Analyst QS. Administrator s Guide. Part Number: B July 2004

Analyst QS Administrator s Guide Part Number: 1001930 B July 2004 http://www.appliedbiosystems.com

This document is provided to customers who have purchased MDS Sciex equipment to use in the operation of such MDS Sciex equipment. This document is copyright protected and any reproduction of this document or any part of this document is strictly prohibited, except as MDS Sciex may authorize in writing. Equipment that may be described in this document is protected under one or more patents filed in the United States, Canada, and other countries. Additional patents are pending. Software that may be described in this document is furnished under a license agreement. It is against the law to copy, modify, or distribute the software on any medium, except as specifically allowed in the license agreement. Furthermore, the license agreement may prohibit the software from being disassembled, reverse engineered, or decompiled for any purpose. Portions of this document may make reference to other manufacturers products, which may contain parts that are patented and may contain parts whose names are registered as trademarks and/or function as trademarks. Any such usage is intended only to designate those manufacturers products as supplied by Applied Biosystems/MDS Sciex for incorporation into its equipment and does not imply any right and/or license to use or permit others to use such product names as trademarks. All products and company names mentioned herein may be the trademarks of their respective owners. Applied Biosystems/MDS Sciex makes no warranties or representations as to the fitness of this equipment for any particular purpose and assumes no responsibility or contingent liability, including indirect or consequential damages, for any use to which the purchaser may put the equipment described herein, or for any adverse circumstances arising therefrom. Applied Biosystems/MDS Sciex is a joint venture between Applera Corporation and MDS Sciex, the instrument technology division of MDS Inc. ISO 9001 REGISTERED COMPANY For Research Use Only. Not for use in diagnostic procedures. SCIEX is a registered trademark owned by MDS Inc. in the United States and certain other countries. QSTAR, ANALYST are registered trademarks owned by Applera Corporation or its subsidiaries in the United States and certain other countries. omaldi is a trademark owned by Applera Corporation or its subsidiaries in the United States and certain other countries. Equipment built by MDS Sciex, a division of MDS Inc., at 71 Four Valley Dr., Concord, Ontario, Canada L4K 4V8. MDS Sciex and Applied Biosystems are ISO 9001 registered. 2004 Edition MDS Sciex, a division of MDS Inc., and Applera Corporation, Joint Owners. All rights reserved. Printed in Canada.

Contents Chapter 1: About this Guide............................... 5 Who Should Read this Guide............................. 5 How this Guide is Organized............................. 6 Related Documentation.................................. 6 Chapter 2: Getting Started with Analyst...................... 7 Reading the Release Notes............................... 7 Understanding Analyst Files.............................. 8 File Structure...................................... 8 File Security....................................... 9 Setting Default Projects.............................. 9 Chapter 3: Configuring Analyst........................... 11 Configuring Attached Peripherals......................... 12 Supported Peripherals.............................. 12 General Device Configuration Tasks................... 12 Configuring a Device............................... 12 Configuring Analyst Security............................ 14 Setting Up User Types.............................. 16 Adding Users to the System.......................... 18 Creating a User Type............................... 19 Assigning Users to User Types........................ 20 Configuring Project Security......................... 21 Configuring Access to Projects and Project Files......... 21 Setting Up Access Rights for Exported Files............. 22 Configuring Access to Instrument Workstations.......... 22 Configuring the Compound Database Editor................ 23 iii

Contents Upsizing to a Microsoft SQL Server.................... 24 Configuring Tuning.................................... 27 Setting the Tuning Options for Mass Calibration......... 27 Setting the Tuning Options for Resolution Optimization.... 28 Setting the Instrument Options........................ 28 Designing Report Templates............................. 29 Designing Headers and Footers....................... 29 Acquisition Elements............................... 29 Quantitation Elements.............................. 30 Configuring ExpressView............................... 31 Configuring Queue Options............................. 33 Setting Queue Options.............................. 33 Configuring the Columns in the Queue................. 34 Chapter 4: Support...................................... 37 Where to Go for Help.................................. 37 Index.................................................. 39 iv

1 About this Guide This guide provides you with the information you need to install and configure Analyst QS, referred to as Analyst from here on in. Analyst provides a Windows based platform for the acquisition and analysis of data derived from mass spectrometers. The interface allows users to perform all of the activities associated with analyzing samples, including configuring attached devices, tuning instruments, performing qualitative and quantitative analysis, and printing reports. Analyst uses the power of the Windows operating system to provide comprehensive security configuration, as well as the ability to operate the system in a networked environment. Who Should Read this Guide This guide is for all personnel who administer hardware and software in the laboratory environment where Analyst is used. The information contained in this guide is intended both for the laboratory administrator, who is concerned with the daily operation and use of Analyst and attached instrumentation from a functional perspective, and the system administrator, who is concerned with system security and data integrity. This guide documents the more common administration tasks. For information specific to particular aspects of the user interface, you should refer to the Analyst online Help. In addition, before proceeding to any of these tasks, you should ensure that you have read the release notes. 5

About this Guide How this Guide is Organized This guide is organized roughly in the chronological order in which tasks should be performed to install, configure, and administer Analyst. In addition, there are chapters containing conceptual information to provide an understanding of the administration of Analyst. Related Documentation Analyst comes with comprehensive online help to assist you in the daily operation of the software. In addition, before you begin installing the software, you should read the documentation packaged with the Analyst QS software CD. The following documentation is also available for reference: Release notes Analyst QS Getting Started Manual omaldi Server Operator s Manual 6

2 Getting Started with Analyst Analyst comes with an installation program that guides you step-bystep through the installation process. While the process is fairly straightforward, you should read the documentation packaged with the Analyst QS software CD, and ensure that you have the basic hardware and software prerequisites before you begin. You should also understand the difference between a data-processing and an instrument workstation because the installation process is slightly different for each type of workstation. To install Analyst, you must have administrator privileges on the workstation on which you are installing the software. For Analyst installation instructions, refer to the documentation packaged with the Analyst QS software CD. Reading the Release Notes Release notes are shipped with the product and should be read before installing the product. The release notes contain information related to: Minimum Hardware Requirements Supported Devices Minimum Software Requirements 7

Getting Started with Analyst Operating System Requirements Note: The release notes can also be found on the installation CD. Understanding Analyst Files When you install Analyst, the software creates a default directory structure to provide a consistent and logical means of accessing project files. In addition, as you create new projects, Analyst sets up a project directory structure automatically. The following default projects are shipped with Analyst as examples of how projects can be set up: API Instrument Default Example File Structure The main project file by default is c:\pe Sciex Data\Projects\Project 1, where Project 1 represents the name of the project. To change the default directory, from the Tools menu, select Project and then Set Root Directory. The table below shows the typical contents of the different subdirectories. Subdirectory Summary Directory Acquisition Methods Acquisition Scripts Batch Data Log Contents All the acquisition methods used by the project. All the acquisition scripts used by the project. A directory for each batch. The Batch Template subfolder contains all the batch templates used by the project. All the raw data (.wiff) acquired by the software for the project. A directory for each batch. (Each directory contains the data acquired with that batch, as well as the batch file containing the information about each sample and its position within the batch.) 8

Analyst QS Administrator s Guide Subdirectory Summary Directory Processing Methods Processing Scripts Project Information Quantitation Methods Results Templates Contents All the logged information. All the processing scripts used by the project. The quantitation settings database. Most other component settings are stored in the Windows registry. All the quantitation methods used by the project. All the quantitation results tables created in the project. All the templates used in the project. File Security Access to all of the files in each project is controlled using the security configuration functions of Analyst. You can control access to projects on a project-by-project basis or even at the file level. For detailed information on security, refer to Analyst Help. Setting Default Projects Note: You must create a PE Sciex Data folder and a project before you can change the default directory for saving project files. Refer to the Analyst online help for information on creating projects. To change the default directory where project files are to be saved 1. From the Tools menu, select Project and then Set Root Directory. 2. Navigate to the directory that you wish to set as the root directory for your projects and click OK. 9

Getting Started with Analyst 10

3 Configuring Analyst After installation, you must configure Analyst. The main configuration tasks are: Configuring attached peripherals. This allows you to describe the peripheral devices attached to the system. Examples of peripheral devices are autosamplers, column ovens, and pumps. Configuring Analyst security. This allows you to set the security and authorizations for your system. You can choose from no security at all to very specific security. Configuring the compound database. This allows you to set the location and name of the compound database. You can also upsize from a Microsoft Access database to a Microsoft SQL Server. Configuring ExpressView. ExpressView allows you to quickly create and submit an acquisition batch. Configure ExpressView to control access to batch information and to require specific information before submitting a batch. Configuring tuning. Tuning allows you to get the most out of your instrument. Configuring the tuning and instrument options allows you to preset mass calibration, resolution optimization, and calibration standard information. Designing report templates. The Report Template Editor allows you to design templates for headers and footers for your reports. You can design new ones, or select and modify existing templates to suit your current needs. 11

Configuring Analyst Configuring queue options. The Queue Manager allows you to set some options governing the sample queue as a whole. For example, you can alter the length of time spent in idle and the maximum number of samples permitted in a single queue. Configuring Attached Peripherals You configure attached peripherals or devices using the Hardware Configuration Editor component of Analyst. The Hardware Configuration Editor provides a streamlined method of setting device configuration parameters and storing them in hardware profiles. You can create multiple hardware profiles for a workstation and select which one to make active depending on the needs of the user at the time. To activate a profile, the device must be connected to your instrument workstation. To configure devices using Analyst, you must first connect them to the workstation and set them up properly. Refer to the device documentation and the Analyst online help for setup information particular to a specific device. Supported Peripherals For a list of the supported devices see the release notes shipped with the product. General Device Configuration Tasks When you install Analyst, all of the device drivers necessary to configure the supported devices are copied over to the workstation. Hardware configuration consists of setting up the device drivers for one or more devices attached to a workstation and saving the results in a hardware profile. Configuring a Device Follow these steps to configure a device using the Hardware Configuration Editor. Before you start to configure a device, attach and configure one or more devices according to the device instructions and any additional instructions provided in Analyst Help. 12

Analyst QS Administrator s Guide Creating a hardware profile The default profile is the mass spectrometer. You create hardware configuration profiles when you add devices to the mass spectrometer. To create a hardware profile: 1. To open the Hardware Configuration Editor, on the Navigation bar double-click Hardware Configuration under Configure. 2. In the Hardware Configuration Editor dialog box, click New Profile. The Create New Hardware Profile dialog box appears. 3. Enter a profile name in the Profile Name field and click Add Device. The Available Devices dialog box appears. 4. Select the appropriate device from the Device Type list. The available devices for the type of device appear in the Devices list. 5. Select the device driver to add to the hardware profile and click OK. You can continue to add device drivers, if necessary, or proceed to configuring the device drivers, as follows. Configuring device drivers After you add device drivers to the hardware profile, you must configure them. To configure a device driver: 1. From the Device in Current Profile list in the Create New Hardware Profile dialog box, select the device to configure and click Setup Device. The appropriate dialog box for configuring your device appears. 2. Enter an alias for the device if desired and select the appropriate settings for your device. Typically you should be able to use the default settings. Refer to your device documentation and port settings to determine whether you need to change any communication settings. 3. Click OK to save your changes to the device driver configuration. 13

Configuring Analyst Activating a hardware profile Once you have created and configured one or more hardware profiles, you need to make one of them active for the workstation. To do this, the device must be connected to the instrument workstation. A blue check mark on a yellow circle indicates the hardware profiles available for activation. Note that only one profile can be active at a time. To activate a profile: 1. From the Hardware Profiles list of the Hardware Configuration Editor, select a profile to activate. 2. Click Activate Profile. The blue check mark on the yellow circle turns bright green when the profile is activated. 3. Click Close to exit the Hardware Configuration Editor. Note: If your profile fails to become active, refer to the Analyst online help for more information. Configuring Analyst Security Analyst provides a comprehensive means of configuring security by integrating its security setup seamlessly with the existing security you have already defined for Windows. Windows users and user groups are available within the Analyst Security Configuration system so that you can control access to the Analyst system. You can configure security at the following levels: Access to Analyst. Access to instrument functionality. Access to specific projects. Access to instrument stations. 14

Analyst QS Administrator s Guide To access Analyst s security configuration component: On the Navigation bar, double-click Security Configuration under Configure. The Security Configuration dialog box appears, from which you can set up Analyst security. If the security mode is single-user mode, the User and User Type tabs disappear. The tabs reappear in fully integrated mode. Choosing a security mode Analyst s security component allows you to choose one of the following modes: Fully integrated mode (in which you make use of the security system you have already defined in Windows). Single-user mode (in which you do not use any security features at all). Fully Integrated Mode Fully integrated mode makes full use of the Windows security you have already set up. Users and user groups defined in Windows are available in Analyst so that you can configure access to the system by specifying the access rights of these users or user groups. In addition, you can define users and user groups as members of user types, each of which has selective access to Analyst functionality based on specific user requirements. You can also define your own user types and control access to the Analyst functionality at the component or even functional level. If you configure Analyst to use fully integrated mode, users must log onto the Analyst workstation, providing a UserID and Password, before being able to access Analyst. Single-User Mode Single-user mode essentially turns off the security portion of Analyst. Any user who logs into a workstation has full access to the software and, essentially, has administrator privileges to the software. This is useful when there are a limited number of users and there are no particular security requirements. 15

Configuring Analyst To set the security mode: 1. From the Security Configuration dialog box, select the Security tab. 2. Select Single User Mode or Integrated Security Mode and click OK. Setting Up User Types Analyst comes with five predefined user types reflecting typical uses of Analyst. You can also choose to define your own user types and configure their access to the system depending on your own specific requirements. Access to Analyst is controlled by user type, not by user, although you can create user types that consist of only a single user. The following is a table of predefined user types and there access. Analyst User Types User Type Typical Tasks Access Admin System administration. Security configuration. Definition of experiments for casual users. Analyst Overseeing instrument operation. Analysis of data for use by end user. All Analyst functionality Acquisition Method Analyst Application Compound Optimization Explore Quantitation Report Template Editor Sample Queue Tune View Status 16

Analyst QS Administrator s Guide Analyst User Types User Type Typical Tasks Access Operator Overseeing daily use of the system, including maintenance, sample organization, data gathering, and processing. End User Providing samples. Receiving processed results. Integrating results with input and output from other applications. Casual User Providing limited number of samples in order to generate required results. Specification of files and conditions used for analysis. Acquisition Method Analyst Application Batch Compound Optimization Explore ExpressView Report Template Editor Sample Queue Tune View Status Acquisition Method Analyst Application Compound Optimization Explore ExpressView Report Template Editor View Status Analyst Application ExpressView View Status 17

Configuring Analyst Adding Users to the System Before you configure user types, both users and user groups must be added to the Analyst security database. To add users to the system: 1. From the Security Configuration dialog box, select the Users tab. 2. Click Add User to open the Add New Account dialog box. 3. From the Accounts list, select the user or user group you wish to add and click OK. The user name appears in the User Name list of the Users tab. 4. Enter a description of the user in the Description field, if desired, and proceed to assign the user or user group to a user type. 18

Analyst QS Administrator s Guide Creating a User Type If you are setting up Analyst s security, you may create one or more user types with capabilities different from the five types created by Applied Biosystems/MDS SCIEX. To create a user type: 1. From the Security Configuration dialog box, select the User Types tab. 2. Click Add User Type. The Add New User Type dialog box appears. 3. Enter a name into the User Type Name field and enter a description, if desired, in the User Type Description field. 4. Click OK. 5. Assign access to Analyst by selecting components and clicking Enable/Disable. To provide selective access to components, expand the Components and Functionality list by clicking the + symbol to the left of the Analyst component. You can then configure access by function. You can now add users to the user types you have defined. 19

Configuring Analyst Assigning Users to User Types After creating user types, you can assign users to those user types. To assign a user to a user type: 1. From the Security Configuration dialog box, select the Users tab. 2. Click Add User. The Add New Account dialog box appears. 3. Select the user you wish to add and click OK. The user appears in the User Name list. 4. From the Not Member Of list, select the user type to which you wish the user to belong and click Add. A user can belong to more than one user type. 5. Click OK. Users who belong to more than one user type have the access rights of all of the user types to which they belong (that is, the access rights are additive). 20

Analyst QS Administrator s Guide Configuring Project Security Using Analyst security configuration, you can configure user access to projects and project files. You can control access by user or by user type. In addition, you can control how files exported to other workstations are accessed by users not defined in the Analyst security database. Note that to use this feature of Analyst security, you must be using NT File Security (NTFS) on your workstations. If you elect not to set up project security, user access to the project files depends on the data setup for each user in NTFS. Configuring Access to Projects and Project Files This procedure describes how you can configure access to projects and project files by users or user types. You can also configure the type of access: read, write, delete, or no access. To configure access to projects and project files: 1. From the Security Configuration dialog box, select the Projects tab. 2. In the Projects list, navigate to the directory or file for which you wish to configure user access. The Project, Root Directory, and File (if applicable) fields display the directories or files you have selected. 3. Click Add to open the Add Permissions dialog box. 4. Select the appropriate access type from the Rights area and then select either a Windows user or user group or a user type from the appropriate list. 5. Click OK. The user type, user, or user group appears in the Permissions list of the Projects tab. 6. To modify access rights for a previously defined permission type, click Permissions and then modify the access rights in the Change Permissions dialog box. Click OK to save your changes. 21

Configuring Analyst Setting Up Access Rights for Exported Files You can set up access rights for files exported to other systems. To set up access rights for exported files: 1. From the Security Configuration dialog box, select the Projects tab. 2. In the Projects list, navigate to the file for which you want to configure user access for exporting. The Project, Root Directory, and Directory/File (if applicable) fields display the file you have selected. 3. Click the appropriate option button: NoAccess, ReadOnly, or ReadWrite. 4. Click Apply. Note: Selecting an access right from the Default list specifies the access right that will be applied as you create new files. Existing files retain their original access right. Configuring Access to Instrument Workstations To control user access to instrument workstations, you must define the workstations in Analyst s security component. This procedure describes how to configure access to an instrument workstation. To configure access to an instrument workstation: 1. From the Security Configuration dialog box, select the Instrument Stations tab. 2. Click Add to open the Add New Instrument Station dialog box. 3. Type the instrument station (IS) name, domain name, and computer name into the appropriate fields. You may also optionally add location and description information. 4. Click OK. The information is displayed in the Instrument Stations tab. 5. Click OK to save your changes. 22

Analyst QS Administrator s Guide Configuring the Compound Database Editor The Compound Database Editor allows you to store information on compounds including the optimization conditions and the compound values or parameters. Note: The defaults for the Compound Database Editor are set during installation. These defaults should be acceptable and do not need to be changed. To set the compound database optimization preferences: 1. In Explore mode, click Settings in the Tools menu. 2. In the list of settings and options, click Optimization Options. 3. In the Optimization Options dialog box, type or browse for the location of the compound database file. Note: If you are accessing the compound database over a file server, the file location must be a mapped drive. 4. In the Name field, type the name of the compound database file. 5. If you are accessing the compound database over a file server, enter your user ID and Password. Sign-on is not required for a local database. 6. Click Test Connection to ensure that the file path and name specified are correct. 23

Configuring Analyst Upsizing to a Microsoft SQL Server Analyst supports the Microsoft Access or SQL server. As the compound database becomes larger, you may find it necessary to upsize to a Microsoft SQL Server. In order to upsize, you must have a Microsoft SQL Server installed. It is recommended that you use the Upsizing Wizard in Microsoft Access to migrate to the SQL Server. Note: You can also use SQL Server s Data Transformation Services (DTS) Import Wizard to import compound database data. However, if you use this wizard there are additional steps, which are not covered in this guide. Refer to the appropriate documentation from Microsoft for more information. The Upsizing Wizard in Microsoft Access upsizes the Access database without additional manual steps. Ensure that you have Microsoft Access installed before you begin the following procedure. To upsize to Microsoft SQL Server 7.0: 1. Using the Microsoft Installation Wizard, install Microsoft SQL Server 7.0. 2. Start Microsoft SQL Server 7.0 and Microsoft Access. 3. In Microsoft Access, from the Tools menu, choose Database Utilities, and then Upsizing Wizard. 4. In the Upsizing Wizard, click Next. 24

Analyst QS Administrator s Guide 5. From the list, select the name of the computer where the SQL server is running. You may choose the (local) server. 6. Type CompoundDB as the name of your new SQL Server database and click Next. 7. Select all of the tables you want to export and click Next. 8. Click Next again to accept the defaults. 9. Select Create a new Access client/server application and in the ADP File Name box, type D:\PE Sciex Data\CompoundDBCS.adp. In this case, D:\ is the drive where the PE Sciex Data folder resides. 25

Configuring Analyst 10. Click Finish. The Data Link Properties dialog box appears. 11. In the Connection tab, select the name of your SQL Server machine from the list. You may also choose (local). 12. Type sa as the User Name. You do not need to specify a Password. 13. Click Test Connection. 14. If the connection is successful, click OK. If the connection is not successful, ensure that the parameters you have specified in the Data Link Properties dialog box match those previously specified in the Upsizing Wizard, and click Test Connection again. The Upsizing Wizard Report appears. Print this report and keep a copy for backup and troubleshooting purposes. Once you close the report, Microsoft Access starts and tries to connect to the SQL server. You may now log in to Microsoft Access to ensure that your data was properly copied. Microsoft Access is 26

Analyst QS Administrator s Guide your interface to the SQL Server. You must reassign any User IDs and Passwords to the newly created SQL Server database. The system administrator s User ID is sa. You do not need to specify a password. In Analyst, you must now specify the location of the SQL server database file. For more information refer to the procedure, To set the compound database optimization preferences. Configuring Tuning Tuning allows you to get the most out of your instrument. Analyst provides three automatic tuning tools: Mass calibration, which automatically ensures that mass peaks are assigned their correct mass-to-charge ratios. Resolution optimization, which automatically adjusts the peak resolution offset values for each selected mass. Quantitation optimization, which automatically optimizes the working parameters for a specific compound or compounds of the instrument with infusion and flow-injection devices. Tuning options and instrument options allow you to configure the mass calibration and resolution optimization. Setting the Tuning Options for Mass Calibration Set the tuning options before you begin a mass calibration. To set the tuning options for mass calibration: 1. In Configure or Tune mode, click Settings in the Tools menu. 2. In the list of settings and options, click Tuning Options. The Tuning Options dialog box appears. 3. In the Calibration tab of the Tuning Options dialog box, select the calibration standard to be used. 4. Select the polarity or polarities to be used. 5. Select the acquisition method and the reference. 6. Click OK. 27

Configuring Analyst Setting the Tuning Options for Resolution Optimization You can choose to perform a mass calibration automatically after optimizing the resolution successfully. You can also choose to update the values of the mass-dependent instrument parameters with the new values resulting from the resolution optimization. Set the tuning options for the resolution optimization before you begin. To set the tuning options for resolution optimization: 1. From the Tools menu, click Settings. 2. In the list of settings and options, click Tuning Options. 3. In the Resolution tab of the Tuning Options dialog box, type the peak width and the height at which the peak width is to be measured for the unit and high resolution definitions. The Mass Shift graph on the Mass Calibration report shows the difference between the value of the expected mass and the found mass on the current calibration. 4. Enter the Acceptable mass difference to determine the acceptance lines in this graphic report. 5. Enter the offset voltage drop from unit-resolution to define the low resolution and click OK. Setting the Instrument Options The instrument options allow you to define the quadrupole, polarity, and resolution to be used in an experiment. You can also adjust the detector instrument parameters. To set the instrument options: 1. From the Tools menu, click Settings. 2. In the list of settings and options, click Instrument Options. 3. In the Instrument Data Editor dialog box, select the quadrupole, resolution, and polarity or polarities. 4. Click OK. 28

Analyst QS Administrator s Guide Designing Report Templates The Report Template Editor provides a way to format reports using headers and footers, and create page layout for printed output. You can print any window, pane, or workspace that you can see on the screen. At this time, the Report Template Editor does not format full reports. Designing Headers and Footers Use design elements in headers or footers to provide additional information and to improve the look of your reports (or to make your report more visually appealing). Analyst allows you to add the following design elements to report headers and footers: Printing date Printing time Page number Operator Workstation Analyst version Custom text or graphics Refer to the online help for details on how to add these elements to report headers and footers. These additional design elements are available for use in report headers and footers: Acquisition elements Quantitation elements Acquisition Elements You can add elements relevant to the chromatogram or spectra to a header or footer. Currently available acquisition elements for use in headers and footers include: 29

Configuring Analyst Acquisition File Acquisition Date Acquisition Time Batch Name Sample Name Sample Comment Sample ID Scan Type and Polarity Scan Mode Scan Masses Dwell Time Pause Time Ion Energy Collision Energy Period & Experiment State Table Parameters For information about each of these items see the Acquisition Elements online help topic. Quantitation Elements You can format headers and footers to include results table and quantitation method information. Currently available quantitation elements include: Results Table Name Results Table Path Method Name Method Path Project Name 30

Configuring ExpressView Analyst QS Administrator s Guide ExpressView makes use of templates to facilitate the submission of single or multiple samples with minimal information. It can prevent inappropriate access to the system by limiting the type of information that can be input or edited. You must have administrator privileges to configure the ExpressView interface. To configure the ExpressView Editor: 1. Log in to Analyst as Administrator. 2. Select the Configure icon in the navigation bar. 3. From the Menu bar select Tools and then Configure ExpressView... The ExpressView Configuration dialog box appears. 4. Select an operation mode. Vial Mode: Select this option to allow users to add single autosampler vials. These vials are added at the next available sample position to an existing autosampler rack. In other words, ExpressView tells the user where the samples must be placed. Plate (or Rack) Mode: Select this option to allow the user to add an entire autosampler rack or plate, but not single samples. This mode is used with those autosamplers that have room for more than one plate or rack. In other words, the user tells ExpressView where the samples are on the plate. ExpressView tells the user where to add the plate. 31

Configuring Analyst 5. Select or clear system settings. Allow multiple samples: Select this option to allow users to specify and submit more than one sample at a time. Samples are placed sequentially according to the arrangement defined in the template. This field is overridden if the number of samples is defined in the batch template. Require custom parameters (if available): Select this option to change any custom parameter from optional to mandatory. The custom parameter(s) must then be defined in the batch template prior to submitting the samples. If this option is cleared, the fields are displayed but need not be completed. If there are no custom parameters in the selected template, the display is not shown and this field is irrelevant. 6. Enter and confirm a password to exit ExpressView and click OK. Password: Enter the password required to exit ExpressView. Creating a password is optional but is useful for preventing unauthorized users from accessing other areas of Analyst. Confirm Password: Enter the password a second time to confirm that you have typed the correct password. 32

Analyst QS Administrator s Guide Configuring Queue Options Setting Queue Options You can set the queue conditions before you begin a batch or sample. To set queue options: 1. In Configure mode, choose Settings then Queue Options in the Tools menu. The Queue Options dialog box appears. Max. Num. Acquired Samples: Type the maximum number of acquired samples that you want to be maintained in the queue. Once this number of acquired samples is reached, Analyst deletes approximately half of the acquired samples starting with the earliest. Max. Idle Time: Enter the maximum amount of time you want an instrument to wait in Ready mode before going into Standby mode automatically. Max. Tune Idle Time: Enter the maximum amount of time you want an instrument to idle in Tune mode before going into Standby mode automatically. Max. Pending Time: This field is currently not in use. 33

Configuring Analyst Disk Space Threshold: Enter the minimum disk space needed to submit the next batch. Failed whole Batch in case of missing vial: Check this box if you wish the whole batch to fail if a sample is missing. 2. To change the default values for any of the queue options, click in the relevant area, enter the new value, and then click OK. Configuring the Columns in the Queue The Queue Manager allows you to specify which of the available columns you wish to see in your project. You can select any combination of columns. You can also change the width of columns in the queue to see all the contents of a column. You can also change the location of a column. To show or hide a column: 1. In Tune mode, choose Sample Queue from the View menu. 2. Right-click anywhere in the column. 3. Choose Column Settings from the menu that appears. The Column Settings dialog box appears. Several types of information are available in this dialog box: Sample information, such as row number, start time, ID number, name, and sample location on rack or plate. Queue information, such as sample status in the queue, project and data file names, and synchronization mode. Batch information, such as batch name, acquisition method used in the batch, and name of the user who submitted the batch. 4. Select the check box beside a column to show it; clear the check box to hide it. All items are read-only. To change the width of a column: 1. Place the cursor on a column divider in the bar above the column. 2. Drag the cursor until the divider shows the desired width. To return the column to its original width, drag the cursor in the opposite direction. 34

Analyst QS Administrator s Guide To change the location of a column: 1. Select the column you wish to move. 2. Drag the column to the new location and release the cursor. A red line between columns indicates the location to which the column has been moved. 35

Configuring Analyst 36

4 Support If you encounter problems configuring or using Analyst, consult the following documentation for assistance before contacting support: Analyst online Help Release notes Where to Go for Help If you have a technical question or request for assistance please contact Applied Biosystems/MDS SCIEX support. Toll Free (North America only): 1-800-831-6844 Web: http://www.appliedbiosystems.com 37

Support 38

Index A access configuring 21 instrument workstations 22 access rights exported files 22 acquisition elements report templates 29 activating hardware profiles 14 adding users 18 adjusting column width 34 assigning users 20 C changing column location 35 choosing security modes 15 column location changing 35 columns adjusting width 34 configuring 34 hiding 34 showing 34 compound database editor configuring 23 configuring access 21 Analyst 11 columns 34 compound database editor 23 device drivers 13 ExpressView 31 peripherals 12 Analyst QS Administrator s Guide project security 21 security 14 tuning 27 creating hardware profiles 13 user types 19 D data-processing workstations 7 default projects 9 design elements report templates 29 devices drivers configuring 13 E exported files access rights 22 ExpressView configuring 31 F files security 9 structure 8 formatting reports 29 H hardware profiles activating 14 creating 13 hiding columns 34 39

I instrument options setting 28 instrument workstations 7 access 22 M mass calibration tuning options 27 O overview configuring Analyst 11 report templates 29 P peripherals configuring 12 project security configuring 21 projects default 9 Q quantitation elements report templates 30 queue options setting 33 R report templates acquisition elements 29 design elements 29 overview 29 quantitation elements 30 reports formatting 29 resolution optimization tuning options 28 S security configuring 14 files 9 security modes choosing 15 setting 16 setting instrument options 28 queue options 33 security modes 16 user types 16 showing columns 34 structure files 8 T tuning configuring 27 tuning options mass calibration 27 resolution optimization 28 U upsizing compound database 24 user types creating 19 setting 16 users adding 18 assigning 20 using SQL server 24 40

Analyst QS Administrator s Guide W workstations data-processing 7 instrument 7 41

Index 42