Agilent 2100 Bioanalyzer System Analyzer User's Guide PDF

Agilent Technologies

Agilent 2100 Bioanalyzer System

2100 Expert Software User's Guide

Notices Agilent Technologies, Inc. 2000-2020 No part of this manual may be reproduced in any form or by any means (including electronic storage and retrieval or transla- tion into a foreign language) without prior agreement and written consent from Agi- lent Technologies, Inc. as governed by United States and international copyright laws.

Document Number SD-UF0000050 Rev. D.00

Edition 02/2020 Published in Germany Agilent Technologies Hewlett-Packard-Strasse 8 76337 Waldbronn

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CAUTION

A CAUTION notice denotes a hazard. It calls attention to an operating procedure, practice, or the like that, if not correctly per- formed or adhered to, could result in damage to the product or loss of important data. Do not proceed beyond a CAUTION notice until the indicated condi- tions are fully understood and met.

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For Research Use Only

Not for use in diagnostic procedures

2100 Expert Software User Guide

In This Guide...

In This Guide...

Welcome to the Users Guide for the Agilent 2100 Expert Software. This manual provides beginners and advanced users with information needed to successfully run electrophoretic assays with the 2100 Bioanalyzer system. The 2100 Expert Software allows the control of the 2100 Bioanalyzer instrument (including diagnostic functions) and, in combination with an analysis kit, the acquisition, interpretation and result presentation of data generated during the analysis of DNA, RNA, and proteins.

1 Typographic conventions in this Manual

This chapter shows you how to make efficient use of this manual.

2 Quick Start

This chapter is meant for experienced users. It briefly summarizes the necessary steps to prepare and run an assay. Please note that in terms of the 2100 Expert Software, a method resembles an extended assay, which also includes additional administrative data such as operator, instrument, reporting, and workflow settings. These additional functions are unlocked with the 2100 Expert Security Pack.

3 Looking at 2100 Expert Software

Before you start running methods/assays on the Agilent 2100 Bioanalyzer system, you should familiarize yourself with the 2100 Expert Software. This chapter shows how to get started with the 2100 Expert Software, and outlines its main operational possibilities.

4 Running and Evaluating Electrophoretic Methods/Assays

This chapter explains how electrophoretic measurements are made using the 2100 Bioanalyzer system, gives detailed descriptions of all steps necessary to run electrophoretic assays, and shows how to analyze and evaluate results using electropherograms and gel-like images.

2100 Expert Software User Guide 3

In This Guide...

5 Working with Chip Data and Methods/Assays This chapter shows you what to do to open, save, import and export files, and how to print the results.

6 Administering System Functions and the Security Pack This chapter is your guideline for configuring the 2100 Expert Software.

7 Running Instrument Diagnostics This chapter shows how to use the diagnostic tests to check the 2100 Bioanalyzer instrument for proper functioning.

8 Performing Verifications This chapter describes how you can validate your 2100 Bioanalyzer system.

9 Products, Spare Parts, and Accessories This chapter lists all parts and accessoriesincluding reorder numbers.

4 2100 Expert Software User Guide

Contents

Contents

1 Typographic conventions in this Manual 7

2 Quick Start 9 Preparing the Agilent 2100 Bioanalyzer Instrument 10 Switching on the Agilent 2100 Bioanalyzer 11 Running a Measurement 12 During the chip run 20 Viewing the Measurement Results 21 What You Can do When the Measurement is Finished 23

3 Looking at 2100 Expert Software 25 Introduction to the Key Features of the 2100 Expert Software 26 Starting the 2100 Expert Software 27 2100 Expert Software Work Area 29 Closing 2100 Expert Software 37 The 2100 Expert Security Pack 38

4 Running and Evaluating Electrophoretic Methods/Assays 51 Principles of Nucleic Acid and Protein Analysis on a Chip 53 Preparing and Running an Electrophoretic Method or Assay 57 Analyzing and Evaluating the Results of an Electrophoretic Method or Assay 85 Result Flagging 145

5 Working with Chip Data and Methods/Assays 157 Working with Chip Data and Methods/Assays 158 2100 Export Data Overview 159 Handling Methods 162 Handling Chip Data 166 Organizing, Backing up, and Archieving 2100 Expert Data 167 Importing Data 169 Exporting Data 173 Printing Reports 180 Configuring Tables 187

2100 Expert Software User Guide 5

Contents

6 Administering System Functions and the Security Pack 191 Administering System Functions and the Security Pack 192 Access Control 193 Pre-configurations for the 2100 Expert Software 198 Configuring the 2100 Expert Software 207 Exporting and Importing Multiple Data Files 215 Archieving Data 217 Using Log Books 220

7 Running Instrument Diagnostics 227 Running Instrument Diagnostics 228 How to Run Instrument Diagnostics Test 230

8 Performing Verifications 233 Performing Verifications 234 Verifications 235

9 Products, Spare Parts, and Accessories 243 Products, Spare Parts, and Accessories 244

6 2100 Expert Software User Guide

2100 Expert Software User Guide

1 Typographic conventions in this Manual

This chapter shows you how to make efficient use of this manual.

7Agilent Technologies

1 Typographic conventions in this Manual In This Guide...

This manual uses convenient online navigation features and follows certain typographic conventions.

If you have any questions this manual cannot answer, please contact Agilent for addtional support at: https://www.agilent.com/en/product/automated-electrophoresis/bioanalyzer-systems.

Table 1 Typographic conventions

Highlight

Italic Emphasis Example: Right-click the ...

Term Example: Dot plots show events as dots.

Reference to another document Example: Refer to the Agilent 2100 Bioanalyzer System Troubleshooting and Maintenance Guide.

Blue Cross-reference or hyperlink Examples: Introduction to the Key Features of the 2100 Expert Software on page 26 https://www.agilent.com/en/product/automated-electrophoresis/bioanalyzer-systems

Courier Code Example: . the command line parameter -port 2 ...

Courier bold

User input Example: Enter 50 MB.

Bold On-screen element Example: ... the OK button.

8 2100 Expert Software User Guide

2100 Expert Software User Guide

2 Quick Start Preparing the Agilent 2100 Bioanalyzer Instrument 10 Switching on the Agilent 2100 Bioanalyzer 11 Running a Measurement 12 During the chip run 20 Viewing the Measurement Results 21 What You Can do When the Measurement is Finished 23

This chapter is meant for experienced users. It briefly summarizes the necessary steps to prepare and run an assay. Please note that in terms of the 2100 Expert Software, a method resembles an extended assay, which also includes additional administrative data such as operator, instrument, reporting, and workflow settings. These additional functions are unlocked with the 2100 Expert Security Pack.

9Agilent Technologies

2 Quick Start Preparing the Agilent 2100 Bioanalyzer Instrument

Preparing the Agilent 2100 Bioanalyzer Instrument

1 Make sure a clean electrode cartridge is installed.

2 If you want to change the cartridge, follow the instructions in Loading the Electrophoresis Chip into the 2100 Bioanalyzer Instrument on page 63 .

10 2100 Expert Software User Guide

Quick Start 2 Switching on the Agilent 2100 Bioanalyzer

Switching on the Agilent 2100 Bioanalyzer

1 Make sure the 2100 Bioanalyzer instrument is connected to line power and connected to the PC.

2 Turn on the line switch at the rear of the instrument.

The status LED at the front of the 2100 Bioanalyzer instrument should light up.

The status LED shows you the current status of the instrument.

Signal Meaning

Green light Instrument is switched on and ready for measurement.

Green blinking Measurement is running.

Orange blinking Instrument is busy (running self-diagnostic, for example).

Red light Instrument is not ready for measurement. Switch the instrument off and on again. If the problem persists, contact Agilent service.

2100 Expert Software User Guide 11

2 Quick Start Running a Measurement

Running a Measurement

1 To start the 2100 Expert Software on the connected PC, go to your desktop and double-click the following icon:

2 The 2100 Environment Checker (see The 2100 Environment Checker on page 28) will validate computer settings in the background. You might have to acknowledge these warnings before the software will start.

3 The access to the 2100 Expert Software and its functionality is controlled by the installed Security Pack. You need to authenticate yourself with your user name and password.

For more information on the user management of 2100 Expert Software, see section Looking at 2100 Expert Software.

12 2100 Expert Software User Guide

Quick Start 2 Running a Measurement

After startup of the software, you enter the Instrument context:

2100 Expert Software User Guide 13

2 Quick Start Running a Measurement

The Instrument tab shows you the status of the 2100 Bioanalyzer instrument:

Icons Meaning

Instrument detected, lid is open.

Instrument detected. Lid is closed, but no chip is inserted.

No instrument has been detected. Check the COM Port setting (see figure under step 3), the RS 232 connection cable, the power cable or the USB connection, and the power switch. For details on how to set up the 2100 Bioanalyzer system and connect it to a PC, see Agilent 2100 Bioanalyzer System Installation and Safety Guide.

NOTE If you started 2100 Expert Software for the first time after installation, you first need to activate the different software modules with your license keys. See How to Activate Software Licenses on page 213 for details.

14 2100 Expert Software User Guide

Quick Start 2 Running a Measurement

4 Make sure that an instrument has been detected before continuing.

5 Select an assay/method for the chip run. On the Instrument tab, click the Assays/Methods button.

OR

Click the Assays/Methods menu.

Both will open a menu, allowing you to select an assay/method for the measurement.

6 Prepare the samples and the chip. Edit destination and data acquisition parameters such as number of samples, and insert sample information in the chip summary table. For detailed information on sample and chip preparation refer to:

Kit Guides that are available for each kit (see Agilent 2100 Bioanalyzer Help Desk)

NOTE You can also select File > Open File to Run. This opens a dialog box allowing you to load either an assay/method (.xsy) or a chip data file (.xad).

NOTE When preparing chip and samples, pay attention to the essential measurement practices described in Essential Measurement Practices (Electrophoretic Methods/Assays) on page 61 or as described in the respective Kit Guide.

2100 Expert Software User Guide 15

2 Quick Start Running a Measurement

7 Insert the chip in the 2100 Bioanalyzer instrument:

a Open the lid.

The status of the instrument is updated on the Instrument tab.

b Check that the cartridge is inserted properly. For details, please refer to Loading the Electrophoresis Chip into the 2100 Bioanalyzer Instrument on page 63 .

c Place the chip into the receptacle.

Figure 1 Electrode cartridge inserted in the instrument (graphic shows an example).

The chip fits only one way. Do not force it into place.

CAUTION Do not force the lid closed. This can damage the cartridge.

If the lid does not close without force, check that chip is inserted correctly. When the software recognizes an inserted chip, the chip is shown on the Instrument tab. If you have closed the lid, and the software has not recognized the chip, verify that the cartridge is properly installed into the instrument. Close the lid.

16 2100 Expert Software User Guide

Quick Start 2 Running a Measurement

d Carefully close the lid.

The electrodes in the cartridge fit into the wells of the chip.

When the chip is detected, the image on the Instrument tab changes to a chip.

If the chip is not detected, open and close the lid again.

8 On the Instrument tab, click .

NOTE The chip that is displayed depends on the assay that was selected in the software, not on the actual chip that was inserted in the bioanalyzer.

2100 Expert Software User Guide 17

2 Quick Start Running a Measurement

9 Before the chip run starts, you are prompted to confirm this action with your electronic signature. This action is then recorded and will be available for reviewing in the signature log and the audit trail.

The chip run starts. The Raw Signals sub-tab shows an electropherogram of the currently measured sample. The name of the sample is displayed above the graph. The graph is a live plot of the migration time against fluorescence units (raw data, including background fluorescence, for example).

18 2100 Expert Software User Guide

Quick Start 2 Running a Measurement

The number of the sample that is currently being measured is indicated on the information bar:

The status bar at the bottom of the window shows the measurement progress for the chip run and the COM port number used for data acquisition.

NOTE The signature must be saved with the correct setting in the Meaning field. If this setting cannot be pre-selected by 2100 Expert Software, you must do this selection manually.

NOTE The 2100 Expert Software Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Modelfor details (Access Control on page 39).

2100 Expert Software User Guide 19

2 Quick Start During the chip run

During the chip run

1 View the chip data file in the Data context by clicking on the name of the Data File.

During the chip run, you can do the following:

Switch to any other context. For example, you can evaluate any chip data file in the Data context, or compare samples in the Comparison context.

If necessary, abort the chip run by clicking on the Stop button. You need to confirm this action with your electronic signature.

All data that was collected up to the stop point will be saved.

2 Switch to any other context. For example, you can evaluate any chip data file in the Data context, or compare samples in the Comparison context.

3 If necessary, abort the chip run by clicking on the Stop button. You need to confirm this action with your electronic signature.

All data that was collected up to the stop point will be saved.

20 2100 Expert Software User Guide

Quick Start 2 Viewing the Measurement Results

Viewing the Measurement Results

To view the results, switch to the Data context. The data file that has just been generated by your chip run is displayed. The Chip Summary tab shows information on your chip data file, and lets you modify or enter comments regarding chip, samples, and study.

2100 Expert Software User Guide 21

2 Quick Start Viewing the Measurement Results

1 In the tree view panel, click any sample name or the ladder.

This selects the Electropherogram tab, which displays a data plot of size/migration time versus fluorescence intensity.

Peaks have automatically been detected, and their characteristics such as size, concentration, purity, or molarity have been calculated and are shown in the Peak Table at the bottom of the window.

22 2100 Expert Software User Guide

Quick Start 2 What You Can do When the Measurement is Finished

What You Can do When the Measurement is Finished

When the measurement is finished, you can:

Document your chip run by entering or modifying sample names, chip comments, and study information, for example.

Evaluate the measurement results by analyzing gel-like images, electropherograms and result flagging.

Analyzing and Evaluating the Results of an Electrophoretic Method or Assay on page 85

Print the results to document them on paper or an electronic format, such as HTML or PDF.

See Printing Reports on page 180.

Export the results or parts of them for further evaluation in other applications.

See Exporting Data on page 173.

Compare the results with the results of other chip runs in the Comparison context. See Comparing Samples from Different Electrophoretic Chip Runs on page 139.

Pass the results through the predefined workflow.

See Workflow Control on page 50

Insert the next chip in the 2100 Bioanalyzer instrument and start a new chip run.

2100 Expert Software User Guide 23

2 Quick Start What You Can do When the Measurement is Finished

24 2100 Expert Software User Guide

2100 Expert Software User Guide

3 Looking at 2100 Expert Software Introduction to the Key Features of the 2100 Expert Software 26 Starting the 2100 Expert Software 27

The 2100 Environment Checker 28 2100 Expert Software Work Area 29

Operating Modes 30 Closing 2100 Expert Software 37 The 2100 Expert Security Pack 38

Access Control 39 Data Integrity 42 Handling of Electronic Signatures 43 Workflow Control 50

Before you start running methods/assays on the Agilent 2100 Bioanalyzer system, you should familiarize yourself with the 2100 Expert Software. This chapter shows how to get started with the 2100 Expert Software, and outlines its main operational possibilities.

25Agilent Technologies

3 Looking at 2100 Expert Software Introduction to the Key Features of the 2100 Expert Software

Introduction to the Key Features of the 2100 Expert Software

The Agilent 2100 Expert Software is characterized by the following key features:

2100 Expert Software provides a single software platform with a common user interface for running, analyzing, evaluating, presenting, and comparing DNA, RNA, and protein parameters.

2100 Expert Software provides an optional Security Pack that needs to be ordered separately as G2949CA and is then activated with a license key. This Security Pack activates user management functions and electronic signature to meet the Food and Drug Administration (FDA) requirements (21 CFR Part 11).

2100 Expert Software provides detailed installation verification and system verification tests on the 2100 Bioanalyzer system.

2100 Expert Software allows having multiple chip data and/or method/assay files open at the same time.

2100 Expert Software features an data evaluation tool (Comparison context) allowing comparison of measurement results (of same method/assay class) from different chips.

2100 Expert Software offers the RNA Integrity Number (RIN), a reliable tool to automatically compare integrity of RNA samples.

2100 Expert Software features improved integration including manual integration (available for DNA and Protein methods/assays only).

2100 Expert Software allows color-coded result flagging with pre-defined or custom result flagging rules. Flagging rules can be applied to measurement results.

2100 Expert Software has customizable result tables and gel-like images.

2100 Expert Software allows to control two 2100 Bioanalyzer instruments from one PC. It is possible to run measurements on two 2100 Bioanalyzer instruments at the same time.

2100 Expert Software has improved printing and reporting functions.

2100 Expert Software has extended instrument diagnostics functionality.

26 2100 Expert Software User Guide

Looking at 2100 Expert Software 3 Starting the 2100 Expert Software

Starting the 2100 Expert Software

1 Go to your desktop and double-click the following icon:

OR

From the Windows Start menu, select All Programs > Agilent 2100 Bioanalyzer > 2100 Expert.

2 The 2100 Environment Checker (see The 2100 Environment Checker on page 28) will validate computer settings in the background. You might have to acknowledge these warnings before the software will start.

3 The access to the 2100 expert and its functionality is controlled by the installed Security Pack. You need to authenticate yourself with your user name and password.

For more information on the user management of 2100 Expert Software, see The 2100 Expert Security Pack on page 38.

The 2100 Expert Software application window appears. 2100 Expert Software Work Area on page 29 gives an overview of the application window.

2100 Expert Software User Guide 27

3 Looking at 2100 Expert Software Starting the 2100 Expert Software

The 2100 Environment Checker At startup of the 2100 Expert Software a few parameters, such as regional settings, setup of a printer and printer margins are checked automatically.

Eventually, a pop-up window will appear that indicates warnings and errors:

Setup a default printer (Setup a default printer on page 198)

Default printer margins (Default Printer margins on page 199)

Configure regional settings (Configure regional settings on page 202)

Display settings (Display settings on page 205)

USB Configuration (USB-to-Serial adapter configuration on page 206)

NOTE For Security Pack users: All changes to above settings have to be performed for the generic 2100 System user account. Please login with this Windows user account and make the according changes.

28 2100 Expert Software User Guide

Looking at 2100 Expert Software 3 2100 Expert Software Work Area

2100 Expert Software Work Area

The 2100 Expert Software has standard elements such as pull-down menus and toolbars, and the main working area, which contains several tabs, some of which have sub-tabs. The 2100 Expert Software area has the following regions (demonstrated at the Data context):

2100 Expert Software User Guide 29

3 Looking at 2100 Expert Software 2100 Expert Software Work Area

Operating Modes The 2100 Expert Software can be operated in six modes, called "contexts":

Instrument Context

Data Context

Verification Context

Comparison Context

Method or Assay Context

System Context

Using the Contexts bar, the Context menu, or the selection list in the toolbar, you can switch between the contexts:

An introduction to the six contexts is given in the following.

NOTE The contexts work independent from each other regarding their data. This means, for example, that you can review data and run measurements at the same time. Please note that in terms of the 2100 Expert Software, a method resembles an extended assay, which also includes additional administrative data such as operator, instrument, reporting, and workflow settings.

NOTE Menus, toolbars, the tree view, and the main working area (tabs) significantly change when you switch between the contexts.

30 2100 Expert Software User Guide

Looking at 2100 Expert Software 3 2100 Expert Software Work Area

Instrument Context On startup, 2100 Expert Software enters the Instrument context, where you can run DNA, RNA or protein methods/assays by selecting a method/assay file and starting the chip runprovided that the 2100 Bioanalyzer instrument is properly connected, a chip is inserted, and the lid is closed.

During the chip run(s), you can view the status of the instrument(s): information and real time acquisition data.

NOTE If two 2100 Bioanalyzer instruments are connected to your PC, you can run both in parallel.

2100 Expert Software User Guide 31

3 Looking at 2100 Expert Software 2100 Expert Software Work Area

In the Instrument context, it is also possible to run hardware diagnostic tests on all connected instruments. Refer to Running Instrument Diagnostics on page 227 for details.

Data Context In the Data context, you can

view, analyze, and evaluate the results of your chip runs that are presented as electropherograms, gel-like images, histograms, dot plots, and result tables.

export and print the results of your chip runs.

The measurement data is stored in.xad files.

32 2100 Expert Software User Guide

Looking at 2100 Expert Software 3 2100 Expert Software Work Area

Verification Context The Verification context is used to run and document qualification tests.

For the 2100 Bioanalyzer instrument and the Expert Software, tests can be run for:

Installation Verification

System Verification

Verification results are automatically saved in .xvd files. You can re-open .xvd files to review verification results.

For details, refer to Performing Verifications on page 233.

2100 Expert Software User Guide 33

3 Looking at 2100 Expert Software 2100 Expert Software Work Area

Comparison Context In the Comparison context, you can open multiple electrophoretic chip data files and compare samples of the same assay class (DNA 1000, for example). It is possible to overlay electropherograms and compare the results.

Comparison results can be saved in .xac files. You can re-open .xac files to review the comparison results and to add further samples for comparison.

34 2100 Expert Software User Guide

Looking at 2100 Expert Software 3 2100 Expert Software Work Area

Method/Assay Context In the Method/Assay context, you can create your own methods/assays based on Agilent templates by modifying certain data (e. g. data analysis setpoints, sample names or result flagging). Within a method/assay, you also define general settings, which include the instrument(s) to be used, the relevant study, the workflow to be followed, and the reporting elements.

Methods/Assays are stored as .xsy files.

2100 Expert Software User Guide 35

3 Looking at 2100 Expert Software 2100 Expert Software Work Area

System Context In the System context, you can

define System Wide Settings for the 2100 Expert Software such as settings for default file names and directories, signal colors, auto export functions, or default export directories

view the contents of the System Log Book

add or delete users and assign the required roles to the users (available to administrators only)

make use of the import/export and archiving functions (available to administrators and backup operators only)

36 2100 Expert Software User Guide

Looking at 2100 Expert Software 3 Closing 2100 Expert Software

Closing 2100 Expert Software

1 From the File menu, select Exit.

If a chip run is in progress, the following message appears:

2 Click OK and wait until the chip run is complete.

3 If the currently open file has not yet been saved, 2100 Expert Software asks for your electronic signature in order to save the file.

After you have confirmed the messages, 2100 Expert Software quits.

NOTE This dialog box may also appear if you try to switch between contexts while there is unsaved data.

HINT When opening a saved data file later, you can always load earlier versions of the file if required.

2100 Expert Software User Guide 37

3 Looking at 2100 Expert Software The 2100 Expert Security Pack

The 2100 Expert Security Pack

The 2100 Expert Software with the Security Pack license provides functionality for

Access Control (Access Control on page 39)

Data Integrity (Data Integrity on page 42)

Handling of Electronic Signatures (How to Sign your Work Steps on page 43)

Workflow Control (Workflow Control on page 50)

With access control functionality, only authenticated and authorized users can access and modify data, i.e. any electronic record created or managed by 2100 Expert Security Pack. It is part of the concept to guarantee the security and integrity of all analytical data created with the 2100 Bioanalyzer instrument and managed by the 2100 Expert Software on a validated PC system. This data security protects all raw data, methods/assays, and results from unauthorized access. Together with the functionality provided for handling of electronic signatures and workflow managment, the security pack renders the 2100 Expert Software compliant to the regulations and guidelines of the Food and Drug Administration (FDA) for electronic records and electronic signature, 21 CFR Part 11.

With the workflow management functions, only dedicated users can perform measurements and create result data. This data must then be reviewed in a way that is configurable, but always requires a 4-eyes principle in order to approve results. The review levels are configurable regarding to who will be allowed to perform them, but also regarding to how many levels of reviews have to be accomplished for a certain method/assay.

38 2100 Expert Software User Guide

Looking at 2100 Expert Software 3 The 2100 Expert Security Pack

Access Control The 2100 Expert Security Pack provides configurable access control and user management functionality to ensure that only authorized users can access the software and the measurement data:

User control (login, access to functionality and data)

Each user must log on to the 2100 Expert Software by entering his/her user name and password. Access to data as well as to functions is only permitted to authenticated and authorized users according to their user roles. Each user is identified and checked for his or her function at all times.

Some program settings (configuration) are specially protected and can only be edited by the 2100 Expert administrators.

Application lock

If the 2100 Expert Software workplace is not used within a specified amount of time, the screen is automatically locked. In such cases, only authorized users can unlock the computer. During a method workflow, only the current user or a special unlock operator can remove the application lock.

Windows user accounts

2100 Expert Software deploys and integrates windows operating system technology for the configuration of user and password management. Thus, options of configuration are versatile and also pre-existing configurations can be easily applied to 2100 Expert Software.

User Role Model The 2100 Expert user role model ensures that every user is allowed to access only those functions he/she is authorized to use (functional security).

User Account The 2100 Administrator takes care of the 2100 Expert Software user accounts. To work with the 2100 Expert Software, you have to log on first (password protected).

2100 Expert Software User Guide 39

3 Looking at 2100 Expert Software The 2100 Expert Security Pack

Roles and Access Rights Depending on your tasks, you are assigned to one or several user roles, for example, administrator, operator, or advanced operator. Rights that are associated with your roles provide access to specific functions of the 2100 Expert Software.

By default, the following roles are used within the 2100 Expert Software:

2100 Administrator

Is responsible for user accounts and roles. Additionally, can perform data export and archiving and can open methods/assays and data files. The 2100 Administrator also has rights to access the secured area with the Windows Explorer for backup and archiving purposes.

Backup Operator

Is responsible for batchwise export and import, archiving and dearchiving, and backup possibilities with external tools. The backup operator also has rights to access the secured area with the Windows Explorer for backup and archiving purposes.

Standard Operator

Can create and run methods/assays and analyze the data, cannot change advanced setpoints nor perform manual integration.

Advanced Operator

Can create and run methods/assays and analyze the data, including changing the advanced setpoints and performing manual integration. Can additionally validate instruments.

Validation Operator

Is responsible for validating the 2100 Bioanalyzer system, usually an Agilent service engineer.

2100 Unlock Operator

Is needed in case of a private lock applied or if another user needs access and the user corresponding to the private lock unexpectedly is not available.

2100 Guest

Merely has got read-only access to methods/assays and data, but no operating functionality.

40 2100 Expert Software User Guide

Looking at 2100 Expert Software 3 The 2100 Expert Security Pack

In most cases 2100 Expert Software displays all data for reviewing independent of the user role. However, only that functionality is available that is associated with the specific role. Note that a user may have more than one role assigned.

If you have several roles and need to perform a task associated with a role other than your current role, you have to log out and log back in with the other role.

Table 2 More specifically, the users with the different roles have access to the following functions

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System User management X Archive/de-archive data X X Import/export multiple files X X X

Verif. Verify system and instruments X X Method/ Assay

Open method/assay files X X X X X X X

Create and modify methods/assays (except advanced setpoints and result flagging rules)

X X

Modify advanced setpoints and result flagging rules

X

Instr. Run methods/assays on instruments X X Data Open data files X X X X X X X

Analyze measurement data (except advanced setpoints and manual integration)

X X

Modify advanced setpoints and use manual integration

X

General Read log books X X X X X X X Change password X X X X X X

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3 Looking at 2100 Expert Software The 2100 Expert Security Pack

Data Integrity 2100 Expert Software provides functionality to ensure the integrity of all data:

Data protection

The measurement data is stored in the restricted area of the file system. It cannot be accessed with the Windows Explorer by ordinary means. This means that viewing files and data with the Windows operating system explorer is restricted.

Audit trails and log books

User actions in the 2100 Expert Software are logged in so-called audit trails and signature logs. These are records of access-controlled actions and cannot be manually modified. They are subject to data protection and are saved within the data files or with the 2100 Expert system file.

The audit trails and signature logs capture the following actions:

Service access and all administration activities

Changes to access rights of users

Modifications to measurement data

The logins and logouts of users, as well as failed attempts to log in and opening and closing of sessions

Additional concepts are provided for

Version control to identify original files and to control versioning of file copies

Archiving functionality and data access for backup purposes for particular users

Disaster recovery

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Looking at 2100 Expert Software 3 The 2100 Expert Security Pack

Handling of Electronic Signatures All activities such as creating or modifying data must be confirmed by the user with his or her electronic signature to proof their authentication.

To ensure data security, no user can sign two consecutive steps in the workflow. If, for example, one user executes a measurement, another user has to review and approve the results.

The different levels of the review workflow are completed by signing them. Once a user has performed a step (for example, reviewed the results), he/she has to sign it. The data is then released for the next workflow level. Then the next user is responsible for the method and the previous user can no longer reject the step. He/she would have to inform the next user to reject the results.

The complete sequence of steps is documented in the audit trail and the signature log, even if the desired result was not achieved.

How to Sign your Work Steps You have performed an action that requires to be signed with your electronic signature such as creating or modifying data.

To sign your work within 2100 Expert Software:

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1 If you choose to save the current data or if you try to switch to another file or context, 2100 Expert Software asks for your signature:

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2 At the top of this dialog, you see the list of changes. Click the plus symbol to expand the sections of the list.

3 The Meaning field is used to state the main purpose of your modifications. In some cases, however, the meaning is unequivocal and you dont need to select it here. This is, for example, when starting a chip run. Then the meaning is already preselected and cannot be changed.

4 To specify your intention in more detail, use the Comment field.

5 Enter your User ID (login name) and your Password in the Signature section. Furthermore, the displayed Domain name must be correct. This is either the local PC name or the network domain, depending where your User ID is defined.

6 To finish the electronic signature, click OK.

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How to Approve/Reject the Current Workflow Level With every method, an appropriate workflow must be defined in order to release it for use. This means that one or several users must be explicitly specified to approve the work of each workflow level. When executing a method, these users can then approve the measured results and move the method to the next workflow level.

To approve the current workflow level:

1 To review the results, switch to the Data context.

As the analyst who was running the method, you now can check the measured results of all samples.

2 Samples can be approved from the Chip Summary tab table (also in a bulk), or individually in the Electropherogram tab.

a In the Approved column of the sample table, specify for each sample whether the results can be approved or must be rejected.

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b Right-click on the sample's electropherogram and select your Approval for the sample.

3 If all samples are approved, you select Approve current workflow from the Workflow menu.

4 Confirm your changes to the state of the samples with your electronic signature.

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5 Additionally, confirm the workflow level approvement with your workflow signature.

The method is moved to the next workflow level (review).

Only the users that are specified in the method for this level are authorized to do the review. The number of required review levels is also specified in the method.

If you are reviewing the method in a later workflow level and the results are not as required, you can also reject the method by selecting Reject current workflow from the Workflow menu. The method must then be taken care of the users of the previous level again.

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If you are assigned to two subsequent workflow levels, you cannot approve both levels. When trying to approve the second subsequent level, the following message appears:

The user doing the final review finalizes the method by approving the final workflow level. However, he/she has the option to revoke this finalization in case errors are observed afterwards. This can also be done from the Workflow menu.

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Workflow Control All measurements follow a determined workflow. This workflow includes steps such as the execution of methods, peer reviews, and the final approval. The workflow also defines that only pre-defined users in certain roles can take these actions and that any other user is restricted from doing so. Every action in the workflow must be signed by the user with an electronic signature, before it can be passed on to the next review/workflow level. The workflow management in particular provides means of reproducibility and traceability for the measurements, thus providing data and result reliability.

For every measurement done with the 2100 Bioanalyzer system, the following workflow must be followed: 1 Method/Assay setup

Methods/Assays are created from method/assay templates and can be modified as required for a particular measurement, typically done by an advanced operator.

2 Method execution The available methods are used to run measurements. This includes the following steps: Preparing the required samples, reagents, chip and the instrument Entering the required administrative information in the method Executing the method The methods are typically executed by a standard operator.

3 Analyst review(s) Every measurement must be evaluated by one of the analyst reviewers. The reviewer decides whether the measurement gets approved (moved to the next workflow level) or rejected (moved one workflow level back).

4 One or more peer reviews and approval (depending on your system configuration) Some labs require the approval of several reviewers. The number of required reviews can be specified in the method.

5 Final review With the evaluation of the final reviewer, the measurement is finished, in case the evaluation results in an approval.

6 Exception route Revoke of the final approval brings back the file into the state, where one of the final reviewers can modify the file and do a changed approval in case of a sample or a setpoint had been accidentally set in a wrong manner and needs to be adjusted before the final state of the document.

This workflow is valid for all methods and measurements and can only be operated in this exact order.

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4 Running and Evaluating Electrophoretic Methods/Assays Principles of Nucleic Acid and Protein Analysis on a Chip 53 Preparing and Running an Electrophoretic Method or Assay 57

Selecting an Electrophoretic Method 58 Preparing Samples, Reagents, and Chips for Electrophoretic Methods/Assays 61 Loading the Electrophoresis Chip into the 2100 Bioanalyzer Instrument 63 Running an Electrophoretic Method or Assay 68 Entering Chip and Sample Information 73 Displaying the Measurement Results (Electrophoresis) 75 Cleaning the Electrodes 83

Analyzing and Evaluating the Results of an Electrophoretic Method or Assay 85

Data Analysis: DNA 86 Data Analysis: RNA and CY5-labeled Nucleic Acids 89 The RNA Integrity Number (RIN) 91 Data Analysis: Protein 100 Smear Analysis 106 Changing the Data Analysis 110 Manual Integration 129 Reanalyzing a Chip Data File 138 Comparing Samples from Different Electrophoretic Chip Runs 139

Result Flagging 145 How to Use the Form Mode 148 Color Indication 150 How to Use the Editor Mode 153 Example: Result Flagging 155

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This chapter explains how electrophoretic measurements are made using the 2100 Bioanalyzer system, gives detailed descriptions of all steps necessary to run electrophoretic assays, and shows how to analyze and evaluate results using electropherograms and gel-like images.

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Principles of Nucleic Acid and Protein Analysis on a Chip

The electrophoretic methods/assays are based on traditional gel electrophoresis principles that have been transferred to a chip format. The chip format dramatically reduces separation time as well as sample and reagent consumption. The system provides automated sizing and quantification in a digital format. On-chip gel electrophoresis is performed for the analysis of DNA, RNA and proteins.

The chip accommodates wells for samples, gel and an external standard (ladder). Micro-channels are fabricated in glass to create interconnected networks among these wells. During chip preparation, the micro-channels are filled with a sieving polymer. Once the wells and channels are filled, the chip becomes an integrated electrical circuit. The 16-pin electrodes of the cartridge are arranged so that they fit into the wells of the chip. Each electrode is connected to an independent power supply that provides maximum control and flexibility. Charged biomolecules like DNA, RNA, or protein/LDS micelles are electrophoretically driven by a voltage gradientsimilar to slab gel electrophoresis. Because of a constant mass-to-charge ratio and the presence of a sieving polymer matrix, the molecules are separated by size. Smaller molecules are migrating faster than larger ones. The detection is based on laser-induced fluorescence detection (LIF). Dye molecules intercalate into

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DNA or RNA strands or protein/LDS micelles. For some applications proteins, RNA or DNA are covalently labeled with a fluorescent dye before separation. The detection is automatically performed by laser induced fluorescence (LIF) detection. Data is translated into gel-like images (bands) and electropherograms (peaks). With the help of a ladder that contains components of known sizes, a standard curve of migration time versus molecule size is plotted. From the migration times measured for each molecule in the sample, the size is calculated. Depending on the assay, one or two internal markers are run with each of the samples. The markers are internal standards used to align the ladder data with data from the sample. This is necessary to compensate for drift effects that may occur during the course of a chip run.

For all DNA methods/assays, quantitation is done with the help of the upper marker. The area under the upper marker peak is compared with the sample peak areas. Because the concentration of the upper marker is known, the concentration for each sample can be calculated. The same principle for quantification based on the upper marker is also used for the Protein 80 and 230 assays. The quantification of the High Sensitivity Protein 250 assay is based on the external ladder. The area under the ladder is compared with the sum of the sample peak areas. Besides this relative quantification, an absolute quantification is available for all protein methods/assays, using standard proteins.

For RNA methods/assays, quantification is also done based on the ladder as described above. In addition, for total RNA methods, the ribosomal ratio is determined, giving an indication on the integrity of the RNA sample. Additionally, the RNA integrity number (RIN) can be utilized to estimate the integrity of total RNA samples based on the entire electrophoretic trace of the RNA sample, including the presence or absence of degradation products.

The 2100 Expert Software plots fluorescence intensity versus size/migration time and produces an electropherogram for each sample:

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The data can also be displayed as a densitometry plot, creating a gel-like image:

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Preparing and Running an Electrophoretic Method or Assay

An electrophoretic chip run requires the following steps:

1 Switch on the 2100 Bioanalyzer instrument and start the 2100 Expert Software. Details are given in Starting the 2100 Expert Software on page 27

2 Select an electrophoretic method/assay.

See Selecting an Electrophoretic Method on page 58.

3 Prepare reagents, chip, and samples.

See Preparing Samples, Reagents, and Chips for Electrophoretic Methods/Assays on page 61 and the appropriate Kit Guide.

4 Load the chip into the instrument.

For details refer to Loading the Electrophoresis Chip into the 2100 Bioanalyzer Instrument on page 63.

5 Start the chip run.

See Running an Electrophoretic Method or Assay on page 68.

6 When the chip run has finished, you can:

Have a first look at the results (see Displaying the Measurement Results (Electrophoresis) on page 75).

Document the chip run (see Entering Chip and Sample Information on page 73).

Analyze and evaluate the results:

See Displaying the Measurement Results (Electrophoresis) on page 75.

See Result Flagging on page 145.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model for details (Access Control on page 39).

NOTE Please note that in terms of the 2100 Expert Software, a method resembles an extended assay, which also includes additional administrative data such as operator, instrument, reporting, and workflow settings.

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Selecting an Electrophoretic Method

To select a method/assay:

1 Switch to the Instrument context.

2 In the Tree View Panel, select the instrument you want to use.

In the upper left of the Instrument tab, an icon shows the status of the instrument. You should see one of the following icons (lid open/closed), indicating that the 2100 Bioanalyzer instrument is detected by the system:

3 If you do not see one of these icons, check that the 2100 Bioanalyzer instrument is switched on and properly connected:

Check the COM port setting.

Make sure the instrument is physically connected to the PC (over the serial interface or the USB-serial adapter).

Check the power connection.

Check the power switch.

If you need additional help, please refer to the Agilent 2100 Bioanalyzer System Maintenance and Troubleshooting Guide.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model ( Access Control on page 39) for details.

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4 Select a method/assay for the chip run.

a On the Instrument tab, click the Methods/Assays button.

OR

Click the Methods/Assays menu.

OR

Select File > Open File to Run. This opens a dialog box, allowing you to load either a method/assay (.xsy) or a chip data file (.xad).

Both will open the Methods/Assays menu, allowing you to select a method/assay from the submenus.

The type of method/assay you have to select depends on the required measurement and the kit you use to prepare your samples. Details on these methods/assays are described in the Kit Guide.

5 Select the desired method/assay, DNA 1000, for example.

The method/assay is loaded and its name appears on the Information Bar:

NOTE After a chip run, the results can be evaluated using parameters from a different electrophoretic chip data file (.xad) of the same method/assay type (DNA 1000 in this example). Refer to Importing Data Analysis Setpoint on page 170.

NOTE The chip data file (.xad) that will be generated as the result of the chip run will be stored the indicated Destination folder in the Secured Area.

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6 Specify an appropriate Destination and File Prefix for this file.

The total number of samples that can be measured varies with the type of method/assay selected.

NOTE With DNA and RNA Nano assays, 12 samples may be run; with RNA Pico assays, 11 samples may be run; and with Protein assays, the maximum number of samples is 10. When preparing the chip (see Preparing Samples, Reagents, and Chips for Electrophoretic Methods/Assays on page 61), keep in mind that you have to follow the sequence of the sample wells.

When preparing the chip, keep in mind that you have to follow the sequence of the sample wells. For example, if you want to measure only 3 samples, you have to fill the wells 1, 2 and 3 of your chip.

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Preparing Samples, Reagents, and Chips for Electrophoretic Methods/Assays Before you can load a chip, you have to prepare the samples and reagents. To find out how to prepare the samples and reagents, refer to the various Kit Guides available for each Kit. Please refer to these documents for further information and analytical specifications.

In general, preparing an electrophoretic method/assay involves the following steps: Check that you have everything that is listed in the appropriate Kit Guide.

Be aware that there can be small but important differences between the different methods/assays even for the same type of molecules (for example, between DNA 1000 and DNA 7500 methods/assays).

Make sure you are familiar with the essential measurement practices (see below next page).

Before running the first RNA method/assay: decontaminate the electrodes. Prepare all the reagent mixtures (for example, the gel-dye mix). Load the gel or the gel-dye mix using the priming station. Load the DNA/RNA marker solution and buffer. Load the destaining solution for protein methods/assays. Load the chip with ladder and samples.

Essential Measurement Practices (Electrophoretic Methods/Assays)

WARNING Toxic and hazardous reagents and samples They may harm your health.

Wear hand and eye protection and follow good laboratory practices.

Prepare and handle reagents and samples with care.

WARNING Handling dye/DMSO reagent Kit components contain DMSO. Because the dye binds to nucleic acids, it should be treated as a potential mutagen and used with appropriate care.

Wear hand and eye protection and follow good laboratory practices when preparing and handling reagents and samples.

Handle the DMSO stock solutions with particular caution as DMSO is known to facilitate the entry of organic molecules into tissues.

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General: Handle and store all reagents according to the instructions given in the Kit

Guides. Avoid sources of dust or other contaminants. Foreign matter in reagents

and samples or in the wells of the chip will interfere with method/assay results.

Always insert the pipette tip to the bottom of the well when dispensing the liquid. Placing the pipette at the edge of the well may lead to poor results.

Protect all reagents from light. Remove light covers only when pipetting. The dye contained in the reagents decomposes when exposed to light and this reduces signal intensity.

Use a new syringe and electrode cleaner with each new Kit. Do not touch the 2100 Bioanalyzer instrument during a chip run and never

place it on a vibrating surface. Allow all reagents and samples to equilibrate to room temperature for 30

minutes before use. Use loaded chips within 5 minutes. Reagents might evaporate, leading to

poor results. Keep all reagents and reagent mixes refrigerated at 4C when not in use.

RNA Methods/Assays: Always wear gloves when handling RNA, and use RNase-free tips, microfuge

tubes and water. Thaw RNA samples on ice. It is recommended to heat denature all RNA samples and RNA ladder before

use (70C, 2 minutes) and keep them on ice. To prevent contamination problems, it is strongly recommended to use a

dedicated electrode cartridge for RNA methods/assays. Perform the RNAse decontamination procedure for the electrodes on a daily basis before running any methods/assays.

Always vortex the dye concentrate for 10 seconds before preparing the gel-dye mix and spin down afterwards.

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Protein Methods/Assays:

Upon arrival make aliquots of the sample buffer and ladder with the typical amount required for the daily use and store them at -20C. Keep the vial in use at 4C to avoid freeze-thaw cycles.

Use 0.5 mL vials to denature samples. Using larger vials may lead to poor results, caused by evaporation.

Loading the Electrophoresis Chip into the 2100 Bioanalyzer Instrument

For electrophoretic measurements, the electrode cartridge is required.

The electrode cartridge contains 16 electrodes that fit into the wells of DNA, RNA, and protein chips. Each electrode in the cartridge has an individual power supply. All electrophoretic methods/assays (DNA, RNA, and protein) require an electrode cartridge. The electrode cartridges will either have an engraved 1 at the front, or will have no engraving at all. Cartridges with a different number are not electrode cartridges.

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Loading Procedures

If you want to change the electrode cartridge If you want to change the electrode cartridge, proceed as follows:

1 Open the lid and pull down the metal locking lever in the open position as shown in the following figure.

The cartridge is pushed out.

2 Gently pull the cartridge out of the lid.

NOTE Store the electrode cartridge in the provided box.

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3 Slide the new electrode cartridge into the lid as shown below.

4 Push the metal front of the cartridge to ensure a tight connection.

5 Push the metal locking lever into the flat (closed) position.

CAUTION Do not touch the electrodes while the cartridge is in the 2100 Bioanalyzer instrument. The electrodes and the high voltage power supplies can be damaged.

Be careful with the electrodes and the high voltage power supplies.

Do not touch the electrodes while the cartridge is in the 2100 Bioanalyzer Instrument.

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To load the prepared chip into the 2100 Bioanalyzer instrument: 1 Open the lid and remove any chip.

2 Place the prepared chip into the receptacle.

The chip fits only one way. Do not force it into place.

Figure 2 Electrode cartridge inserted in the instrument (graphic shows an example).

3 Carefully close the lid.

When the chip is detected, the image on the Instrument tab changes to a chip.

CAUTION Do not force the lid closed. This can damage the cartridge.

If the lid does not close without force, check that the cartridge and chip are inserted properly.

When the software recognizes an inserted chip, the chip is shown on the Instrument tab. If you have closed the lid, and the software has not recognized the chip, verify that the cartridge is properly installed into the instrument. Close the lid.

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If the chip is not detected, open and close the lid again.

NOTE The displayed image depends on the method/assay selected in the software, not the type of chip inserted. If you would like to run a DNA chip but a protein chip appears, you have selected the wrong method/assay.

NOTE If the AutoRun option is active, the chip run starts automatically once a chip has been inserted and the lid has been closed.

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Running an Electrophoretic Method or Assay

NOTE You can stop a chip run at any time, for example, if errors occurred or if you are not satisfied with the quality of the measurement results that you can observe during the chip run. See Stopping a Chip Run on page 72.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

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Starting and Stopping an Electrophoretic Chip Run

Starting a Chip Run When you have loaded the chip, you can start the chip run:

1 On the Instrument tab, click

2 To start the chip run, you need to confirm this action with your electronic signature, which will be recorded in the audit trail.

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The chip run starts. The Raw Signals sub-tab shows an electropherogram of the currently measured sample. The name of the sample is displayed above the graph. The graph is a live plot of the migration time against fluorescence units (raw data, including background fluorescence, for example).

The number of the sample that is currently being measured is indicated on the information bar:

The status bar at the bottom of the screen shows the measurement progress for the chip run and the COM port number used for data acquisition.

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3 During the chip run, you can do the following:

View the chip data file in the Data context e.g. clicking on the name of the Data File:

Switch to any other context. For example, you can evaluate any chip data file in the Data context, or compare samples in the Comparison context.

If necessary, abort the chip run by clicking on the Stop button. You need to confirm this action with your electronic signature.

All data that was collected up to the stop point will be saved.

4 After the chip run is completed, you can:

Switch to the Data context, where you can view, analyze, and evaluate the results of your chip run (see Displaying the Measurement Results (Electrophoresis) on page 75 and Analyzing and Evaluating the Results of an Electrophoretic Method or Assay on page 85).

Stay in the Instrument context and start a new method/assay, for example.

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Stopping a Chip Run You can stop a chip run at any time, for example,

if the quality of the measurement results does not meet your expectations,

if, for example, after three samples you already have the information you desired and you want to start another chip run.

To stop the method/assay:

1 Click the button.

OR

From the Instrument menu, select Stop.

b Click Yes to stop the chip run.

NOTE You cannot resume a stopped chip run.

NOTE If you stop a chip run, automatic export (see Exporting Chip Run Data Automatically on page 176) and automatic print (see How to Turn on and Configure Automatic Printing of Chip Run Reports on page 185) does not take place.

The following message appears:

NOTE Data acquisition of the current sample will be aborted.

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2 When the chip run is aborted, you can:

Switch to the Data context, where you can view, analyze, and evaluate the results (if any) of your chip run (see Displaying the Measurement Results (Electrophoresis) on page 75 and Analyzing and Evaluating the Results of an Electrophoretic Method or Assay on page 85).

Stay in the Instrument context, where you can start the next chip run.

Entering Chip and Sample Information

Before and after a chip run, you can document the run by entering information on chip and samples.

1 In the Data context, select the Chip Summary tab.

2 On the Sample Information sub-tab, you can enter or modify additional information such as sample names and comments. On the Study Information sub-tab, you can enter information such as the name of the current study, the laboratory location, and the experimenter, for example.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

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For details on all input fields, refer to Chip Summary tab.

3 From the File menu, select Save.

NOTE You may find some input fields already filled in, because chip, sample, and study information are taken over from the base method/assay or chip data file or sample information was already entered in the Instrument context.

HINT You can import chip, sample, and study information from .txt or .csv files. This is especially helpful and time-saving, if you already have documented a similar chip run in another chip data file. Refer to Importing Chip and Sample Information on page 171 for details.

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Displaying the Measurement Results (Electrophoresis)

You can view the measurement results of an electrophoretic chip run as electropherograms or gel-like images. You can display the electropherograms either one sample at a time, or all

samples at the same time to get an overview of the chip run, for example, to see the progress of a reaction. See How to Switch Between Single View and Grid View on page 75.

You can navigate through the samples. See How to Navigate Through the Samples on page 76.

You can change the display of electropherograms and gel-like images to make details better visible. See How to Change the Display of Electropherograms and Gel-like Images on page 77.

How to Switch Between Single View and Grid View To switch between single view and grid view: 1 From the Electropherogram menu, select View Single Sample or View All Samples.

OR

Click the View Single Sample or View All Samples button on the Electropherogram toolbar. OR Click the All Samples entry in the Tree View Panel to switch to the grid view, or any sample name to switch to the single view. OR Double-click any electropherogram in the grid view to switch to single view:

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

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How to Navigate Through the Samples At any timeeven during a chip runyou can scroll though all sampleseither in electropherogram or gel view.

Navigation Procedures

To navigate through samples using the Lower Panel: 1 If the lower panel is not visible, select View > Lower panel.

The lower panel appears in the lower left corner.

2 Electropherogram view: Click any lane of the small gel image.

OR

Gel view: Click any well on the chip icon.

To navigate through samples using the TreeView Panel: 1 If the tree view is not visible, select View > Tree View.

The tree view panel appears to the left of the tabs, and shows all chip data and method/assay files as nodes.

2 Click any sample name.

Electropherogram view: the electropherogram of the selected sample is shown in single view

Gel view: the lane of the gel-like image corresponding to the selected sample is highlighted.

To browse through samples: 1 From the Electropherogram or Gel menu, select Next Sample or Previous Sample.

OR

Click the Next Sample or Previous Sample button in the electropherogram or gel toolbar.

To switch between electropherogram and gel view 1 Click the Electropherogram or Gel tab to display the results of the selected

sample as an electropherogram or as a gel-like image.

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How to Change the Display of Electropherograms and Gel-like Images It is possible to change the display of electropherograms and gel-like images.

In electropherograms and gel-like images you can:

zoom (enlarge or reduce using the mouse) the graphs to display details, for example.

In electropherograms, you can additionally:

change the peak labeling, e.g. peak size

switch the x-axis description between size and migration time

switch enhanced RNA view on and off

show data points.

pan and scale the graph using the mouse.

change the background from a gray-to-white gradient to white.

add a grid to the electropherograms.

In gel-like images, you can additionally:

change the exposure

change the gel color.

change order of gel lanes in gel like images.

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How to change the display

How to zoom into an electropherogram 1 From the Electropherogram menu, select Graph Mode > Zoom (default setting).

2 Position the mouse pointer in the electropherogram.

3 Click and hold down the left mouse button.

The mouse pointer changes its shape to a magnifying glass:

4 Drag the mouse.

A rectangle shows the part of the an electropherogram to be enlarged.

5 Release the mouse button.

How to pan and scale an electropherogram 1 From the Electropherogram menu, select Graph Mode > Pan or Scale.

2 Position the mouse pointer in the electropherogram.

3 Click and hold down the left mouse button.

The mouse pointer changes its shape to a double-arrow or to a double crosshair.

4 Drag the mouse.

As you drag the mouse, the electropherogram curve moves in the drag direction (Pan mode), or the scales of the X and/or Y axes change (Scale mode).

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5 Release the mouse button.

a You can perform several zoom, pan and scale steps in a row.

b To undo the last zoom, pan, or scale step: Click the Undo Zoom button or double-click in the electropherogram.

c To undo all zoom, pan, and scale steps: Click the Undo All button.

d To remove the gray-to-white gradient from the background of an electropherogram: From the Electropherogram menu, select Show Gradient.

The color gradient disappears and a white background is displayed.

e To show/hide the grid lines on an electropherogram: From the Electropherogram menu, select Show Grid.

How to undo the last zoom, pan, or scale step

1 Click the Undo Zoom button or double-click in the electropherogram.

How to undo all zoom, pan, and scale steps

1 Click the Undo All button:

NOTE You can perform several zoom, pan and scale steps in a row.

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How to display data points in an electropherogram:

1 From the Electropherogram menu, select Show Data Points or click the button in the toolbar.

Data points used to generate the graph are now shown as bullets. Data points are 0.05 seconds apart.

How to change the peak labeling or remove the labeling:

1 Click on the dropdown menus in the toolbar.

How to switch the x-axis between size or migration time:

1 Click on the button in the toolbar.

How to switch the enhanced RNA view on and off:

1 Click on the button in the toolbar.

The greyscale of the gel image is recalculated while excluding the marker peak intensity. This will enhance band visibility for faint samples with low fluorescence intensity.

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How to remove the gray-to-white gradient from the background of an electropherogram 1 From the Electropherogram menu, select Show Gradient.

The color gradient disappears and a white background is displayed.

How to show/hide the grid lines on an electropherogram 1 From the Electropherogram menu, select Show Grid.

How to zoom into a gel-like image: 1 Position the mouse pointer in the gel.

2 Click and hold down the left mouse button.

The mouse pointer changes its shape to a magnifying glass and a horizontal line appears.

A second horizontal line appears showing the part of the gel to be enlarged.

3 Release the mouse button.

You can perform several zoom steps in a row. To undo the last zoom step:

1 Click the Undo Zoom button or

OR

double-click in the gel.

To undo all zoom steps:

1 Click the Undo All button .

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How to change the order of the gel lanes: 1 Position the mouse pointer on top of a gel lane.

The mouse pointer changes its shape to a hand.

2 Click and hold down the left mouse button.

3 Drag the mouse left or right.

The mouse pointer changes its shape to a pointing hand and a vertical line appears.

4 Release the mouse button.

The lane is inserted in the new position.

How to switch between displaying sizes or migration time [sec]: 1 Select Gel > Show Sizes or

OR

click on the Show Sizes button in the toolbar.

How to change the exposure of the gel: 1 Move the exposure slider right to the gel up and down to change the

"exposure" of the gel.

How to change the gel color: 1 Select Gel > Gel Color or

OR

click on the Gel Color button in the toolbar and select a color scheme from the list.

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Cleaning the Electrodes When the method/assay is complete, remove the used chip from the instrument and dispose of it according to the guidelines established by your laboratory safety officer. Remove the chip quickly to prevent a buildup of residues from the solutions on the electrodes.

Then perform the cleaning procedure to ensure that the electrodes are clean (i.e., no residues left from the previous method/assay). The cleaning procedures are described in detail in the appropriate Kit Guide and in the Agilent 2100 Bioanalyzer System Maintenance and Troubleshooting Guide.

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Good Practices

1 Empty and refill the electrode cleaner at regular intervals (e.g., every five methods/assays).

The electrode cleaner can be used for 25 methods/assays.

CAUTION Electronic Discharge Electrostatic discharge could damage the high-voltage power supplies.

Always use the electrode cleaner for cleaning the electrodes.

Never use a cloth to clean the electrodes.

CAUTION Damage of power supply by wet electrodes Wet electrodes can cause severe damage to the on-board high voltage power supplies.

Always make sure the electrodes are dry before inserting them into the 2100 Bioanalyzer instrument again.

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Analyzing and Evaluating the Results of an Electrophoretic Method or Assay

The purpose of electrophoretic methods/assays is to separate sample components and determine their size, concentration, purity, or molarity. Results for a particular sample are calculated after all data for that sample has been read.

The steps in data analysis differ depending on the type of method/assay in use:

Data Analysis: DNA on page 86

Data Analysis: RNA and CY5-labeled Nucleic Acids on page 89

The RNA Integrity Number (RIN) on page 91

The data analysis process for protein methods/assays consists of the following steps: on page 100

Smear Analysis on page 106

Further steps in analysis are:

Changing the Data Analysis on page 110

Manual Integration on page 129

Reanalyzing a Chip Data File on page 138

Comparing Samples from Different Electrophoretic Chip Runs on page 139

How to Use the Form Mode on page 148

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

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Data Analysis: DNA 1 Raw data is read and stored by the system for all individual samples.

2 The data is filtered and the resulting electropherograms are plotted. You can change the settings of the data analysis after the run and reanalyze your data.

3 Peaks are identified and tabulated by peak ID. You can change the settings of the peak find algorithm and reanalyze the data after the run has finished. (Note that peak find settings can be changed for all or only certain samples.)

4 A sizing ladder (see the following example electropherogram), which is a mixture of DNA fragments of known sizes, is run first from the ladder well. The concentrations (ng/L) and sizes (bp) of the individual fragments are preset in the method/assay and cannot be changed.

5 A standard curve of migration time versus DNA fragment size is plotted from the DNA sizing ladder by interpolation between the individual data

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points. The standard curve derived from the data of the ladder well should resemble the one shown below.

6 Two DNA fragments, the lower and upper marker, are run with each of the samples, bracketing the DNA sizing range. The markers are internal standards used to align the ladder data with data from the sample wells. The figure below shows an example of assigned marker peaks in a sample well.

NOTE The software performs alignment by default. Turning automatic data analysis off suspends data analysis until you turn it on again.

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7 The standard curve, in conjunction with the internal markers, is used to calculate DNA fragment sizes for each sample from the migration times measured.

8 To calculate the concentration of the individual DNA fragments in all samples, the upper marker, in conjunction with a method/assay-specific concentration against base-pair size calibration curve, is applied to the individual sample peaks in all sample wells.

9 If the check box Rest. Digest on the Chip Summary Tab is enabled, the 2100 Expert Software flags peaks that may have co-migrated:

Since it is assumed that the molarity of all the fragments in a restriction digest should be the same, any peaks or clusters having a molarity that is significantly larger than the rest are flagged as potentially co-migrating peaks, allowing you to examine them in more detail.

NOTE The software allows you to redefine the peaks chosen as upper and lower markers. A change in marker selection will cause quantitative changes in the calibration procedure, and therefore in the entire data evaluation.

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Data Analysis: RNA and CY5-labeled Nucleic Acids 1 Raw data is read and stored by the system for all individual samples.

2 The data is filtered and the resulting electropherograms are plotted. You can change the settings of the data analysis after the run and reanalyze your data.

3 Peaks are identified and tabulated by peak ID. Fragments, such as ribosomal RNA, are also tabulated. You can change the settings of the peak find algorithm for any or all samples and reanalyze the data.

4 An RNA ladder (containing a mixture of RNA of known concentration) is run first (see the electropherogram below). The amount and individual sizes are preset in the assay and cannot be changed.

Electropherogram of RNA Nano 6000 Ladder

5 The lower marker is run as internal standard with each of the samples and is used to align the ladder with the samples.

NOTE Peak ratios for the RNA ladder may vary from one batch of RNA 6000 ladder to the next. Method/assay performance will not be affected by this variation.

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6 For the Eukaryote or Prokaryote Total RNA, the ribosomal RNA fragments (either 18S and 28S for eukaryotic RNA or 16S and 23S for prokaryotic RNA) are detected and displayed in the Fragment Table sub-tab. After detection, the ratio of the fragment areas is calculated and displayed in the Results sub-tab.

7 For the mRNA method/assay, the ribosomal RNA, if present, is detected and displayed in the Fragment Table sub-tab. The ribosomal RNA contamination is calculated and displayed in the Results sub-tab.

8 The RNA integrity number is automatically determined and displayed in the Results sub-tab and below the gel-like image.

9 To calculate the concentration of the RNA, the area under the entire RNA electropherogram is determined. The ladder, which provides the concentration/area ratio, is applied to transform the area values into concentration values.

10 For the small RNA small and miRNA regions are determined and average size, size distribution, concentration and % of total are displayed in the Region Table sub-tab.

11 For the Small RNA method/assay, the small RNA and miRNA concentration and the miRNA/small RNA ratio [%] is calculated and displayed in the Results sub-tab.

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Alignment of RNA Samples The marker solution that is part of each RNA kit, contains a 50 bp DNA fragment. This fragment is used as lower marker to align all samples. By default the RNA alignment and the subtraction of the lower marker are enabled for RNA Nano methods/assays. The marker is displayed as the first peak in the electropherogram.

The RNA Integrity Number (RIN) The RNA integrity number (RIN) is a tool designed to help scientists estimate the integrity of total RNA samples. The RIN extension automatically assigns an integrity number to a eukaryote total RNA sample analyzed on the 2100 Bioanalyzer system. Using this tool, sample integrity is no longer determined by the ratio of the ribosomal bands alone, but by the entire electrophoretic trace of the RNA sample, including the presence or absence of degradation products. In this way, interpretation of an electropherogram is facilitated, comparison of samples is enabled and repeatability of experiments is ensured.

Scope What the RIN can do: Obtain an assessment of the integrity of RNA. Directly compare RNA samples (e.g. before and after shipment, compare

integrity of same tissue across different labs, etc.). Ensure repeatability of experiments (e.g. if RIN shows a given value and is

suitable for microarray experiments, then the RIN of the same value can always be used for microarray experiments given that the same organism/tissue/extraction method/assay was used).

What it cannot do: Tell a scientist ahead of time whether an experiment will work or not if no

prior verification was done (e.g. RIN of 5 might not work for microarray experiments, but might work well for an appropriate RT-PCR experiment. Also, an RIN that might be good for a 3' amplification might not work for a 5' amplification).

The computation of the RIN is part of data analysis for total RNA samples. The computed RNA integrity number is shown on the Results sub-tab of the Gel or Electropherogram tab of the Data context. It is also included in XML export files and in printed reports.

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Although the lower quantitative limit of the RNA 6000 Nano method/assay is specified as 25 ng/L it is recommended to use at least 50 ng/L for a meaningful RNA integrity number. When using lower concentrations, higher sample to sample variances of the RIN may be observed.

NOTE Until now, the computation of the RIN has only been validated for eukaryote total RNA Nano samples. The 2100 Expert Software also calculates the RIN for prokaryote and plant total RNA samples and for the RNA 6000 Pico method/assay. Be aware that for these samples, the RIN has not been validated in extensive downstream experiments.

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Examples for RNA Integrity Numbers A database of about 1300 mammalian total RNA samples was created using the RNA 6000 Nano method/assay. The samples came from different species (mainly human, rat and mouse), tissues, preparation methods/assays, concentrations and degradation states. All samples were classified according to their degradation state. Numbers from 1 to 10 were used as labels. 10 stands for a perfect RNA sample without any degradation products, whereas 1 marks a completely degraded sample. The labels in-between are used to indicate progressing degradation states of the RNA sample. The following figure shows typical representatives for each of the 10 RNA integrity classes.

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Computation of the RNA Integrity Number For the computation or the RNA integrity number, the electropherogram is partitioned into regions as shown in the figure below. The lower marker and the 18S and 28S fragments divide the electropherogram into nine regions:

Signal Anomalies In addition to the computation of the RIN, the data analysis detects various unexpected signals, disturbing the computation of the RIN. Such disturbances are called anomalies. Region anomaly detectors recognize unexpected signals in each region. If detected, the anomaly is displayed in the Error sub-tab of the Electropherogram and Gel tab.

Anomaly Description Critical? Unexpected baseline signal Yes Unexpected signal in pre-region No Unexpected signal in 5S-region Yes Unexpected signal in fast-region Yes Unexpected signal in inter-region Yes Unexpected signal in precursor-region No Unexpected signal in post-region No Unexpected ribosomal ratio Yes Unexpected sample type Yes Unexpected lower marker (compared to previous well) No

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Two categories of anomalies were introduced, critical and non-critical. Anomalies in regions interfering with the customer sample RNA are considered critical. The corresponding gel lane is flagged red.

The baseline anomaly, for example, is detected for signals with fluctuating or steep baseline. The ribosomal ratio anomaly detects unexpected ratios of the 28S fragment area and the 18S fragment area. The unexpected sample type anomaly is detected for samples which do not fit the standard total RNA profile.

If a non-critical anomaly is detected, the RIN can still be computed accurately. Therefore non-critical anomalies are not flagged. Non-critical region anomalies are pre-region anomaly, precursor-region anomaly and post-region anomaly. The electropherogram below gives an example for a non-critical anomaly in the post-region.

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To take full advantage of the RIN feature, a 2 step use-model is suggested: 1 Determine the threshold value for the RIN that results in meaningful

downstream experiments:

Correlate RIN with downstream experiment and determine threshold RIN for meaningful results (iterative process)

2 Run standard experiment and use RIN to determine if sample integrity is sufficient:

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Troubleshooting the RIN To obtain meaningful and reproducible results, the lower marker must be identified correctly. On details on how to adjust the lower marker, please refer to Changing the Data Analysis on page 110.

In rare cases, the RIN value for a sample might not be shown in the Results tab but marked as not available (N/A). Such results are typically related to unexpected signals and thus critical anomalies, see Signal Anomalies on page 95.

The root cause should be investigated by checking:

Is the correct assay selected for this experimental run?

Is the marker correctly assigned by the software?

Are the ribosomal fragments correctly assigned by the software?

Are the samples correctly treated and heat-denatured?

Details about the critical signal anomaly are shown in the Errors tab, see Figure on page 99.

If critical anomalies have been detected during the analysis, in many cases RIN values can still be displayed by increasing the thresholds. The user can modify predefined thresholds for anomaly detection. The higher the threshold the less anomalies are detected. Valid threshold values range from 0 to 1.

How to create your own assay file with adapted anomaly thresholds by default is described in How to modify a custom assay method on page 165. A customized assay will not change the RIN value, which is calculated by an independent algorithm.

RNA Integrity Number Setpoints Various setpoints are available to customize the display of the RIN (RNA Integrity Number). With these setpoints, you can modify the predefined thresholds for anomaly detection. You can find them in the advanced user mode of the setpoint explorer.

NOTE RIN N/A is a warning that the RIN may not be reliable for a particular sample (such as due to unusual noise/signals, ribosomal ratio, and other factors). Clearing the critical error message may yield a RIN, but Agilent does not guarantee the accuracy of this value. It is recommended to also perform a visual inspection of the data.

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To adjust the setpoints for a single sample, switch to the Local tab of the setpoint explorer and open the RNA Integrity Number group.

To adjust the setpoints for the whole chip, switch to the Global tab of the setpoint explorer and open the RNA Integrity Number group in the Sample Setpoints group. For the chip, you can additionally switch between integer and decimal representation of the RIN.

For more information on how to use the setpoint explorer, see About the Setpoint Explorer ( Changing the Data Analysis on page 110).

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Data Analysis: Protein

The data analysis process for protein methods/assays consists of the following steps: 1 Raw data is read and stored by the system for all samples. 2 The data is filtered and the resulting electropherograms are plotted. You can

change the settings of the data analysis after the run and reanalyze your data. 3 Peaks are identified and tabulated by peak ID. You can change the settings of

the peak find algorithm and reanalyze the data after the run has finished. (Note that peak find settings can be changed for all or only certain samples.)

4 A sizing ladder (see the example electropherogram below), which is a mixture of proteins of different known sizes, is run first from the ladder well. The sizes of the individual proteins are preset as kDa in the method and cannot be changed. Please note that the individual protein concentrations may vary slightly from ladder lot to ladder lot.

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5 A standard curve of migration time versus size is plotted from the sizing ladder by interpolation between the individual protein size/migration points. The standard curve derived from the data of the ladder well should resemble the one shown below.

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6 Depending on the protein method/assay, one or two internal marker proteins are run with each of the samples. The lower marker and/or upper marker proteins are used to align the ladder data with data from the samples. The figure below shows an example of assigned marker peaks in a sample well.

7 The standard curve, in conjunction with the markers, is used to calculate protein sizes for each sample from the migration times measured.

NOTE The software performs alignment by default. Turning automatic data analysis off suspends analysis until you turn it on again.

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8 To calculate the concentration of the individual proteins in all samples of the Protein 80 or the Protein 230 assay, the upper marker with known concentration is used. The concentration is calculated based on the time corrected area underneath each sample peak and the upper marker in the same sample. The protein concentration of the High Sensitivity Protein 250 assay is determined similar to the RNA methods/assays. The relative protein concentration is determined based on the area measuered underneath the individual sample peak and the area measured for the ladder on the same chip. For all protein methods/assays it is possible to perform absolute quantification (See Absolute Protein Quantitation on page 103).

9 In addition to the concentration of the individual proteins, which is listed in the Peak Table, the total relative protein concentration (ng/L) is determined as displayed in the Results sub-tab.

10 The purity (in % total) is calulated for the individual protein of each sample based on the ration to the total protein concentration.

Absolute Protein Quantitation Absolute quantification is calculated based on the relative concentration of a sample and user-defined standards and the known concentration of this standards.

For protein samples you can enable the use of calibration for each sample and enter the concentration of the standard protein. This allows you to generate a calibration curve, which is used to analyze and quantitate this protein within different samples on the same chip. The generated standard curve can also be used to quantitate any other sample protein relative to the standard protein.

NOTE The software allows you to define the markers yourself. A change in the selection of the markers will lead to quantitative changes in the calibration procedure, and therefore in the entire data evaluation.

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Using Calibration in Protein Assays The calibration feature for protein assays allows quantification based on external standard calibration.

On the Chip Summary tab, use the sample table on the Sample Information sub-tab to define the samples that you want to use as calibration standards by clicking the checkmark box Use for Calibration and enter a concentration.

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The calibration standard should be run at least in three different concentrations to generate a calibration curve. The software will automatically produce this calibration curve to determine the actual concentration of the corresponding protein in all other samples within the same chip. In the peak tables of the samples, a remark is added to the observation column to identify the calibration protein and the calibrated proteins:

The calibration curve can be displayed by switching to the Calibration Curve sub-tab on the Chip Summary tab.

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Smear Analysis The 2100 Expert Software allows to perform a smear analysis for all electrophoresis methods/assays.

When the smear analysis is enabled (in the advanced setpoints), the software allows you to define regions of interest. These regions are used to define the area of broad peaks and determine their part of the total area. Smear analysis provide a means to analyze broad signals that can be hardly evaluated with the normal peak assignment.

You therefore can define regions that contain the peaks of interest. The regions are defined by size, e.g. base pairs or kDa. For these regions you can determine the region area in relation to the total area.

Enabling and Performing Smear Analysis

To enable smear analysis: 1 Go to the Electropherogram tab in the Data context

2 Go to the Setpoint Explorer and select the Local or Global tab, depending on which samples should be analyzed.

3 Select the Advanced mode from the dropdown menu.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

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4 Under Smear Analysis, select the check box Perform Smear Analysis.

The Region Table sub-tab is added to the Electropherogram tab.

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Performing Smear Analysis After enabling the smear analysis in the setpoint explorer, you are able to insert regions of interest in the electropherogram.

To do so:

1 Select the Region Table sub-tab in the Electropherogram tab.

2 Right-click the electropherogram and select Add region.

A region will be inserted into the electropherogram. The Region Table shows the values for the inserted region.

3 Repeat the previous step until the number of required regions is inserted.

4 Adjust the regions by directly moving the dashed lines in the electropherogram.

5 To remove a region, right-click the dashed line in the electropherogram and select Remove Region from the context menu.

NOTE The smear analysis table can be directly edited by selecting the region table under Smear Analysis in the setpoint explorer. It can also be opened when right clicking on the table in the Region Table sub-tab or in the electropherogram. In the region table it is possible to define the regions by entering upper and lower limits.

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In the smear region table, you can edit the Region Start Size and Region End Size, for example:

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Changing the Data Analysis

Different sets of parameters (data analysis setpoints) can be changed in the software in order to modify the data evaluation for sample analysis:

Filtering parameters

Peak find parameters for all samples/peak height for individual samples

Enabling smear analysis

Align to upper and/or lower marker

Adding/deleting ribosomal fragments (for RNA assays/methods only)

Manual integration (for protein and DNA assays/methods only)

Absolute quantification (for protein assays/methods only)

These settings can be made before a new run is started or when reanalyzing a previously saved data file.

About the Setpoint Explorer The tool allowing you to modify the data analysis setpoints is the Setpoint Explorer. The Setpoint Explorer is accessible from:

Assay Properties Tab

Electropherogram Tab (Single/Grid View)

Gel Tab

On the Assay Properties tab, the Setpoint Explorer is always visible and lets you modify setpoints globally (for all samples):

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model ( Access Control on page 39) for details.

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If the Setpoint Explorer is not visable on the Electropherogram/Gel tab, click the vertical bar on the right edge of the application window:

The Setpoint Explorer appears.

For electrophoretic assays/methods, you can modify the setpoints

globally, that is, for all samples (Global tab)

locally, for the current sample (Local tab)

Setpoints can be modified in a normal mode (normal user) and advanced mode (experienced user). Click the + nodes to expand, and the nodes to collapse branches. Setpoints that you can change are white. To edit a setpoint, double-click the value, enter the new value, and press enter. The changes are applied automatically.

NOTE On the Assay Properties tab the Local tab can be enabled by clicking on the individual sample in the Tree View panel.

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When you try to change any global setpoints where local settings have been applied, the software prompts you as to whether you want to overwrite the local (custom) settings.

If you decide to overwrite the custom sample settings, all local settings you made will be discarded. If you decide not to overwrite the custom sample settings, the global settings will not be applied where local settings have been changed.

Changing setpoints requires that you confirm the action with your electronic signature.

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Color Coding of Setpoint Values Specific color coding indicates differences between local setpoint values and global setpoint values. The following differences are indicated:

One local setpoint value differs from the global setpoint value as defined for this assay. On the Local tab, a yellow background indicates that a local setpoint value has been modified and differs from the current global setpoint value.

A tooltip displays the global value defined for this assay.

Right-click the local setpoint value to access the following functions:

Copy to Clipboard: The currently loaded local setpoint values are copied to the clipboard as flat table.

Restore Default: The local setpoint value is reset to the setpoint value as currently defined on the Global tab.

Set as Default: The local setpoint value is set as new global setpoint value, but not automatically applied to all other samples.

On the Global tab, the corresponding global setpoint value for which a local setpoint value has been modified is displayed in blue font color.

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A tooltip displays the corresponding local values of all samples in sequential order.

Local setpoint values differ from the global values as preset by Agilent but match the global setpoints as currently defined for this assay.

On the Global tab, a yellow background indicates that the global setpoint value differs from the value as preset by Agilent but all local setpoints have the same value as the current global value.

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A tooltip displays the global value as preset by Agilent.

Local setpoint values differ from the global values as preset by Agilent as well as from the global setpoints as currently defined for this assay.

On the Global tab, a blue font color on yellow background indicates that the global setpoint value differs from the global setpoint values as preset by Agilent and at least one local setpoint value.

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Right-click the global setpoint value to access the following functions:

Copy to Clipboard: The currently loaded global setpoint values are copied to the clipboard as flat table.

Apply to All: The current global setpoint will be applied to all samples and override their current value.

Restore Default: The current global setpoint will be reset to default as preset by Agilent, but will not override current local setpoint values.

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Filtering Setpoints The first step the software takes in analyzing the raw data is to apply data filtering. The following filtering setpoints can be changed in the advanced mode under Filter Settings:

Filter Width [s]: Defines the data window, given in seconds, used for averaging. The broader the filterwidth, the more raw data points are used for averaging. As a result, the noiselevel will decrease, but peaks will become lower and broader. Overall, changing the Filter Width has more effect on the result of the filtering procedure applied then does changing the Polynomial Order.

Polynomial Order: This setting isused to define the power series applied to fit the raw data. The higher the number, the more the fit function will follow the noisy raw data curve. As a result, the noise level of the filtered curve will increase.

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Integrator Setpoints After data filtering, the peak find algorithm locates the peaks and calculates the local peak baselines. The algorithm begins by finding all the peaks above the noise threshold in order to determine the baseline, after which any peaks below the noise threshold are rejected. A local baseline is calculated for each peak to allow for baseline drift.

Setpoints can be modified in a "normal" mode (normal user) and "advanced" mode (experienced user).

The integrator setpoints that can be changed are:

Slope Threshold: The Slope Threshold setpoint determines the difference in the slope that must occur in order for a peak to begin. The inverse of this value is used to determine the peak end.

Area Threshold: The Area Threshold determines the minimum amount of peak area that must be detected before a peak is recognized.

Height Threshold [FU]: The Height Threshold setpoint determines whether a peak is kept. It represents the minimal peak height. For each peak, the difference between the start point value and the center point value (local baseline) must be greater than the Height Threshold value.

Width Threshold [s] The Width Threshold determines whether a peak is kept. It represents the minimal peak width. For each peak, the difference between the start and end point (local peak baseline) must be greater than the Width Threshold value.

Peak Filter Width [s]: The Peak Filter Width setpoint determines the minimum amount of time that must elapse before a peak is recognized.

Baseline Plateau [s]: The Baseline Plateau setpoint is a parameter that assists in finding peaks. The signal is recognized to be at baseline whenever the slope of the data is less than the Slope Threshold setpoint (either positive or negative) for longer than the time set for the Baseline Plateau. This setting rejects brief, low slope areas such as between non-baseline-resolved peaks.

Peak Filter Polynom The Peak Filter Polynom setpoint defines the order of the polynom which is used to filter the data to find peaks. The larger this whole number value is the more sensitive is the filter and the more peaks get detected. The peak filter polynom is directly linked to the peak filter width. The entered value multiplied by 0.05 (data rate) must be less or equal the peak filter width.

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List of setpoints that can be changed General Assay Setpoints

Electrophoresis Properties

Gel Color: Select gel color from dropdown menu

Ladder Concentration

Ladder and/or Sample Setpoints

Baseline Calculation

Zero Baseline (on/off): Zero signal to baseline

Flat Baseline (on/off): If selected, baseline level will be equal to start baseline level.

Filter Settings

Filter Width [s]: Defines the data window used for averaging.

Polynomial Order: Defines the power series applied to fit the raw data.

Baseline Correction

Perform Baseline Correction (on/off)

Integrator

Slope Threshold

Area Threshold

Height Threshold [FU]

Width Threshold [s]

Baseline Plateau [s]

Peak Filter Width [s]

Peak Filter Polynom

Calibration

Calibrate All ( on/off)

Smear Analysis

Perform Smear Analysis (on/off)

Regions Table

RNA Fragment

Fragment Detection Table: Structure to provide molecular fragment type.

Use Dynamic Time Window (on/off): Use dynamic window for detection of ribosoms.

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RNA Integrity Number

Pre Region Anomaly Threshold: Sensitivity for detection of signal anomalies before lower marker.

5S Region Anomaly Threshold: Sensitivity for detection of signal anomalies between lower marker and the fast region.

Fast Region Anomaly Threshold: Sensitivity for detection of signal anomalies between 5S region and 18S.

Inter Region Anomaly Threshold: Sensitivity for detection of signal anomalies between 18S and 28S fragments.

Precursor Region Anomaly Threshold: Sensitivity for detection of signal anomalies between 28S fragment and post region.

Post Region Anomaly Threshold: Sensitivity for detection of signal anomalies after precursor region.

Baseline Anomaly Threshold: Sensitivity for detection baseline signal anomalies.

Ribosomal Anomaly Threshold: Sensitivity for detection of unexpected ribosomal RNA ratios.

Unknown Sample Type Threshold: Sensitivity for detection of unknown sample types.

Marker Anomaly Threshold: Sensitivity for detection of marker anomalies.

Single Decimal Represe. (on/off): Show the RIN as integer or with one decimal place.

Threshold Prerequisite: Threshold for minimum total RNA concentration to show RIN.

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Manually Moving Fragment Start and End Points (RNA and Cy5-Labeled Nucleic Acids) It is possible to alter the integration start and end points manually for individual fragments in an RNA or Cy5-labeled nucleic acids assay/method. The integration borders of detected RNA-fragments are displayed in the Fragment Table sub-tab. Zooming in on the base of a particular fragment allows you to see the start and end points. Placing the cursor over one of these points changes the cursor to a pointing hand, allowing you to click and drag the point along the line of the fragment until it is positioned as desired.

Move any other start or end points as desired. This is only required if the automated integration needs some adjustment.

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HINT The fragment table can be directly edited in the setpoint explorer in the advanced mode, RNA Fragment > Fragment Detection Table:

NOTE Changing the start or end points of the fragment will change the calculated rRNA ratio and rRNA concentration. The calculated RNA Integrity Number (RIN) is not affected.

It might be convenient to pause the automatic analysis (Electropherogram > Pause Automatic Analysis) until all changes are done.

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Setting the Baseline for Calculation of RNA Concentration At low signal-to-noise ratios, the baseline that defines the area used for calculating the concentration of RNA assays/methods is highly dependent on the settings for the Start and End Time. You can adjust the Start and End Times manually (thereby adjusting the baseline) to ensure a good result even at very low signal-to-noise ratios. Choose a single sample in the Electropherogram Tab, Results Sub-tab. Two vertical green long-dashed lines indicating the setpoints for the Start and End Times (with the baseline drawn between them) are displayed in the window.

Move the cursor over the long-dashed line on the left (Start Time setting) and drag the line to the desired position. Do the same with the long-dashed line on the right (End Time setting) until you have a flat baseline.

NOTE Changing the start or end points of the fragment will change the calculated rRNA concentration and rRNA ratio. The calculated RNA Integrity Number (RIN) is not affected.

It might be convenient to pause the automatic analysis (Electropherogram > Pause Automatic Analysis) until all changes are done.

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Assigning Upper and Lower Marker Peaks (all electrophoretic assays) For each sample, the upper and/or lower marker peaks are assigned first and then the data is aligned so that the sample markers match the ladder markers in time, allowing the size and concentration of the sample peaks to be determined.

The first peak is assigned to be the lower marker and is then offset to match the lower marker in the ladder. The upper marker, if present, is then assigned to the last peak in the sample or to the peak nearest the ladders upper marker.

If you get unexpected peaks in the ladder analysis, unexpected sizing results or find that the markers have been set incorrectly, you may exclude peaks manually from the ladder or set a peak to be used as a marker. Right-clicking in the peak table causes a context menu to appear, allowing you to do so:

In case the 2100 Expert Software did not detect the markers in the samples correctly, you are able to manually assign them in the same way.

NOTE Excluding a peak or manually setting a peak to be an upper or lower marker may cause errors during analysis.

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Aligning or Unaligning the Marker Peaks The upper and lower are aligned to the ladder markers by resampling the sample data in a linear stretch or compression using a point-to-point fit.

Data before alignment:

Markers aligned to the ladder:

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If the sample marker peaks are either more than twice as far apart or less than half as far apart as the ladder markers, they are assumed to be the wrong peaks, and analysis of the sample stops, producing the error Marker peaks not detected.

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NOTE With DNA and protein assays/methods, the height of marker peaks is assay/method dependent. Ladder peaks are analyzed to calculate a marker peak threshold that is used to locate the marker peaks in the sample wells. If the marker peaks found using this calculated assay/method fail to align with those of a sample, the 2100 Expert Software will use the minimum peak height threshold setting instead (if this value is lower than the value for the marker peak). For example, the calculated threshold might be too high to find the sample's markers if they happen to be very small for some reason. Either no markers will be found or the wrong peaks will be assumed to be markers and these may not align with the ladder markers. Consequently, the software attempts to use the minimum peak height threshold that, if it is set low enough, will catch the real markers, allowing the sample to align.

NOTE After alignment, peaks are shown with relative migration times that are different from the real migration times with data unaligned.

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Manual Integration For DNA and Protein assays/methods, the 2100 Expert Software allows to manually integrate peaks. This is only required if the integration results do not reflect the expectations. Manual integration allows you to move, add or delete peak baselines.

Examples for Manual Integration

Example: Adjusting peak baselines To manually change peak baselines:

1 Switch to the Electropherogram tab in the Data context and zoom into the electropherogram to enlarge the peak of interest.

2 Select Electropherogram > Manual Integration to switch on the manual integration.

OR

As an alternative you can click the Manual Integration button in the toolbar.

The baseline points become visible as blue or green dots. Highlighted baseline points are labelled green and can be moved either along the vertical line (press CTRL key and left mouse button) or along the signal trace (left mouse button). The blue baseline points are fixed and cannot be moved. To highlight a baseline point, click it.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

HINT To move a peak baseline, point along the vertical line, press the CTRL key and left mouse button. To move a peak baseline, point along the signal, press the left mouse button only.

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3 If you want to change several baseline points, deactivate the automatic analysis by clicking the Pause Analysis button in the toolbar.

This way, the software will not recalculate the data analysis with every change.

Once you have changed all baseline points, click the Pause Analysis button

again to activate automatic analysis.

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4 Adjust the baseline points as appropriate.

To move a peak baseline point along the signal or the vertical dotted line, press the left mouse button.

If the new peak baseline point is not on the signal trace, create a new dotted vertical line by press the CTRL key and the left mouse button and move the point along this line.

5 Click the Automatic Analysis button to enable the integration again.

The integration results in the result and peak tables will change according to the changes done.

HINT To move a peak baseline point along the vertical line, press the CTRL key and the left mouse button. To move a peak baseline point along the signal, press the left mouse button only.

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Example: Removing peaks To remove peaks in the Manual Integration Mode:

1 Switch to the Electropherogram tab in the Data context and zoom into the electropherogram to enlarge the peak of interest.

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2 Select Electropherogram > Manual Integration to switch off the automatic integration. As an alternative you might click the Manual Integration button

in the toolbar.

The baseline points become visible as blue or green dots.

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3 Right-click a baseline-point and select Remove Peak from the context menu.

The two baseline points and the connecting line will disappear and the integration results shown in the result and peak tables will be updated:

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Example: Inserting peak baselines To insert peaks in the Manual Integration Mode:

1 Highlight the Electropherogram tab in the Data context and zoom into the electropherogram to enlarge the peak of interest.

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2 Right-click the electropherogram and select Add Peak from the context menu.

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3 Two baseline points and the connecting line will appear and the integration results shown in the result and peak tables will be updated.

4 Adjust the baseline points as described in Example: Adjusting peak baselines on page 129.

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Reanalyzing a Chip Data File

To do this: 1 To open a chip data file (.xad), click File > Open.

2 Choose the filename from the list of data files.

3 Click OK.

The items that can be changed for reanalysis are: All assay setpoints see Changing the Data Analysis on page 110,

sample and study information,

marker peak assignment,

manual integration see Manual Integration on page 129,

result flagging see Result Flagging on page 145,

quantification.

If you save the data file after making changes, it will keep a record of the changes such as gel color, sample names, and peak find settings that were in effect at the time the file is resaved. If you do not want to change the original file, choose File > Save As and give the file a new name or save it to a different location.

NOTE Occasionally you may wish to open and view or reanalyze a chip data file that was run and saved previously. The raw data values are saved in the data file, along with the analysis settings that were chosen for the run, so that the data can be reanalyzed with different settings.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model ( Access Control on page 39) for details.

HINT When applying modified data analysis setpoints, performing manual integration or changing the RNA fragment analysis, the software will (by default) immediately recalculate the raw data, which takes some time. Select Dont Analyze from the Gel Menu or Electropherogram Menu to temporarily switch off automatic data analysis while you modify setpoints.

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Comparing Samples from Different Electrophoretic Chip Runs The 2100 Expert Software allows you to compare the measurement results of samples from different electrophoretic chip runs. Samples to be compared must be from chip runs of the same method/assay type.

In the Comparison context, you can create comparison files, include samples from different chip runs, and compare the samples by overlaying electropherograms, for example.

To compare samples from different electrophoretic chip runs:

1 Switch to the Comparison context.

2 From the File menu select Open, and open all chip data files (.xad) that contain the samples you want to compare.

The .xad files appear in the Select Data Files list of the Tree View Panel.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See for detail User Role Model (Access Control on page 39)

NOTE The Select Data Files list also contains all electrophoretic .xad files that are currently open in the Data context.

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3 Select a .xad file from the Select Data Files list to display a list of its samples.

4 Right-click a sample name and select Add Sample to New Comparison File.

You need to confirm this action with your electronic signature.

A new comparison file appears in the upper part of the tree view containing the sample. The sample is selected and its electropherogram is shown.

HINT Double-clicking a sample name in the lower part of the tree view or dragging a sample name into the tree view adds the sample to the comparison file that is currently selected in the upper part of the tree view. Or, if no comparison file is selected, creates a new comparison file and adds the sample to it.

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Note that the Electropherogram Tab (Single/Grid View) has the same functionality as in the Data context.

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5 You can now add further samples from any of the open .xad files to the comparison file.

You are notified if you try to add a sample of a .xad file that has the wrong method/assay type.

6 To remove samples from a comparison file, right-click the sample name and select Delete Sample from Comparison File.

You need to confirm this action with your electronic signature.

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7 To compare the electropherograms of samples, go to the Electropherogram tab, click Overlaid Samples in the toolbar and select the samples to be compared.

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8 Select the Gel tab to display a comparison of the gel-like images of the samples.

Note that the Gel tab has the same functionality as in the Data context.

9 From the File menu, select Save to save the comparison file (.xac) under the default name, or select Save As to save it under a new name.

The default name is derived from the method/assay class: ComparisonFileX [Method Class].xac where X is an autoincremented number. Example: ComparisonFile0 Protein 230.xac

You need to confirm this action with your electronic signature.

NOTE You can re-open comparison files to review the comparison results, and to add/remove samples.

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Result Flagging

Result flagging can be used to assign a user-defined color codeto a sample. This lets you easily identify samples with certain properties immediately after a chip run, e.g. all total RNA samples with RIN above 7.5 are marked in green.

The color assignment is carried out by applying a sequence of rules to the measurement results obtained for the sample. The rules are defined on chip level and are applied to all samples of the chip.

Two modes are available to define result flagging rules:

Form Mode

In this mode, you can choose an application specific result flagging rule from a given list. Additional attributes, such as size or concentration are entered in the preset forms.

Editor Mode

This mode is more flexible and allows you to write arbitrary complex expressions by using functions, variables and operators.

Regardless of how you create the result flagging rules, there are two options available for the order in which the rules are applied:

In Normal mode, the rules are applied in the given order, and the first matching rule will determine the color of the sample. All rules are applied subsequently. The first rule which applies to the sample defines its color. So you should start with the most specific rule. If that one does not apply, a less specific one may apply. If none of the defined rules apply, the final default rule defines the color code.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles.

See User Role Model ( Access Control on page 39) for details.

HINT You can export and import result flagging rules from other method/assay or chip data files. See Exporting Result Flagging Rules on page 179 and Importing Result Flagging Rules on page 172.

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In Target mode, all rules are applied subsequently. If the next rule applies, the color code changes to the color code defined by the rule, otherwise the previous color code is kept. Therefore, the last matching rule defines the color code of the sample. This mode is called target mode because later rules refine the result color code. The first default color code is the most general and the last one the most specific.

You can switch between the Normal or Target mode using the Result Flagging

menu or the or button in the toolbar. You can define the flagging rules already in the method, orafter the chip run is finishedmodify these rules or define new rules in the chip data file, and apply the rules to the measurement results. Defined rules can also be saved, loaded and applied to other data files.

HINT The examples shown in this chapter are taken from the demo method/assay Demo Protein 230 Series II.xsy, that comes with the 2100 Expert Software. You can find this demo method/assay in the ..\methods\demo\electrophoresis subdirectory of the 2100 Expert Software installation folder. In the ..\data\samples\resultflagging subdirectory of the 2100 Expert Software installation folder, you can find further examples for result flagging rules (.xml), which you can import in the Protein 230 Series II demo method/assay.

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Defining Result Flagging Rules The rules can be defined on the Result Flagging tab. This tab is available in the Data context if an electrophoretic chip data (.xad.) file is selected and in the Assay context if an electrophoretic assay (.xsy) file is selected.

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How to Use the Form Mode The Form Mode provides some pre-defined rules (forms) that you can use to define the result flagging rules to colorcode your samples. You can set up any number of rules for evaluation. As a typical example of how these forms are used, you can flag DNA samples that have a fragment purity of 10% for fragment sizes of 150 bp. To do this, proceed as follows:

1 Open the chip data file that contains the results to be analyzed in the Data context and switch to the Result Flagging tab.

2 Switch to the Form mode going to Result Flagging > > > Form or by clicking

the icon in the toolbar. 3 Choose the Search Fragment with Purity form the Select Form list.

The Search Fragment with Purity form is displayed.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model on page 39 for details.

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4 Fill out the form following the 3 steps:

a Specify the fragments to search for

Define the fragment size(s) to be searched for by clicking on the (+) button to add a fragment and then enter the size in bp for the first fragment. It is possible to add several fragments to the list.

b Specify options

Enter the required purity for the fragment size(s) and the tolerance, both in % in the section. If you defined several fragment sizes and want all of these to be present in the flagged samples, select the option All of them must be present. If you only require that one of the sizes is present, select the option Any of them can be present.

c Specify Results

Select the color with which the samples that meet the criteria should be marked. If desired modify the labeling text.

Optionally select the color with which samples that do not meet the criteria should be marked and modify the labeling text.

5 Apply this rule to the samples by going to Result Flagging > > > Apply Result

Flagging or clicking the icon in the toolbar.

All samples are re-evaluated according to the result flagging rule and displayed with the respective colors.

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Color Indication The results are displayed:

On the Chip Summary Tab:

The colors in the Result Flagging column show which sample matches which rule.

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On the Gel Tab and on the small gel image on the Lower Panel:

The spot on top of the lane is colored if the sample matches a result flagging rule.

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On the Resultssub- tab in the Electropherogram or Gel Tab:

Result Flagging Color: color of the result flagging rule that the current sample matches.

Result Flagging Label: label of the result flagging rule that the current sample matches.

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How to Use the Editor Mode The editor mode for result flagging is a powerful way for advanced users to create your own result flagging rules.

To define a result flagging rule for a selected chip data file:

1 Open the chip data file in the Data context and switch to the Result Flagging tab.

2 Switch to the Editor mode going to Result Flagging > > > Editor or by clicking

the icon in the toolbar.

3 Edit a rule that was created within the Form mode. -OR-

OR

Create a new rule going to Result Flagging > > > Create New Rule > or >

Duplicate Selected Rule by clicking the icon or icon.

4 Click the Edit button next to the Label field and enter or modify the result label for this rule.

The result label can be any arbitrary text.

5 Click the Edit button next to the Condition field and enter or modify the logic expression for this rule.

Expressions are built up of functions, variables, operators, and values. You can manually type in the expressions. But you can also double-click the items in the Functions, Variables, and Operators lists, to insert them in the respective fields. As an example for a logic expression for the rule condition, enter NumberOfPeaks > 9 AND PeakFoundAuto(150). With this rule, all samples can be found that have more than nine peaks while one of them has a size of 150 bp 10%. Detailed descriptions of the available functions as well as the required syntax and examples are shown in the Help field at the bottom of the screen.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model ( Access Control on page 39) for details.

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6 Click the Edit button next to the Comment field and enter or modify a comment for this rule.

7 Click the Edit button next to the Color field and select a color. If you check the Gradient check box, you can assign a color gradient to the rule. It is useful for example to use this gradient function for purity or concentration.

8 If necessary, generate additional rules.

a To rearrange the order of the rules go to Result Flagging > > > Move

Selected Rule > or > Move Selected Rule Down or click the and icons in the toolbar.

b To reset the form go to Result Flagging > > > Reset Form or click on the icon in the toolbar.

9 To apply the rules to your measurement results, go to Result Flagging > > >

Apply Result Flagging or click the icon.

If there still are syntax errors in the rule definitions, an error message appears. All samples are re-evaluated according to the result flagging rules and displayed with the respective colors. See Color Indication on page 150 for more information on the color codes.

You can reuse result flagging rule definitions, see Exporting Result Flagging Rules on page 179 and Importing Result Flagging Rules on page 172.

NOTE If the entered syntax is not correct, the invalid part is displayed in red color.

NOTE Additional information is available in the Help panel at the bottom of the screen. This panel provides context-specific help, including examples.

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Example: Result Flagging Sample 1 contains 100 g/mL proteins. The electropherogram shows 2 peaks for 2 different proteins, which could be separated. One peak can be found at 32 kDa (LDH).

Sample 2 contains 60 g/mL proteins and shows 3 peaks.

Sample 3 contains 80 g/mL proteins and shows 5 peaks.

Now, the following rules are defined:

1 Is there a peak at 30 kDa +/- 7%?

Rule 1: PeakFound(30, PER, 7)

2 Is the total concentration of proteins higher than 90 g/ml?

Rule 2: TotalConcentration > 90

3 Were 5 to 10 peaks found?

Rule 3: NumberOfPeaks >= 5 AND NumberOfPeaks <= 10

Alternative Rule 3: NumberOfPeaks BETWEEN (5,10)

Applying these rules in the given order (in Normal mode) leads to the following results:

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

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For sample 1, rule 1 matches and defines the color. Rule 2 would also match, but is not checked, because the procedure stops at the first match.

For sample 2, none of the rules match, if there is no peak at 30 kDa +/- 7%. Therefore, this sample will get the default color.

For sample 3, only rule 3 matches and defines the color.

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5 Working with Chip Data and Methods/Assays Working with Chip Data and Methods/Assays 158 2100 Export Data Overview 159 Handling Methods 162

Handling Methods 162 Handling Chip Data 166 Organizing, Backing up, and Archieving 2100 Expert Data 167 Importing Data 169

Importing 2100 Bioanalyzer System Files 169 Importing Data Analysis Setpoint 170 Importing Chip and Sample Information 171 Importing Result Flagging Rules 172

Exporting Data 173 Exporting Chip and Sample Information 174 Export Chip Run Data 174

Printing Reports 180 How to Print a Chip Run Report 181 How to Turn on and Configure Automatic Printing of Chip Run Reports 185

Configuring Tables 187 Configuring... 188

This chapter shows you what to do to open, save, import and export files, and how to print the results.

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Working with Chip Data and Methods/Assays

You can make efficient use of the chip and method/assay data generated by the 2100 Expert Software, if you know the following fundamentals and operating techniques:

2100 Export Data Overview on page 159

Handling Methods on page 162

Handling Chip Data on page 166

Organizing, Backing up, and Archieving 2100 Expert Data on page 167

Importing Data on page 169

Exporting Data on page 173

Printing Reports on page 180

Configuring Tables on page 187

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

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2100 Export Data Overview

The 2100 Expert Software manages data in the following different formats:

Method/assay files (.xsy)

Chip data files (.xad)

Comparison files (.xac)

Verification result files (.xvd)

Diagnostics result files (. xdy)

Result flagging rule files (.xml)

Method/Assay files Method/Assay files (.xsy) contain the following information:

Data acquisition and analysis setpoints

Acquisition setpoints are instrument commands and acquisition parameters. Analysis setpoints are evaluation parameters, some of which you can modify.

Method/Assay information

All parameters defined by the method/assay, such as method/assay type, title, and version.

This information includes:

Method/Assay type, title, version, and all other parameters defined by the method/assay.

Study configuration

Instrument configuration

Reporting configuration

Workflow configuration

Chip and sample information

These are sample names, sample and chip comments, and lot numbers.

Ladder table and peak table

Result flagging rules

The audit trail and the signature log with all signatures of the involved users.

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Chip data files Chip data files (.xad) contain the following information:

Measurement results

After each chip run, the measurement resultsalso called raw dataare automatically saved in a new chip data file. Electrophoretic measurement results are pairs of migration time and fluorescence intensity values.

Base method/assay information

Because a chip run is always based on a method/assay file, all information from the method/assay file becomes part of the chip data file.

Run log

Events occurring during the chip run, such as the start and end time, or any errors or problems are entered in a run log, which is also saved in the chip data file.

Evaluation information

These are modifications you made during data evaluation, such as modified gel coloring, manually set markers, manual integration, modified setpoints, modified result flagging rules, or definitions of new markers and regions.

The audit trail and the signature log with all signatures of the involved users

Comparison files You can compare the measurement results from different chip runs (data files of same method/assay class only) by collecting samples from different chip data files (.xad) and storing them in a comparison files (.xac). It is then possible to overlay electropherograms of these samples, for example, but also to compare gel-like images or data tables.

Comparison files also contain an audit trail and a signature log with all signatures of the involved users.

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Verification result files Verification result files (.xvd) contain results of qualification tests regarding the 2100 Bioanalyzer system hardware and software. The files are stored in the ..\validation subfolder of the 2100 Expert Software installation directory. For each verification run, an .xvd file is generated.

Date and time of the verification run are included in the file name. Example: Verification_23-05-2005_10-28-40.xvd.

Verification files also contain an audit trail and a signature log with all signatures of the involved users.

Diagnostics result files To ensure proper functioning of the 2100 Bioanalyzer instrument you should run hardware diagnostics tests on a regular basis. The results of these hardware tests are stored in diagnostics results files (.xdy) in the ..\ diagnosis subfolder of the 2100 Expert Software installation directory.

Result flagging rule files You can export and import result flagging rules from other method/assay or chip data files. Result flagging rules are stored in .xml files.

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Handling Methods

Method Templates The 2100 Expert Software provides method templates. They are designed for measurements using the available kits. They are not suited to be run directly, but must be adapted into custom methods. For example, a necessary adaption for these methods might be to add an instrument.

Predefined Assays Predefined assays are provided with 2100 Expert Software. They are meant and prepared for measurements using the available Analysis kits.

Predefined assays such as DNA 1000 are write-protected. Although you can open predefined .xsy files and edit some of their properties, you cannot save any changes under the original file name.

Methods You can derive your own methods from the predefined methods as described in How to create a custom method: on page 163.

The main benefit of custom methods is that you have to do the following only once in the method file, instead of doing it again and again in the chip data files:

Enter the general properties of the method such as the configuration of study, instrument, reporting, and workflow.

Modify method setpoints (data analysis setpoints).

Enter information on chip and samples.

For example, if your sample names are to be the same for a series of chip runs.

Define rules for result flagging.

NOTE When creating a method from a template or from a pre-existing method, it initially has the state method development. The user who saved it as a new method, will automatically be set up as an analyst in the workflow. In this state only he/she can run the method after adding an instrument. This way the method can be tested without the need to change the state to ready to use.

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You can modify methods at any time. See How to modify a custom assay method on page 165.

How to create a custom method:

To create a method:

1 Switch to the Method context.

2 From the Methods menu, select a method.

OR

Select File > Open and open a method (.xsy) file.

The file appears in the TreeView Panel.

3 Switch to the General Properties tab to specify the Study Configuration settings.

To add a new study to the list of studies, click Add. Then fill the remaining fields.

To modify the settings of an existing study, select it from the list, click Modify and edit the fields in question.

4 On the Instrument Configuration sub-tab, you see a list of all validated instruments.

Select the instruments allowed for this method and click the Add button to move them to the list of Allowed Instrument Configurations.

To remove an instrument from this list, select it and click the Remove button.

NOTE If you just want to view the properties of a method, you can open the method file in read-only mode, ensuring you do not make accidental changes.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

NOTE You can also import the instrument settings from another method file (for example, a similar method). Click the Import button and select the method file to be used.

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5 On the Reporting Configuration sub-tab, define the items that are to be included in the report.

6 Switch to the Assay Properties Tab to modify the method setpoints if required.

7 Switch to the Chip Summary Tab to enter chip and sample information.

8 Define flagging rules on the Result Flagging Tab.

9 Select Save As from the File menu.

The Save As dialog box appears.

10 Under Save as type, select (.xsy), and enter a name and location for the new method.

11 To create the new method, click Save.

12 You need to confirm this action with your electronic signature.

NOTE You can also import the report settings from another method file (for example, a similar method). Click the Import button and select the method file to be used.

NOTE When creating a method from a template or from a pre-existing method, it initially has the state method development. The user who saved it as a new method, will automatically be set up as an analyst in the workflow. In this state only he/she can run the method after adding an instrument.

NOTE This way the method can be tested without the need to change the state to ready to use. In this state the method can also be run on instruments that are not validated.

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How to modify a custom assay method To modify a custom assay method:

1 From the File menu select Open.

The Open dialog box appears.

2 Select a method (.xsy) file and click Open.

The method appears in the TreeView Panel and the Assay Properties Tab is displayed.

3 Modify the method by making changes on the following tabs:

Modify study, instrument, reporting, and workflow settings on the General Properties Tab.

Modify method setpoints on the Assay Properties Tab.

Modify or enter additional chip, sample, and study information on the Chip Summary Tab.

Define or modify flagging rules on the Result Flagging Tab.

4 If the method is now completely set up, switch back to the General Properties tab and click the Release for use button.

5 From the File menu select Save to save the method with the current name or Save as to save it with a new name.

You need to confirm this action with your electronic signature.

NOTE You cannot save modifications to predefined assays method templates.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

NOTE The study description is stored in the 2100 Expert system file. Altering the study description of a method will not affect the entries in the data files that were previously generated from this method. To update this information in the data files, too, they must be opened, and the study must be assigned again.

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Handling Chip Data

Chip data (.xad) files are automatically generated at the end of a chip run. The .xad files are given names that correspond to the choices you have made in the Options dialog box (see How to Specify Data File Names and Directories on page 207).

Modifying and saving chip data files 2100 Expert Software allows to re-open chip data files, reanalyze them using different evaluation parameters and store the new results. You can save modifications either to the original file (File > Save) or under a new file (File > Save As).

If you alter the data shown in any way after it has been saved and try to exit the program or switch to a different context (to acquire new data, for example), a dialog box will appear asking whether or not you wish to save the changes.

Opening chip data files as read-only A chip data file can be opened as read-only; the Title Bar will show (Read-Only) at the end of the filename. The read-only file can be edited but may not be saved under the same name. If you attempt to save an edited read-only file, and error message will be displayed explaining that the file is a read-only file.

The benefit of opening chip data files as read-only is to prohibit you or other users from making changes that would alter the file in any way. Because the 2100 Expert Software allows you to open chip data files, modify data, and save them, you may prefer to ensure that the original parameters that were used to create the file are not altered.

NOTE Raw data acquired from the 2100 Bioanalyzer system is not changedonly evaluation and display of the results can be changed and saved.

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Organizing, Backing up, and Archieving 2100 Expert Data

As you begin to work with the 2100 Expert Software, it is good practice to organize your files. If you are not the only user of the bioanalyzer, creating a directory within which to save your files is recommended; having each person save files to their own directory will speed the process of finding a particular file when someone wishes to examine the data again. Even if only one person uses the 2100 Expert Software, it is still wise to review your files periodically, archive files you are no longer using but wish to save, and discard unneeded files.

With the Security Pack installed, the 2100 Expert Software takes this task over from you and saves all the created data files in the Secured Area directory. In the data folder you will find folders for each assay class and each assay subclass. Underneath each assay subclass you can find a folder for each method and finally in this method folder you will find a folder for each data file created on your system.

Organizing 2100 Expert Data Each user in your laboratory may want to specify a particular prefix that will easily differentiate their data files from any others.

To do this, switch to the System context, go to the System Wide Settings tab, and select Data Files in the tree navigation. Then activate the Prefix check box, and edit the prefix string as you require. Note that you can also modify the file prefix before you start a chip run. Additionally, you may specify that a new directory is created each day for storage of that days runs. To do this, activate the Create Daily Subdirectories check box on the same screen.

You can specify the file prefix every time before you start a chip run in the Instrument context.

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5 Working with Chip Data and Methods/Assays Organizing, Backing up, and Archieving 2100 Expert Data

Backing up 2100 Expert Data It is strongly recommended to save your files to a backup drive or on CD/DVD on a regular basis. This allows to retrieve the data in case of a system crash or other cases of data loss. For users of the 2100 Expert Security Pack, data backup is in the responsibility of the backup operators or the 2100 Administrators. 2100 Expert Software provides these users with the rights to access the Secured Area of the file system with the Windows Explorer and backup tools for this purpose.

Archiving 2100 Expert Data The difference between archiving and backing up is that in the archiving process the data will be removed from its original place and moved while during the backup process only a copy is taken (depending on the tools you use).

It is a good idea to periodically archive your files to a CD/DVD to remove them from your hard disk. Depending on the amount of hard disk space available to the 2100 Expert Software, you may need to clear space on your hard drive to ensure that you will have enough room to save upcoming chip run data.

For users of the 2100 Expert Security Pack, archiving is done by the backup operators or the 2100 Administrators. 2100 Expert Software provides archiving functionality to users with either of these roles. Additionally, these users have the rights to access the secured area of the file system with the Windows explorer and tools for this purpose.

See Archieving Data on page 217 for details.

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Importing Data

When working with method/assay (.xsy) or chip data (.xad) files, you enter specific information that you may want to reuse. To support the reuse of data, 2100 Expert Software has the following import capabilities:

Importing 2100 Bioanalyzer System Files on page 169

Importing Data Analysis Setpoint on page 170

Importing Chip and Sample Information on page 171

Batchwise importing files into a secured state (To import multiple 2100 Expert data files: on page 216)

You can import result flagging rules definitions for result flagging into electrophoretic method/assay or chip data files:

Importing Result Flagging Rules on page 172

Importing 2100 Bioanalyzer System Files You can import data, assay and method files that were generated with other Agilent 2100 Bioanalyzer systems.

How to Import Assay, Method and Chip Data Files

To import assay or method files:

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

NOTE Note that the imported files have the state method development and cannot be used directly for a measurement. If you imported an assay file that was generated with 2100 Expert Software without security pack, the missing information (such as allowed instruments or workflow information) has to be added. If you imported a method file from 2100 Expert Software with security pack, information such as the instrument to be used and the workflow settings need to be updated.

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1 Switch to the Method/Assay context.

2 From the File menu, select Import to display the Open dialog box.

3 Select a .xsy (2100 Expert method/assay file) file.

4 Click Open.

5 You need to confirm this action with your electronic signature.

The imported file appears in the Tree View Panel, and the Method Properties/Assay Properties tab shows information about the method/assay.

Upon importing, the file gets converted to a new 2100 Expert method/assay file (.xsy).

To import chip data files: 1 Switch to the Data context.

2 From the File menu, select Import to display the Open dialog box.

3 Select a .xad (2100 Expert chip data file) file.

4 Click Open.

5 You need to confirm this action with your electronic signature.

The imported file appears in the Tree View Panel, and the electropherogram grid view shows an overview of all samples.

Upon importing, the file gets converted to a new 2100 Expert chip data file (.xad).

Importing Data Analysis Setpoint Importing Data Analysis Setpoint

You can import data analysis setpoints from other method/assay (.xsy ) or chip data (.xad) files of the same type.

Note the following when importing:

Electrophoresis files to be imported must be of the same assay/method type. This means that you cannot import setpoints from a DNA 1000 assay/method into a DNA 7500 assay/method, for example.

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To import data analysis setpoints: 1 On the Assay Properties/Method Properties tab, click Import Setpoints.

The Open dialog box appears.

2 Select the file from which you want to import, and click Open.

All files: the setpoint values are updated in the setpoint explorer, and immediately applied to the measurement results (if any).

3 From the File menu, select Save to make the changes permanent.

Importing Chip and Sample Information On the Sample Information and Study Information sub-tabs of the Chip Summary tab, you can enter names and comments regarding chip, samples, and study. The information you enter here may be very similar for further chip runs or other assays/methods. Once you have entered the information, you can export it into a separate file (see Export Chip Run Data on page 174), which you can then import into other chip data (.xad) or assay (.xsy) files instead of typing it anew.

The import/export files can have the extension .txt or .csv, and have a fixed form.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

NOTE Importing data analysis setpoints overwrites all current setpoint values.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

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To Import Chip and Sample Information 1 On the Chip Summary tab, click Import.

The Import Sample Information dialog box appears.

2 Select the file that contains the information you want to import, and click Open.

The Sample Information and Study Information sub-tabs of the Chip Summary tab update to show the imported data.

3 From the File menu, select Save to make the changes permanent.

Importing Result Flagging Rules You can import result flagging rules into electrophoretic assay/method (.xsy) or chip data (.xad) files. Result flagging rules can be stored in.xml files (see Exporting Result Flagging Rules on page 179).

To Import Result Flagging Rules 1 Open an electrophoretic assay/method or chip data file in the respective

context.

2 Switch to the Result Flagging Tab.

3 In the Result Flagging toolbar click .

The Load Rules dialog box appears.

4 Select the.xml file that contains the set of result flagging rules, and click Open.

The imported rules are applied to the data of the assay or data file.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

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Exporting Data

2100 Expert Software allows you to export the results of your chip runs in a variety of formats. The exported data can be used for further evaluation with other applications, such as text processors, graphic tools, or Microsoft Excel.

You can export the chip run data of the currently loaded file either manually or automatically:

Export Chip Run Data on page 174

More powerful functions for exporting data files are found in the System context. See:

To export multiple 2100 Expert data files: on page 215 for exporting multiple data files.

Archieving Data on page 217 for archiving complete directories (data files and .PDF reports).

If you want to export only parts of your measurement results:

Exporting Tables on page 176

Exporting Graphs or Gel-like Images on page 177

Copying Graphs, Gel-like Images and Tables into the Clipboard on page 178

Information that you have entered to document a chip run can be exported for reuse in future chip runs:

Exporting Chip and Sample Information on page 174

From electrophoretic assay/method or chip data files, you can also export rule definitions for result flagging:

Exporting Result Flagging Rules on page 179

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See Access Control on page 39 for details.

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Exporting Chip and Sample Information On the Sample Information and Study Information sub-tabs of the Chip Summary tab, you can enter names and comments for the chip and the samples. The information you enter here may be very similar for further chip runs or other methods/assays. Once you have entered the information, you can export it into a separate file, which you can then import into other chip data (.xad) or method/assay (.xsy) files instead of typing it anew.

The import/export files can have the extension .txt or .csv, and have a fixed form, which differs for electrophoretic assays.

To export chip and sample information to a file:

1 On the Chip Summary tab, click Export.

The Export Sample Information dialog box appears.

2 Specify a file name and location for the file to which you want to export.

3 Click Save.

Export Chip Run Data

1 Switch to the Data context.

2 In the Tree View Panel, select a chip data (.xad).file or load a file.

3 From the File menu, select Export.

The Electrophoresis Export Options dialog box appears.

4 Select the export categories, and specify a target directory.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See Access Control on page 39 for details.

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5 Click Export.

Several system dialog boxes appear, one for each export category, allowing you to check and modify names and locations of the export files. Clicking the Save button in these dialog boxes finally starts the export.

6 Confirm this action with your electronic signature.

Several system dialog boxes appear, one for each export category, allowing you to check and modify names and locations of the export files.

The Export tab of the System context allows you to export multiple data files without having to load them first.

See To export multiple 2100 Expert data files: on page 215 for details.

NOTE Keep in mind that exporting a chip data file can require up to 20 MB of disk space. In particular, exporting electropherograms and gel-like images as .tif or .bmp files may take up a lot of disk space.

NOTE If you want to access these exported files and you do not have admin rights, please keep in mind to specify a target directory outside the Secured Area folder.

NOTE Otherwise the data will get exported but you will not be able to access it with the Windows Explorer since access is only granted to 2100 Administrators and 2100 Backup Operators.

HINT Chip run data can be automatically exported every time a chip run has finished. Refer to Exporting Chip Run Data Automatically on page 176 for details.

NOTE Chip run data can be automatically exported every time a chip run has finished. Refer to Exporting Chip Run Data Automatically on page 176 for details.

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Exporting Chip Run Data Automatically

1 Switch to the System context and select Auto Export in the tree navigation.

2 Activate the Auto Export check box.

3 Specify the export categories that are to be included in the exported files.

4 Switch to Default Export Directories in the tree navigation and specify the target directories.

5 To leave the System context, you need to confirm this action with your electronic signature.

From now on, chip run data is automatically exported every time a chip run has finished.

Exporting Tables You can export:

Result, peak, fragment, region, and ladder tables as .csv files or .xls files.

Log book tables as .html or .txt files.

NOTE Keep in mind that exporting a chip data file can require up to 20 MB of disk space. In particular, exporting electropherograms and gel-like images as .tif or .bmp files may take up a lot of disk space.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

NOTE If you stop a chip run, auto export does not take place.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model ( Access Control on page 39) for details.

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To export a result, peak, fragment, region or ladder table: 1 On the Assay Properties/Method Properties, Electropherogram, or Gel tab,

right-click the heading row of a table.

2 From the context menu, select Export.

The Export Data dialog box appears.

3 Enter a file name and choose the destination directory.

4 Select .csv or .xls as export file format.

5 Click Save.

To export a log book table: 1 On the Log Book tab, right-click a table.

2 From the context menu, select Export.

The Export Data dialog box appears.

3 To specify the file name, the destination directory, and the file type, click the ... button. You can choose between HTML file for .html output and Tabbed text file for .txt output.

4 Specify whether you want to export the Selected rows only or All visible rows.

5 Click OK

Exporting Graphs or Gel-like Images You can export graphs or gel-like images as individual graphic files.

NOTE Result tables can be automatically exported every time a chip run has finished. Refer to Exporting Chip Run Data Automatically on page 176 for details.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

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To export a graph or a gel-like image:

1 Right-click the graph and select the appropriate entry (e.g. Save Gel or Save Electropherogram) from the Context menu.

OR

Click the button in the toolbar.

The Save As dialog box appears.

2 To enter a name and choose the destination directory, click File name.

3 To select a graphic file format: .bmp, .jpg, .wmf, .tif or .gif, click Save as type

4 Click Save.

The graph or gel-like image is written to the specified file.

Note the following:

Electropherograms:

if the grid view is active, an overview image of the electropherograms (of all samples and the ladder) is exported.

Copying Graphs, Gel-like Images and Tables into the Clipboard You can copy graphs and gel-like images into the clipboard. This applies to most graphs that can be displayed in the 2100 Expert Software, such as electropherograms or standard curves.

You can also copy tables (or parts of tables) into the clipboard. This applies to most of the tables that can be displayed in 2100 Expert Software, such as result tables or log book tables.

To copy a graph, gel-like image or table into the clipboard:

HINT Electropherograms and gel-like images can be automatically exported every time a chip run has finished. Refer to Exporting Chip Run Data Automatically on page 176 for details.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

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1 Right-click the graph, gel or table.

2 From the context menu, select Copy Gel/Copy Electropherogram or Copy To Clipboard (tables).

OR

Click the button in the toolbar.

You can now switch to a word processing, spreadsheet, graphics, or other application, and paste the graph/gel or table there.

Exporting Result Flagging Rules You can export result flagging rules for reuse in other electrophoretic assay/method (.xsy) or chip data (.xad) files (see Importing Result Flagging Rules on page 172). Result flagging rules are stored in.xml files.

To export result flagging rules:

1 Open the electrophoretic assay/method or chip data file with the desired result flagging rules in the respective context.

2 Switch to the Result Flagging tab.

3 In the Result Flagging toolbar click the icon (Export Rules to File).

The Save Rules dialog box appears.

4 Browse for a folder where you want to store the rules, and specify a name for the.xml file.

5 Click Save

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

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Printing Reports

For documentation and presentation purposes, you can print reports for method/assay (.xsy), chip data (.xad), verification results (.xvd), and comparison (.xac) files.

You can print all reports manually, see How to Print a Chip Run Report on page 181. When printing manually, a preview function allows you to view the printout before starting the print job.

The 2100 Expert Software can also be set to print customized chip run reports automatically at the end of the run. These reports can be set up to contain different information (settings for the manual and automatic print functions are maintained separately). See How to create a custom method: on page 163 for more information.

The 2100 Expert Software can also be set to print customized chip run reports automatically at the end of the run. These reports can be set up to contain different information (settings for the manual and automatic print functions are maintained separately). See How to Turn on and Configure Automatic Printing of Chip Run Reports on page 185 for more information.

HINT Beside sending reports to a printer, you can also create .pdf and .html files.

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How to Print a Chip Run Report The following information can be included in a chip run report:

You can always include:

Run summarygeneral data about the method/assay, and sample information.

Assay detailscomplete list of data analysis setpoints.

Run Logbook

Signature Logbook

Audit Trail

For electrophoretic chip data files (.xad), depending on the method/assay type you can include:

Electropherograms

Gel-like image

Result tables

Standard curve

Calibration curve

To print a report:

1 Switch to the Data context.

2 In the Tree View Panel select the chip data (.xad) file you want to generate a report of.

NOTE The contents of the report are specified during the method/assay setup. If a chip run was made based on a method/assay that was released for use, you cannot alter the pre-defined contents of the report.

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3 From the File menu select Print.

Depending on the file type different dialog boxes appear.

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4 You generally have the following possibilities:

select the items to be included in the report from the Print Item section

select the wells to be included from the Wells (electrophoretic assays) section

select the appropriate options

specify whether you want to generate the report as a file (PDF or HTML) and specify the file path

5 Use the Page Setup and Printer buttons to access system dialog boxes, allowing you to select a printer, and specify the print medium and page layout.

6 To get a preview of the printouts or files to be generated, click the Preview button.

7 To print out the pages or generate the file(s), click Print.

The following example shows the Run Summary part of an RNA chip run report.

NOTE Security Pack: You can only select the included Print Items and the additional Options only unless the method is released for use.

NOTE Your selections here are separate from the Auto Print selections (they do not affect each other). Both are used by default the next time you print (even after restarting the program).

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How to Turn on and Configure Automatic Printing of Chip Run Reports

A report can be automatically printed on a printer or generated as a file at the end of each chip run. Saving reports as files can be helpful for documentation purposes.

To enable and configure automatic printing:

1 Switch to the System context.

2 Select Run and Result in the tree navigation.

3 Activate the Auto Print check box and click the Settings button next to this check box.

The Auto Print dialog box appears.

NOTE The Auto Print settings are independent from those made via the Print command of the File menu.

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4 Adjust the settings:

In the Print Item section, select the options that are to be included in the report.

In the Save To File section, you can redirect the automatic printouts to .pdf and .html files.

Note that no print output is generated if you select the PDF and/or HTML option.

Using the Page Setup and Printer buttons, you can access system dialog boxes, allowing you to select a printer for the automatic print, and specify the print medium and page layout.

5 Click OK to confirm the automatic print settings.

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Configuring Tables

2100 Expert Software uses various tables to present data:

Result tables

Peak tables

Fragment tables

Region tables

Log book tables

In some cases, you might want to reorganize the way the data is presented. To do so, you can hide or show columns, change the column sequence, and adapt the table height.

The following example demonstrates how to add the migration time to the Peak Table.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

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Configuring...

Showing and Hiding Columns To add the Aligned Migration Time column to the table:

1 Right-click the heading row of a table and select Configure Columns from the context menu.

The Configure Columns dialog box opens:

2 Move any desired column headers from the Available list to the Displayed list.

3 Configure the order of the column headers in the Displayed list by using the Up and Down buttons.

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4 Click OK.

A new column Aligned Migration Time is inserted in the table:

To change the column sequence of a table:

1 Position the mouse pointer on a column header.

2 Click and hold the left mouse button to drag the header cell to the desired position.

While dragging, a green arrow indicates the target position.

3 Release the mouse button.

The column has moved to its new position:

NOTE You can set the column sequence also using the Up and Down buttons in the Configure Columns dialog box.

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To increase or reduce the column width: You can customize the view by changing the column width.

1 Position the mouse pointer between two columns and move it until the cursors shape changes to a double arrow.

2 Click and hold the left mouse button and drag left or right.

3 Release the mouse button.

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6 Administering System Functions and the Security Pack Administering System Functions and the Security Pack 192 Access Control 193

How 2100 Expert Software Manages Users and Data Access 193 Managing User Accounts and Roles 194

Pre-configurations for the 2100 Expert Software 198 Setup a default printer 198 Default Printer margins 199 Configure regional settings 202 Display settings 205 USB-to-Serial adapter configuration 206

Configuring the 2100 Expert Software 207 How to Configure the 2100 Expert Software 207

Exporting and Importing Multiple Data Files 215 Exporting and Importing Multiple Data Files 215

Archieving Data 217 Archieving Data 217

Using Log Books 220 How to change the display of the logbooks 224 How to Search the Log Book 226

This chapter is your guideline for configuring the 2100 Expert Software.

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6 Administering System Functions and the Security Pack Administering System Functions and the Security Pack

Administering System Functions and the Security Pack

The 2100 Expert Software provides the following configuration options and system functions:

Users can be added, removed, and assigned various roles. See Access Control on page 193 for details.

Default data file names and directories can be specified. Also, settings such as for automatic printing or automatic data export can be set up. See Configuring the 2100 Expert Software on page 207 for details.

Chip data files can be exported and imported. See Exporting and Importing Multiple Data Files on page 215 for details.

Data can be archived to free system space. See Archieving Data on page 217 for details.

Log books are provided that record all important actions and messages in the 2100 Expert Software. See Using Log Books on page 220 for details.

NOTE The 2100 Expert Security Pack restricts access to data and functionality to users who are logged in with certain roles. See User Role Model (Access Control on page 39) for details.

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Access Control

Among others, the 2100 Expert Software with the Security Pack license provides functionality for access control. With this access control functionality, only authenticated and authorized users can access and modify data, i.e. any electronic record created or managed by 2100 Expert Security Pack.

How 2100 Expert Software Manages Users and Data Access 2100 Expert Security Pack does not add another level of user management. It utilizes the user accounts setup which is managed by the operating system. The users can either be managed locally (user accounts on the computer) or in a company environment (user accounts managed by a directory service).

Analogously, password management is taken from the Windows operating system. The requirements in respect to user and password management posed in controlled environments, must be achieved by configuring the operating system account and password policies accordingly.

However, not all the users set up at the local PC or domain service are allowed to access the 2100 Bioanalyzer System. During its setup, the 2100 Expert Software will be configured to grant access only to those operating system users, which have been selected by a 2100 adminstrator.

Here it is also defined, which data and functionality a user is allowed to access. The 2100 Expert Software uses roles to determine which data and functions a user is allowed to access. Unless a user has already been assigned a particular role within the 2100 Expert Software, this user has no access to the 2100 Expert data.

There are direct consequences for a user management that is performed by the operating system: When a user changes his/her password within the company's directory service, this new password is also valid for the 2100 Expert Software.

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To protect the data generated with the 2100 Bioanalyzer System from access via the Windows environment, a so-called Secured Area is defined. The Secured Area is a file directory where all Security Pack data gets stored in. It is defined as a folder belonging to the generic 2100 System account. This account perfoms the underlying security management tasks and is not visible inside the 2100 Expert Software. The System account is not assigned to any roles.

As a consequence the data in the Secured Area is controlled by the 2100 Expert Software. Access to the directory through Windows Explorer should only be granted via the software provided user roles "Administrator" and "Backup Operator" as this is recorded in the audit trail. Other users, including Windows users are not granted access to the secured data.

As an example, you may have a PC with 15 user accounts set up in the operating system plus the 2100 System account. Only 5 of these users are also set up as 2100 Expert Software users and, therefore, can access data through the 2100 Expert Software. But only one of them has the role 2100 Administrator and can, thus, access the data also with the Windows Explorer.

Managing User Accounts and Roles With the Security Pack license installed, the user management functions are activated. These functions are only available to users with the role administrator.

For more information on the various user roles, see User Role Model (Access Control on page 39).

To Add a New User to the 2100 Expert Software:

1 Switch to the System context and go to the Users and Roles tab.

2 Select Users and Roles > Add User.

The Select User dialog box opens.

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The appearance of this window depends on the installed operating system.

3 Select the user you want to add either from the local users or from your companys domain server.

4 To add him/her to the list of selected users, click Add. You can add several users to this list.

5 To create user accounts for all selected users in the 2100 Expert Software, click OK

6 You need to confirm this action with your electronic signature.

The new users now appear in the tree view panel.

NOTE To select a user for 2100 Expert Software, his/her user account must already be set up in the operating system environment. This can only be done by an operating system administrator.

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To assign roles to a user or to remove roles from a user: 1 Switch to the System context and go to the Users and Roles tab. 2 Click the name of the user in question in the tree view panel.

The User Information of the selected user is displayed. 3 Check the roles that you want to assign to the user. Uncheck the rules that

you want to remove from the user. 4 When leaving the Users and Roles tab, you need to confirm the changes with

your electronic signature.

How to Enable and Disable a User Account A 2100 Expert Software user account may be disabled. Two possible cases cause a 2100 Expert user account to be disabled: If the operating system user account is disabled, the respective 2100 Expert

account is also disabled. This can happen, for example, due to several failed attempts to log into the operating system.

The operating system user account may still be working, but the 2100 Expert account is disabled. The account could have been actively switched off by the 2100 administrator, if access for a certain user should be prohibited. Additionally, also 2100 expert may disable the account after too many failed attempts at login or signing.

A disabled account can only be enabled by a 2100 administrator. If the user account cannot be enabled again within 2100 Expert Software, the operating system administrator must check the users account in the operating system and enable it again.

To enable or disable a user account within 2100 Expert Software: 1 The User Information including the current status of the selected user is

displayed. 2 Switch to the System context and go to the Users and Roles tab. 3 To enable or disable a user account, right-click the users name in the tree

view panel and select the appropriate entry from the context menu. The status of the user changes accordingly.

4 When leaving the Users and Roles tab, you need to confirm the changes with your electronic signature.

HINT If you are unsure whether you selected the correct user in the tree view panel, you can click the Full Name button to retrieve the users full name from the Windows user account.

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How to Change Your Password If for security reasons a user needs to change the password immediately, for example if it has been spied upon, this can be done directly in the 2100 Expert Software.

To change your password:

1 From the File menu in any context, select Change Password.

The Change Password dialog box opens.

2 Enter your old password to authenticate yourself.

3 Enter the new password twice to verify the correct spelling.

4 To finish the password change, click OK.

NOTE The 2100 Expert Security Pack uses the user accounts from the Windows environment. Thus, changing your password from within the 2100 Expert Software will cause that this new password will also be required for future logins to the Windows operating system.

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6 Administering System Functions and the Security Pack Pre-configurations for the 2100 Expert Software

Pre-configurations for the 2100 Expert Software

Setup a default printer The 2100 Expert Software requires a printer to be setup for the printing of reports and for some software features, like result flagging, to function properly. This can either be a physical printer, connected to the PC or laptop the 2100 Expert Software is running on, a network printer or a virtual printers, like PDF or XPS printers.

To setup a printer on your PC or laptop, please follow the instructions below:

1 Windows 7 OS: To setup a default printer, log on to the operating system with an administrative account, select the Start button and then Devices and Printers. Add or select a printer, then select Set as default printer.

OR

Windows 10 OS: To setup a default printer, log on to the operating system with an administrative account, select the Start button and then Settings. Go to Devices and add or select a printer. Then select Make default.

NOTE Security Pack Users: Please be aware that you have to setup a printer by logging into the generic 2100 System account. Then follow the instructions for your operating system.

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Default Printer margins

Configure XPS properties in Windows 7

1 In the 2100 Expert Software, open File > Page setup, then set the margins to 0.5 inches each and click OK. Make sure the paper size is Letter and Source is Automatically Select.

NOTE When working with 2100 Expert Software B.02.08 and Operating System Windows 7, certain page margins are not compatible with the document printer.

To modify the printer margins, please follow the instructions below.

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2 Log on to the operating system with an administrative account, select the Start button and then Devices and Printers. Right click on Microsoft XPS Document Writer, select Printing preferences.

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3 Select the Layout tab and choose Orientation: Portrait. Then click on Advanced and select Paper/Output and under Paper Size choose Letter and confirm with OK.

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Configure regional settings

1 Log on to the operating system with an administrative account, select the Start button and then Control Panel.

2 Select the Clock, Language, and Region category.

NOTE Certain issues in the 2100 Expert Software can be solved by ensuring that your computers regional and language settings are correct.

To review and change the regional settings please follow the instructions below.

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3 Select Region and Language.

4 Ensure that the format is set to English (United States) and click on the Additional Settings button.