ⓔ is connected to the used standard and is not connected to the
concentration level. Setting a peak on already used number will overwrite the
values with a newly added one.

Note: When using any type of Broad calibration, Add Broad Peak will be enabled instead
of Add Narrow Peak.
7. Fill in the appropriate molecular weight values for the respected peaks into the M
column ⓕ .
8. Save the calibration file: from File - Save or click on ⓖ.

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19.1.2 Applying a GPC calibration to a chromatogram

If the calibration file is not assigned to the template method, the measured
chromatogram will not have it linked either. To link a calibration file to a
chromatogram do as follows:
1. Switch to the GPC Results tab ⓐ at the bottom part of the Chromatogram
window.

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2. To link the calibration file to the Chromatogram, click the Set… button ⓑ , so that
the Open GPC Calibration dialog window will emerge. You can select calibration
file from your current project or you can navigate to other folders.
3. Select the desired calibration file from the list and click OK.
4. Check that the Calibration File (Peak Table) field contains the name of the
calibration file ⓒ .
Note: When no calibration file is linked to a chromatogram, the field Calibration
File (Peak Table) contains inscription (None).

5. Save the chromatogram by selecting File - Save or clicking on ⓓ.

19.1.3 Setting a GPC calibration in the template method
Setting a GPC calibration in the template method allows you to automatically
calibrate all measured chromatograms using such method during analyses.

1. Open the Method Setup - GPC Calculation dialog by selecting Method -

GPC Calculation... in the Instrument window.
2. Open the template method by selecting the Open... icon ⓐ .

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3. Click the Set… button ⓑ to set a GPC calibration file for the template method, or
create a new one by clicking the New… button ⓒ .
4. Click OK ⓓ to apply and save the changes made to the template method.

19.2 PDA Operation

Pick the desired topic in the following chapters.

19.2.1 How to set Clarity instrument to display PDA data

l To switch an Instrument to PDA mode, select the LC-PDA, GC-PDA, CE-PDA or
GPC-PDA option from the Instrument Type Setting dialog.
l Instrument Type Setting dialog is invoked by clicking on the button in the
System Configuration dialog.
l Options that are technically possible and have been purchased are enabled by
default. Otherwise they are automatically disabled.

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19.2.2 How to open PDA chromatogram

1. In the Chromatogram window, click the Open Chromatogram icon .
2. Choose a chromatogram that has PDA data.
Note: Notice that the presence of PDA data is noted in the chromatogram
details at the bottom part of the dialog.
3. After choosing chromatogram(s) click Open (or one of the other options when
selecting multiple chromatograms).
Note: For more information regarding the opening options refer to chapter
Open Chromatogram in the Reference Guide.
4. Next suggested topic is: "How to work with PDA chromatogram" on the next
page.

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19.2.3 How to work with PDA chromatogram

Instrument Type must be set to PDA - see the chapter "How to set Clarity
instrument to display PDA data" on pg. 235.
l To open PDA Chromatogram window navigate to Window - PDA Window ①
in the Chromatogram window alternatively click the PDA Window icon
②.

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How to display PDA data

1. Spectra are automatically displayed in the PDA Chromatogram window upon
opening chromatogram that contains PDA data.
2. By default, PDA Chromatogram is divided into 4 separate panes, each with a
different information. You can change number of panes from the View menu

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3. To change a view of a pane, right mouse click and select one of the views. For a
more specific example, see the chapter "How to search in PDA library" on pg.
244..
4. Numbers ① to ④ correspond to different views in the picture above.

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How to use markers in PDA Chromatogram

Panes in the PDA Chromatogram contain graphs with markers (thin lines of inverse
color crossing the data plot ① ② ③ ④ ). Corresponding data are displayed
according to the marker positions.
Note: Moving marker in one pane moves it accordingly in other ones. For example,
moving marker ① in Chromatogram View will result in corresponding shift of
marker ③ in Isoplot View.

l To change spectral data based on time: drag the vertical marker ① or ③

to the desired time. Note that the cross cursor changes to once the
move is possible.
l To change wavelength: drag the horizontal marker ② or ④ to desired

position. Notice that the cross cursor changes to or respectively once

the move is possible.
l To change both: wavelength and time, move to the junction where the two

markers ② and ③ meet. Once the cross symbol changes to , left

mouse click + hold + drag to your desired position.
l In the 3D View you can move the whole graph to your area of interest -
simply left mouse click + hold + drag. Note that markers in other panes will
change accordingly to the moved area.

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Caution: Increasing the zoom may cause that the markers to be out of the current view. To
move them to the current zoom, right mouse click in the pane and use Move
Markers Here from context menu.

19.2.4 How to set PDA method

This section deals only with method setup related only to PDA options. For a
method setup see "Setting up a method"
1. PDA Method tab ① is available only when PDA Extension is configured on
the given instrument.
2. From the drop down ② box select PDA Spectrum - if chromatogram
contains more than one (typically DAD and FLD).
3. For the Peak Purity Options there are several settings which can restrict the
evaluation of peak purity. It can be restricted based on the Restrict
Wavelength Range ③ check- box and filling the range of wavelength in
which it will be evaluated.
4. Another restriction can be made using the Absorbance Threshold ④ . This
determines which part of peak will be used. For 0% spectra from entire peak
will be included in calculation. For 5%, spectra which has less than 5% of
absorbance compared to spectrum in apex will be excluded from calculation
etc.
5. Used Points ⑤ specifies the number of points peak purity will be evaluated,
either from the All the points or from the Five most significant.
6. In the Library Search Options ⑥ select criteria according to which the
Search in Library command, described in see pg. 244., will be performed.
7. To add another PDA library to search in, click the icon ⑦ and then click
, from the dialog choose a library.
8. List of libraries that will be searched in is listed ⑧ . Alternatively
enable/disable the search for specific library using the check-box.

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19.2.5 How to display peak purity

Displaying peak purity is one of the fundamental tasks when ensuring that no co-
eluting or co-migrating impurities contribute to the peak's response.
1. Used views: Chromatogram View, Peak Purity Spectra View, Peak Purity View
and Isoplot View.
Note: See chapter "How to work with PDA chromatogram" on page 237 for
more information about using the PDA Chromatogram window functions.
2. Move the marker ① to the peak for which you want to display peak purity.
3. In the menu Chromatogram - click the Display Peak Purity ② command or click
the icon in the toolbar.
Note: No peak selected in the Peak Purity View means that the marker from
step 2 is not positioned on any peak.
4. Peak Purity View: displays signal for selected peak and its calculated Peak
Purity ③ .
5. Peak Purity Spectra View: displays spectra in several significant points ④ of the
peak selected in the Peak Purity View.

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19.2.6 How to work with PDA library

PDA Library serves for storing compounds along with their PDA data such as
spectrum. Working with PDA libraries and data is possible from PDA
Chromatogram window.
Note: It works on a similar basis as calibration. Search In Library command, searches
the PDA library for similar spectrum as defined by your cursor axis in the
chromatogram.
PDA library can be managed either from the menu Library or using the toolbar
which is shown below:

Manage libraries:
l
Create a new library: click the New Library icon.
l
Open existing library: click the Open Library button and in the dialog
choose your desired library.

Add compounds:
1. Add a spectrum into the library: click the Add Spectrum icon which opens
Spectrum Property. In the dialog you can specify compound name and
additional comment.

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2. Add all identified peaks: click the command from the menu Spectrum - Add All
Identified Peaks.

Note: Identified peaks are those that correspond to peaks identified and named in the
calibration file. Peaks are added into the currently opened library.

3. Save library: to keep any changes made in the library, click the Save Library
icon.
4. Close library: click the Close Library icon. If you have unsaved changes you
will be prompted to either save the changes or discard them.

View library:
1. Spectral Library View: to view contents of your library, right mouse click in any
pane of PDA Chromatogram windo and choose Spectral Library View. It
contains a table with spectrum name, retention time and other parameters.

19.2.7 How to search in PDA library

To search for a matching compound in the PDA library, there is number of ways.

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Most common way to search in library:

1. Move marker ① to peak for which you want to search in library.
2. Right mouse click to a pane you don't need and select Spectral Search View to
display pane which shows search results.
3. Use the Search in Library ② icon from the toolbar. Spectral Library Search
Options dialog will pop-up where you can further refine match criteria as well as
searching across multiple libraries.
Note: Same can be achieved by pressing F3 or CTRL + F on the keyboard.
Alternatively you can use Spectral Search Viewcommand from context or
Spectrum menu.

Search in library is based upon multiple requirements (mainly on Match Factor), if

any of the requirements fails, the compound will not be displayed in the result of the
search.

1. Invoke Spectral Library Search Options dialog according to steps 1- 3 at the

beginning of this topic.

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2. Set the search parameters in the top half of the dialog.

3. Note that Restrict Retention Time check-box ③ should be enabled only when
the PDA library has been created under same conditions as the measured
chromatogram.
4. You can add new library entry using the ④ and use ⑤ to select library
which may containt.
5. Once criteria are set up, click OK to apply them and to perform the search.

Possible problem during library search:

l After performing search, you may notice that the blue ribbon ⑥ at the
bottom of the window that states 0 spectra found during the search and
Library Search View is also empty ⑦ .
l Possible reason for such behavior can be that the Library Search Options
are incorrectly set up e.g., selected library does not contain matching
spectrum.

19.2.8 How to view specific spectra in overlay

To view specific spectra from PDA library in overlay and thus have the opportunity
to compare current spectrum against spectra from the PDA library, follow the steps
below.

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1. Used views: Chromatogram View, Spectral Library, Spectral View and Isoplot
View.
Note: How to change views is shown in "How to work with PDA chromatogram"
on page 237
2. Move the marker to your desired position ① .
3. In the Spectral Library View check the Spectrum Name for each ② spectrum
that you want to show in the Spectral View.
4. Spectral View displays current spectrum along with other spectra ③ checked in
the PDA library.
5. You can move the marker ④ in the Isoplot View to move alongside both
wavelength and retention time axes.
Note that those steps can be also performed on results from the Search in Library -
thus having spectra from the search in overlay.

Note: To compare spectra it is recommended to normalize their view. Right click into
Spectral View and select Properties. In PDA Properties dialog navigate to
Chrom&Spectral View tab and select Normalization: At Current Range ⑤ .

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19.3 MS Operation
Pick the desired topic in the following chapters.

19.3.1 Creating and filling your own MS library

Own MS Library can be created using external program NIST MS Search
accessed either from the MS toolbar or from the MS menu in the MS
Chromatogram window:
l
Use the Manage Libraries button to open the MS Search.
l Switch to the Librarian tab ⓐ .
l
Use the Create Library button ⓑ to create your own library, and Add to
Library button ⓒ to add the selected compounds into it.

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To be able to add selected compounds (or spectra) to own library, such compounds
must be selected in the Librarian tab. To do so, you can either perform the Single
Compound Search or use Add Spectrum to Library icon or command from the
MS Chromatogram window.

Add Spectrum to Library

After clicking the Add Spectrum to Library icon or command, the view will lock in the
graph and will let you select the spectrum. After selecting the spectrum the Add MS
Spectrum to Library dialog for inserting that particular MS Spectra appears:
l Set the Averaging Time Range field to perform averaging and smoothing of
the spectra inserted into the library – if not selected, the actual spectra as
clicked into the graph will be stored.
l Set a Compound Name under which you want to add the spectrum into the
library.
l Press the OK button.
l The MS Search program will open, which allows you to add the spectrum
into the library upon switching to the Librarian tab and using the Add to
Library button.

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Single Compound Search
After clicking the Single Spectrum Search icon or command, the view will lock in the
graph and will let you select the spectrum. After setting the desired parameters and
clicking the Search button the MS Search program will open. Switch to the
Librarian tab and using the Add to Library button add the spectrum into the
library.
Note: For more details on Single Search Compound please see the chapter "MS
Libraries" in MS Extension manual.

19.3.2 Integration of signals in MS

In MS Extension, two types of signals can be integrated: Quantification Signals and
Result Table Signal.

Result Table Signal

Result Table Signal serves for filling the Result Table with peaks other than those
mentioned in MS Method. Any signal from the detectors configured on the particular
Instrument can be selected as Result Table Signal.
l Switch to Integration tab in Chromatogram window.
l In the drop-down list select Result Table Signal (as defined on MS Method
tab). If the Result Table Signal is not selected, integration table will not be
shown at all.
l Apply integration operations as desired.

Quantification Signal
Quantification Signal serves for quantification of compounds mentioned in MS
Method. Integration table is unique for each quantification signal. When multiple
compounds are quantified on the same quantification signal they will share the
same table.
l Switch to MS Integration tab in Chromatogram window.
l In the drop-down list select desired compound (defined by m/z ion and the
name). Chromatogram will be focused on the compound's peak.
l Apply integration operations as desired.

Note: Even if you select Result Table Signal, e.g. TIC also as your Quantification Signal
for any of your compounds, the integration table from Result Table Signal will not
be used for such Quantification Signal. Each quantification signal has its own
integration table.

19.3.3 MS Search and improving Match probability

This topic describes how MS Search, a library search is done and how to improve
Match probability with library compounds.

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19.3.3.1 MS Search - library search for compounds in MS

MS Search - Single Compound Search

Performs a simple search of a single spectrum in one or more spectral libraries.
l Open MS Search dialog using the MS - Single Compound Search menu or
icon in the Chromatogram window.
l Cursor will be focused into the chromatogram.
l Select desired search area, either an exact retention time or an interval
(while holding CTRL key when clicking).
l MS Search dialog will be opened with filled in the selected search interval.
l In Max Hits select how many results (up to) shall be shown.
l Click on Search.
l Select the desired compound by checking the checkbox and possibly add
such compound to your MS Method.

MS Search - Automatic Compound Search

Serves for searching of possible compounds of interest on a defined signal.
l Open MS Search dialog using the MS - Automatic Compound Search menu
or icon in the Chromatogram window.
l In the drop-down list select a signal to be searched and define the search
retention time interval.
l Select Libraries to be searched in.
l Optionally set some Search Options and hit Search button.
l In the search results, you can select any compound at each peak found at
specified retention time, sorted by the best matches.
l After selecting some compounds, you can add the to your MS method by
clicking the Add All Selected to Method button.
l When selecting any of the compounds, you can compare the spectrum with
the spectrum from library in the graph below the search results.

MS Search - Target Compound Search

Performs a simple search of a single spectrum in one or more spectral libraries.
l Open MS Search dialog using the MS - Target Compound Search menu or
icon in the Chromatogram window.
l By clicking the Select Compound... button open Select NIST Compound
dialog.
l Enter the name of the desired compound and select it from the table below. If
you use more than one library, select the library to be searched in the
combobox on the left side.

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l Select retention time or whole chromatogram to be searched in and hit the
Search button.
l You will get results - exact retention times of peaks with the highest
probability.
l You can filter the results by Filter by Min Match Factor slider/editbox, based
on Match probability.
l Select the desired compound and add such compound to your MS Method.

19.3.3.2 Improving Match probability

Restrict m/z Range

Serves for narrowing the m/z range to be searched. Provided you know the range of
compounds' m/z you are interest in, you can omit the remaining m/z from the
search, thus raising the Match probability. In case you enter wrong m/z range, a
dialog will appear and will tell you what the m/z range of the current chromatogram
is.

Use Selected m/z

Defines what m/z should or should not be searched.
l Search Only Selected will search only for the defined m/z. Suitable when you
know typical m/z for the compounds you are interested in.
l Search All But Selected will omit selected m/z from search. Suitable e.g.
when you don't want the used solvent to interfere with the search results.

Background subtraction
Defines exact points and/or intervals of retention time to be omitted from the
search. Such values can be inserted manually or selected directly in the graph.

Preview Spectrum in Library

Shows the search results, based on the above-mentioned options, directly in the
NIST library. You can check here, whether your setting were right, or even find out
the typical m/z for selected compounds.

19.4 SST operations

Following chapters describe specific procedures concerning SST.

19.4.1 Using SST for quality control

The optional SST Extension allows to set up limits for selected parameter. It
compares measured values against those preset limits and perform actions based
on the result. The SST works with calibrated chromatograms and the evaluation is
based on the compound name in calibration.

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Here we provide an example on how to create SST method which can be used to
check if the control samples are within expected limits and how to set up sequence
to be checked by different SST methods.
Caution: In order to get desired reactions to passed or failed limits for this scenario it is
necessary to have chromatogram Overlay Mode switched off.
1. Create a SST method in the Chromatogram window using the:
l SST - SST Result to display the SST tab
l SST - New to create a new SST method
l SST - Update from Calib to load the list of peaks from a calibration file
(There has to be calibration linked to the chromatogram on the Results
tab)
l Than the screen will look similar to this:

2. As the second step, fill in the necessary parameters for the limits. (In this case
Tetrachlormethane peak is the one used to check actual against expected value
in Control sample., Expected Amount is 1.2, lower limit is 1.1, upper limit 1.3.)
l Select the checkbox of the Tetrachlormethane in the table on the left.
l Double-click the Amount column in the table on the right to activate it.
l Set the 1.1 value in the Lower Limit cell of the column, 1.3 into the Upper
Limit cell.
l Right-click the table and select the SubParameters item. On it uncheck
the %RSD Limit item (as you do not need it) and select the Each
Individual Value.

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More Info:
l When the SST Result is based on Each Individual Value than it
compares each evaluated value with the Upper Limit or Lower Limit.
l When the SST Result is based on Mean of All Values than it
compares average value of all opened chromatograms with linked
calibration with the Limits. So pay attention to all opened
chromatograms.
l You may hide the inactive rows and columns by using the SST - Show All
Columns and SST - Show All Rows items in the menu.
l The result of the check is displayed by the green tick mark or red cross.
You can validate several different parameters at the same time.
l You should see similar result now:

3. In another step you can set reaction to the test result:

l Use the SST - Events command to open the SST Properties dialog
again.
l Set the tab as on next picture (sequence will stop and beeping sound will
be played if SST fails):

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lIt is possible to trigger any external program wanted and set different
events on failed or passed check etc.
4. Save the created method by using the SST - Save item (I used HighControl.sst
file name).
5. You can create other SST methods in the same manner. For example if you use
multiple calibration levels it is possible to create methods which control each
level against its own limits.

How to set up sequence to be checked by different SST methods

l Set the sequence accordingly:
l Right-click the sequence table and select the Setup Columns item.
l Set the columns Open, Run Program, Program to Run, Parameters and
Include in SST as visible. Any other columns may be displayed as
desired.
l Set the columns for the rows with High Control and Low Control samples
as shown on the next picture:

l This will force Clarity to open the correct SST method for the row and
perform the check.
Caution: Parameters like %Self% are case sensitive. All 3 checkboxes
Open, Run Program and Include in SST must be checked for
SST to work correctly.

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