xcalibur 2.1 and 21 cfr part 11 compliance administrator...

Thermo Xcalibur Xcalibur System and 21 CFR Part 11 Compliance

Administrator Guide

XCALI-97208 Revision A January 2009

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Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
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The contents of this document are subject to change without notice. All technical information in this document is for reference purposes only. System configurations and specifications in this document supersede all previous information received by the purchaser.

Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might result from any use of this document, even if the information in the document is followed properly.

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Release history: The Xcalibur manuals support Xcalibur version 2.1 and above.

For Research Use Only. Not regulated for medical or veterinary diagnostic use by U.S. Federal Drug Administration or other competent authorities.

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Contents

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ixAbout This Guide. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ixRelated Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xSafety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xContacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi

Chapter 1 Configuring and Setting up Xcalibur System Components . . . . . . . . . . . . . . . . . . .1Configuring Xcalibur Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Opening the Xcalibur Configuration Dialog Box . . . . . . . . . . . . . . . . . . . . . . 2Selecting Default Folders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2Updating Customer Information. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3Configuring Fonts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4Selecting a Default Peak Detection Algorithm. . . . . . . . . . . . . . . . . . . . . . . . . 5Selecting Default Mass Options. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6Selecting Default Labeling and Scaling Options . . . . . . . . . . . . . . . . . . . . . . . 8Selecting Error Handling Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9Defining the Dataset List. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Converting File Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Chapter 2 Preparing Your Data System to be 21 CFR Part 11 Compliant . . . . . . . . . . . . . . . .13Major Requirements of 21 CFR Part 11 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Prevention of Data Falsification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14Data Reconstruction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14System Security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

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Xcalibur Software and Compliance with 21 CFR Part 11 . . . . . . . . . . . . . . . . . 17Configuring Software Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Configuring the Auditing Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17Protecting Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17Setting Up User Access Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Security Features Within the Software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18Becoming 21 CFR Part 11 Compliant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Chapter 3 Using the Database Configuration Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .21

Chapter 4 Establishing Secure File Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25Turning Off Fast User Switching for Local Workstations . . . . . . . . . . . . . . . . . 25Confirming the Properties of System Services . . . . . . . . . . . . . . . . . . . . . . . . . . 26Configuring Security Settings for Folders and Files . . . . . . . . . . . . . . . . . . . . . . 31

Working with Accounts Set up by Xcalibur. . . . . . . . . . . . . . . . . . . . . . . . . . 32Adding Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32Removing Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34Setting Permissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35Setting Permissions for Xcalibur Folders . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36Sequential User Logon and Automatic Logoff . . . . . . . . . . . . . . . . . . . . . . . . 38

Configuring Security Settings for the Database Registry Key . . . . . . . . . . . . . . . 40Removing and Archiving Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Chapter 5 Defining Secure User Groups and Adding Users . . . . . . . . . . . . . . . . . . . . . . . . . .45Planning User Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46Using the Authorization Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Defining User Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47Editing User Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49Setting Permissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Setting the Permission Levels for an Individual Feature . . . . . . . . . . . . . . . 50Setting All Permissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52Inheriting Permissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52Exporting and Importing Permissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Specifying Predefined Comments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53Viewing the Authorization Manager History Log . . . . . . . . . . . . . . . . . . . . . . . 54Printing the Security Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54Saving the Security Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Chapter 6 Using the CRC Validator. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55Checking Files With the CRC Validator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

Xcalibur System and 21 CFR Part 11 Administrator Guide Thermo Scientific

Contents

Selecting Files Using Database Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58Selecting Files Using a Pattern. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Chapter 7 Auditing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61Accessing the Auditing Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

Accessing the Global Auditing Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62Accessing an LCquan Workbook Database . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Viewing Audit Viewer Pages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64Filtering Audit Viewer Entries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65Sorting Audit Viewer Entries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66Printing the Audit Viewer Entries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

Printing the Audit Trail for the Global Auditing Database . . . . . . . . . . . . . . 67Printing the Audit Trail for an LCquan Workbook Database . . . . . . . . . . . . 67

Appendix A Installing an Oracle Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .69Installing the Oracle Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70Installing the Oracle Client . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

Appendix B Reference Tools. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .87Command Line Arguments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87ExcelExp.exe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90XConvert.exe. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92

Appendix C System Administration Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .95

Thermo Scientific Xcalibur System and 21 CFR Part 11 Administrator Guide v

Xcalibur System Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95Configuring Xcalibur. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96

Xcalibur Configuration Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96Configuring the System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

Add Programs To Tool Menu Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . 104Add Tool Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104Comment Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105Customize Toolbar Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105Dataset Name Selector Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106File Converter Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106File Save - Audit Trail Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110File Summary Information Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . 110Password Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110Print Selection Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111Select Directory/Select Data Directory Dialog Box . . . . . . . . . . . . . . . . . 111Supervisor Permission Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112View Audit Trail Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112Spectrum Ranges Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112

Configuring Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113Instrument Configuration Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . 113Out Of Date Instrument Drivers Detected Dialog Box . . . . . . . . . . . . . . 115

Instrument Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116File Menu for the Instrument Setup Window . . . . . . . . . . . . . . . . . . . . . 118Instrument menu for the Instrument Setup Window . . . . . . . . . . . . . . . . 119Help Menu for the Instrument Setup Window . . . . . . . . . . . . . . . . . . . . 119Instrument Setup Window Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120

Xcalibur Administrator Utilities for Compliance with 21 CRF Part 11 . . . . . . 121Audit Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122

All Page, Audit Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123History Page, Audit Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124Event Page, Audit Viewer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125File Tracking Page, Audit Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126Instrument Error Page, Audit Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127Sort Entries Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129Print Options Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129Filter Entries Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130

Auditing Database Configuration Manager . . . . . . . . . . . . . . . . . . . . . . . . . 131Xcalibur Authorization Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133

Choose Secure Group Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147Create Private Group and Edit User List Of Private Group Dialog Boxes 147Edit Comment List Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148Users In Group Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148New Comment Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148

CRC Validator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149

Contents

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

Thermo Scientific Xcalibur System and 21 CFR Part 11 Administrator Guide vii

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i Xcalibur System and 21 CFR Part 11 Administrator Guide Thermo Scientific

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Preface

This administrator guide describes how to provide system administration for standard system operation using the Thermo Xcalibur™ mass spectrometry data system and how to configure specific Xcalibur applications to help an organization become compliant with the Electronic Records and Electronic Signatures Rule, published by the United States Food and Drug Administration as 21 CFR Part 11.

To provide us with comments about this document, please click the link below. Thank you in advance for your help.

About This GuideThis Administrator Guide has the following topics:

• Configuring and Setting up Xcalibur System Components

• Preparing Your Data System to be 21 CFR Part 11 Compliant

• Establishing Secure File Operations

• Defining Secure User Groups and Adding Users

• Using the CRC Validator

• Installing an Oracle Database

• System Administration Reference

Contents

• About This Guide

• Related Documentation

• Safety and Special Notices

• Contacting Us

Thermo Scientific Xcalibur System and 21 CFR Part 11 Administrator Guide ix

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Preface

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Related DocumentationThermo Fisher Scientific provides these documents for Xcalibur:

• Xcalibur Getting Started (Quantitative Analysis)

• Acquisition and Processing User Guide

• Quantitative Analysis User Guide

• Qualitative Analysis User Guide

• Creating and Searching Libraries User Guide

• XReport User Guide

• Xcalibur System and 21 CFR Part 11 Compliance Administrator Guide

• Help from within the software

Safety and Special NoticesMake sure you follow the precautionary statements presented in this guide. The safety and other special notices appear in boxes.

Safety and special notices include the following:

CAUTION Highlights hazards to humans, property, or the environment. Each CAUTION notice is accompanied by an appropriate CAUTION symbol.

IMPORTANT Highlights information necessary to prevent damage to software, loss of data, or invalid test results; or might contain information that is critical for optimal performance of the system.

Note Highlights information of general interest.

Tip Helpful information that can make a task easier.


Preface

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Contacting UsThere are several ways to contact Thermo Scientific for the information you need.

To contact Technical Support

Find software updates and utilities to download at mssupport.thermo.com.

To contact Customer Service for ordering information

To copy manuals from the Internet

Go to mssupport.thermo.com and click Customer Manuals in the left margin of the window.

To suggest changes to documentation or to Help

• Fill out a reader survey online at www.thermo.com/lcms-techpubs.

• Send an e-mail message to the Technical Publications Editor at [email protected].

Phone 800-532-4752Fax 561-688-8736E-mail [email protected] base www.thermokb.com

Phone 800-532-4752Fax 561-688-8731E-mail [email protected] site www.thermo.com/ms

hermo Scientific Xcalibur System and 21 CFR Part 11 Administrator Guide xi

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1

Configuring and Setting up Xcalibur System Components

To configure and set up Xcalibur system components for use, read these topics.

Configuring Xcalibur SoftwareConfigure Xcalibur using the Xcalibur Configuration dialog box. Use the pages in the dialog box to define the location of data, methods, and report templates on your data system; to edit customer information; to select the fonts that you want to use; and to select error handling options.

To configure Xcalibur, do these procedures:

1. Opening the Xcalibur Configuration Dialog Box

2. Selecting Default Folders

3. Updating Customer Information

4. Configuring Fonts

5. Selecting a Default Peak Detection Algorithm

6. Selecting Default Mass Options

7. Selecting Default Labeling and Scaling Options

8. Selecting Error Handling Options

9. Defining the Dataset List

Contents

• Configuring Xcalibur Software

• Converting File Formats

Thermo Scientific Xcalibur System and 21 CFR Part 11 Administrator Guide 1

1 Configuring and Setting up Xcalibur System ComponentsConfiguring Xcalibur Software

2

Opening the Xcalibur Configuration Dialog Box

To open the Xcalibur Configuration dialog box

1. Choose Start > Programs > Thermo Xcalibur > Xcalibur from the Windows™ desktop. The Home Page window opens.

2. Choose Tools > Configuration from the Roadmap view of the Home Page window. The Xcalibur Configuration dialog box opens.

Selecting Default Folders

To select Xcalibur default folders

1. Click the Folders tab. The Folders page of the Xcalibur Configuration dialog box opens (see Figure 82).

Figure 82. Folders page

2. To locate and select your data folder, click Browse.

3. To locate and select your method folder, click Browse.

4. To locate and select the default folder for your report templates, click Browse.

5. To save your settings, click OK.



Updating Customer Information

The Customer Info page of the Xcalibur Configuration dialog box displays the current licensing information for your Xcalibur MS detector. If this information is not already entered or it is incorrect, update the current entries.

To update customer information

1. Click the Customer Info tab. The Customer Info page of the Xcalibur Configuration dialog box opens (see Figure 83).

Figure 83. Customer Info page

2. If the information on the Customer Info page is incomplete or incorrect, type the new information.




4

Configuring Fonts

Grid plots in Xcalibur use both a fixed pitch font and a proportional font. The Xcalibur default fixed pitch font is Courier New with a minimum size of 7 points and a maximum size of 12 points. The Xcalibur default proportional font is Arial with a minimum size of 7 points and a maximum size of 12 points. To use other fonts, font styles, or font sizes, change the font settings.

To configure Xcalibur Fonts

1. Click the Fonts tab. The Fonts page of the Xcalibur Configuration dialog box opens (see Figure 84).

Figure 84. Fonts page

2. [Optional] To select a fixed pitch font, select a font name in the Fixed Pitch Font list. The selected font name is displayed at the top of the list.

a. Enter the minimum size of the selected font in the Min list.

b. Enter the maximum size of the selected font in the Max list.

c. View the font sample, minimum size (top) and maximum size (bottom), in the Fixed Pitch Font Preview area.

3. [Optional] To select a proportional font, select a font name in the Proportional Pitch Font list. The selected font name is displayed at the top of the list.

a. Enter the minimum size of the selected font in the Min list.



b. Enter the maximum size of the selected font in the Max list.

c. View the font sample, minimum size (top) and maximum size (bottom), in the Proportional Pitch Font Preview area.


Selecting a Default Peak Detection Algorithm

Use the Peak Detection page of the Xcalibur Configuration dialog box to view or change the default peak detection algorithms for all data types.

To specify peak detection parameters

1. Click the Peak Detection tab. The Peak Detection page of the Xcalibur Configuration dialog box opens (see Figure 85).

Figure 85. Peak Detection page

2. To select the Default Peak Detection Algorithm for MS Data, click an algorithm name from the corresponding list.

Note In the Spectrum list view, if Xcalibur displays the elemental composition values in light gray, close Qual Browser and choose Xcalibur Roadmap > Tools > Configuration to display the Configuration page. Select the Fonts tab and set all font sizes to a minimum of 10 points.



6

3. To select the Default Peak Detection Algorithm for PDA/UV Data, click an algorithm name from the corresponding list.

4. To select the Default Peak Detection Algorithm for Other Data Types, click an algorithm name from the corresponding list.


Selecting Default Mass Options

Use the Mass Options page of the Xcalibur Configuration dialog box to view or specify default parameter values that affect mass calculations and library searches.

To specify mass options

1. Click the Mass Options tab. The Mass Options page of the Xcalibur Configuration dialog box opens (see Figure 86).

Figure 86. Mass Options page

2. Specify a default value for mass tolerance:

a. Select the Use user defined check box in the Default Mass Tolerance area. This activates the Mass tolerance box.

b. Type a value from 0.1 to 50000 in the Mass tolerance box.

c. Select either mmu (millimass units) or ppm (parts per million) from the Units options.



3. To specify a default value for mass precision, type a value from 0 to 5 in the Decimals box.

4. To specify the Default mass defects for lower values of mass, type a value from -2500 to 2500 in the first Defect box. Then, type a mass value from 0 to 10000 in the first at mass box.

For example, enter a value of 50 in the Defect box for a value of 200 in the at mass box.

5. To specify the Default mass defects for higher values of mass, type a value from -2500 to 2500 in the second Defect box. Then, type a mass value from 0 to 10000 in the second at mass defect mass box.

For example, enter a value of 1000 in the Defect box for a value of 5000 in the at mass box.




8

Selecting Default Labeling and Scaling Options

Use the Labeling and Scaling page of the Xcalibur Configuration dialog box to view or change default parameter values for labels and scales of the Y-axes in spectrum and chromatogram plots.

To specify labeling and scaling parameters

1. Click the Labeling and Scaling tab. The Labeling And Scaling Page of the Xcalibur Configuration dialog box opens (see Figure 87).

Figure 87. Labeling and Scaling page

2. In the Labeling options area, to specify the Label for MS Data, select From Detector or Custom from the corresponding list.

If you select Custom, enter a label in the adjacent box.

3. To specify the Label for PDA/UV Data, select From Detector or Custom from the corresponding list.


4. To specify the Label for Other Data Types (other than MS and PDA/UV), select From Detector or Custom from the corresponding list.


5. In the Use Absolute Scale area, select the data types to display on the Y-axis.



6. In the Retention time precision area, type the number of decimal places to include when reporting retention times.


Selecting Error Handling Options

Use the Intelligent Shutdown (Error Handling) page of the Xcalibur Configuration dialog box to define how Xcalibur responds when an error occurs during data acquisition.

To change the error handling option

1. Click the Intelligent Shutdown tab. The Intelligent Shutdown (Error Handling) page of the Xcalibur Configuration dialog box opens (see Figure 88).

Figure 88. Error Handling page

2. Select the error handling option, Attempt to stop the devices and pause the sequence.




10

Defining the Dataset List

As administrator, use the Dataset List page of the Xcalibur Configuration dialog box to define or edit the list of dataset names that the user can choose from when selecting a dataset.

To define the list of dataset names

1. Click the Dataset List tab. The Dataset List page of the Xcalibur Configuration dialog box opens (see Figure 89).

Figure 89. Dataset List page

2. To specify the name for Xcalibur to use for a dataset, either select a name from the Display Name list, or add a new name to the list by doing the following:

a. Click Add New Dataset Name. The Create New Dataset Name dialog box opens.

b. Type a name in the box and click OK. The new name appears in the Study list to the left.

3. If necessary, repeat steps a and b to add more names to the list.

4. To delete a name from the list, select the name in the Study list and click Remove Selected Dataset Name.

Note If you change the display name to something besides Dataset, Xcalibur renames the parameters on this page to reflect the change.


1 Configuring and Setting up Xcalibur System ComponentsConverting File Formats

5. To specify whether a blank study name is a valid selection:

• Select the Blank Dataset name is a valid selection check box to allow a user to select a blank name when asked to select a dataset in the Dataset Name Selector dialog box.

• Clear this check box to require the user to select a valid dataset.

6. To specify whether the selection is restricted to the entered names:

• Select the Selection restricted to entered names check box to specify that only the names listed in the Study List appear in the Dataset Name Selector dialog box.

• Clear this check box to specify that the names listed in the Study List as well as a those obtained from the database appear in the Dataset Name Selector dialog box.

7. To specify the maximum number of names to display in the Dataset Name Selector dialog box, type a number in the Maximum number of names to display box.


Converting File FormatsTo convert files from one file format to another using the File Converter dialog box

1. Choose Tools > File Converter from the Roadmap view of the Home Page window. The File Converter Dialog Box opens (see Figure 90).

Figure 90. File Converter dialog box


1 Configuring and Setting up Xcalibur System ComponentsConverting File Formats

12

2. To specify the source data type of the files you want to convert, select from the Source data type list in the Conversion source area.

You can only batch process files with one source data type and one destination data type at a time. You can perform other data type conversions in separate batches.

3. To select the files to be converted, click Browse and select the folder that contains the files.

The files appear in the Conversion Source list. Xcalibur displays the File Name, Type, Size, and Date.

4. Create a list of files to convert using one of the following options:

• To convert all of the files in the Conversion Source list, click Select All. All of the files appear on the Jobs page in the Conversion destination area at the bottom.

• To convert a single file from the Conversion Source list, select the file and then click Add Job(s).

• To delete a file that appears in the Conversion source list, select the file and then click Clear Selection.

5. To specify the destination data type of the files you want to convert, select from the Destination data type list in the Conversion destination area.

6. To select a destination folder, click Browse to search for a folder to hold the converted files.

The source files remain in their original directories.

7. To start the file conversion using batch processing of the files on the Jobs page, click Convert.

You can monitor progress by clicking the Status tab in the Conversion Destination area.

Xcalibur continues file conversion processing until all files are converted and stored in the specified destination folder.

• To convert other source files with a different format, go to step 8.

• If you are done converting files, go to step 9.

8. To convert a different source data type, click Clear Selection to clear all files displayed in the Conversion source list.

Repeat steps 2 through 7 for the other source data type.

9. To close the File Converter dialog box, click Close.


2

Preparing Your Data System to be 21 CFR Part 11 Compliant

Read this chapter to configure specific Xcalibur applications to help an organization become compliant with the Electronic Records and Electronic Signatures Rule, published by the United States Food and Drug Administration as 21 CFR Part 11.1

Compliance with 21 CFR Part 11 requires both technical and procedural compliance. To achieve technical compliance, the organization must use software that contains the required security features and functions. To achieve procedural compliance, the organization must establish standard operating procedures and policies that define how to use processes and systems in a compliant manner.

1Code of Federal Regulations, Title 21, Food and Drugs, Part 11 “Electronic Records: Electronic Signature Final Rule,” Federal Register 62 (54) 1997, 13429-13466. The final rule is also available electronically at http://www.fda.gov/ora/compliance_ref/part11/.

Contents

• Major Requirements of 21 CFR Part 11

• Xcalibur Software and Compliance with 21 CFR Part 11

• Becoming 21 CFR Part 11 Compliant


2 Preparing Your Data System to be 21 CFR Part 11 CompliantMajor Requirements of 21 CFR Part 11

14

Major Requirements of 21 CFR Part 11In August 1997, the United States Food and Drug Administration published a rule for electronic records and electronic signatures under the current good manufacturing practice (cGMP) regulations in the Code of Federal Regulations (21 CFR Part 11). To make electronic records and electronic signatures equivalent to paper records and handwritten signatures, an organization must follow the rule. This rule also permits the widest possible use of electronic technology.

An important implication in 21 CFR Part 11 is that organizations must implement rules to confirm that proper methods, procedures, and controls are in place. As a result, these issues must be addressed:

• Prevention of Data Falsification

• Data Reconstruction

• System Security

Prevention of Data Falsification

Electronic data can be falsified in several ways: through direct modification; indirectly, through record deletion; or indirectly, through use of readily available tools.

To prevent falsification, the organization must implement a number of controls. These controls can be procedural in nature or can be functionally implemented within the system generating the electronic records. Normally, a system combines both methods to achieve compliance.

To help prevent data falsification, Xcalibur (designed for compliance with 21 CFR Part 11) uses audit trails and system security.

Data Reconstruction

Although it is important to demonstrate that data has not been falsified, it is just as important to show how it has been generated. Raw data cannot be reconstructed; however, it is possible to regenerate all other records derived from the original raw data files.

To confirm that all electronic records generated from the raw data can be regenerated, an efficient and comprehensive audit trail must fulfill these criteria:

• Account for all events and actions that are required to regenerate the records.

• Add new audit trail entries to existing records only. Do not overwrite or obstruct other records.

• Prevent the user from having any control of the audit trail records or modifying the configuration of the audit trail.

The audit trails that Xcalibur creates meet these requirements.



System Security

Most organizations implement strict security procedures for their computer networks to prevent unauthorized access to data. In this context, unauthorized access means:

• Access by an individual (external or internal to the organization) who has not been granted the authority to use, manipulate, or interact with the system

• Access through the use of the identity of another individual, for example, by using a colleague’s username and password

Controls to confirm appropriate access of records

The 21 CFR Part 11 rule defines a number of controls to confirm that the systems that generate electronic records can be accessed only by individuals who have some level of responsibility towards those records. The rule includes both procedural controls and functionality controls.

Xcalibur (designed for compliance with 21 CFR Part 11) implements some of these controls directly and relies on the security functions in your computer operating system for other parts. For example:

• The Finnigan Security Server controls secure file operations.

• The administrator restricts user access through the Xcalibur Authorization Manager (a Thermo Fisher Scientific-supplied administrative tool).

• The administrator controls software feature access through the Xcalibur Authorization Manager.

• Your computer security functions manage user authentication.

• Your computer security functions and, in particular, the NTFS permission rights maintain electronic record security.



16

Configuring Antiviral Software to support 21 CFR Part 11

To configure Antivirus software on data acquisition computers, use these suggestions for best results. This information is not intended to replace or supersede procedures on computer configuration and validation.

• Avoid running full system scans with the antivirus software while acquiring data. Some antiviral software routines make very aggressive use of system resources, interfering with data acquisition routines and causing loss of communication. Consider full system scans as maintenance—to be done when the system is not acquiring.

• Avoid running optimization utilities, such as hard disk defragmentation, while acquiring. These can also monopolize computer resources and cause loss of communication.

• Make sure the firewall settings include exceptions for the instruments in use. Most instrument software now configures the required exception for the Microsoft™ Windows firewall automatically upon installation. If the firewall exception is not configured, the computer cannot communicate with the device.

These exceptions might include these executables:

• TSQInstManager.exe (Quantum™ mass spectrometer)

• LTQManager.exe (LTQ™ ion trap mass spectrometer)

• Agilent1100.exe (Agilent™ 1100 HPLC systems)

• Surveyor.exe (Surveyor™ HPLC systems)

• Waters2795VI.exe (Waters™ HPLC systems)

• Note the directories typically used during acquisition:

• C:\Documents and Settings\(Current user)\Local Settings\Temp

• C:\Documents and Settings\Xcalibur_system\Local Settings\Temp

• C:\Xcalibur\methods [or the directory where instrument and processing method files (.meth and .pmd) are stored]

• C:\Xcalibur\data [or the directories where raw files (.raw) are stored]

• C:\Xcalibur\system\programs\

• C:\Thermo\system


2 Preparing Your Data System to be 21 CFR Part 11 CompliantXcalibur Software and Compliance with 21 CFR Part 11

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Xcalibur Software and Compliance with 21 CFR Part 11Xcalibur incorporates security features and functions to enable Xcalibur applications to comply with 21 CFR Part 11. It is crucial that the laboratory administrator configures the software properly to fully implement these security features.

This section contains the following topics:

• Configuring Software Applications

• Security Features Within the Software

Configuring Software Applications

Configuring Xcalibur software applications for compliance with 21 CFR Part 11 involves three steps:

• Configuring the Auditing Database

• Protecting Records

• Setting Up User Access Controls

Configuring the Auditing Database

The auditing database is critical in enabling Xcalibur applications to comply with 21 CFR Part 11. The database confirms that data cannot be deleted or altered without a record being kept and keeps an audit log of parameter changes made in Xcalibur applications.

See Chapter 3 for the procedure on configuring the auditing database.

Protecting Records

To establish secure file operations, the laboratory administrator must grant access permissions for specific folders, files, and registry keys. System permissions must be set so that only an administrator can delete or alter security related records, such as the Authorization Manager and Database Configuration settings. These settings make sure unauthorized users cannot alter the security settings for Xcalibur applications.

See Chapter 4 for the procedure on creating protected folders, files, and registry keys.

hermo Scientific Xcalibur System and 21 CFR Part 11 Administrator Guide 17

2 Preparing Your Data System to be 21 CFR Part 11 CompliantXcalibur Software and Compliance with 21 CFR Part 11

18

Setting Up User Access Controls

To control user access, the laboratory administrator must define secure user groups and grant access permissions for each group. The administrator can restrict defined groups of users from performing various functions within the application software. This restriction can range from complete prohibition, through several levels of password-required access, to no restrictions. User access controls are set through the Xcalibur Authorization Manager.

After the security settings are defined for at least one group, users who are not in a secure group are denied access to the application. However, when no secure groups are defined, all users can access all features of the software!

See Chapter 5 for the procedure on defining user groups and granting access permissions.

Security Features Within the Software

After an administrator has defined the appropriate file protections and user access controls, Xcalibur applications use a number of built-in features to confirm the security of the data and to meet 21 CFR Part 11 requirements.

Xcalibur includes a file tracking system that maintains a database of the files created in or used by Xcalibur applications. The file tracking system uses the file journaling features of the Windows operating system, recording all changes or deletions made to files stored in the database, even if the changes are made using a non-Xcalibur application such as Windows™ Explorer™.

With Xcalibur’s comprehensive audit trail you can regenerate all electronic records generated from the raw data. The audit trail consists of two parts: the history log and the event log. The history log contains information about every parameter change that a user has made within the application. The event log contains information about all of the events that have occurred within the application, such as the creation of a sequence or the saving of a file.

The CRC Validator performs Cyclic Redundancy Checks (CRCs) to protect against malicious changes to data files. A CRC can detect file corruption and attempted changes to data files outside of Xcalibur applications. The CRC calculates checksums for sets of data using mathematical formulas and stores the value in the auditing database. When data are modified or processed within the application, CRC calculates and stores new checksums. The stored checksums can be compared with checksums calculated from the files stored on the disk using the CRC Validator application. A mismatch between the stored and computed checksums might indicate file corruption or tampering.


2 Preparing Your Data System to be 21 CFR Part 11 CompliantBecoming 21 CFR Part 11 Compliant

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Becoming 21 CFR Part 11 CompliantThese chapters provide the following information:

• How to configure the auditing database

• How to establish secure file operations

• How to define secure user groups and add users

Complete the procedures that are outlined in Table 1 and described in detail in the identified chapters. This table also serves as a checklist to make sure you do all of the tasks to configure Xcalibur applications for compliance with 21 CFR Part 11.

Table 1. Checklist of tasks for configuring Xcalibur software applications for compliance with 21 CFR Part 11

Task See Topic Completed?

Install the latest version of Xcalibur and Xcalibur Foundation software.

Install the layered software applications.

If necessary, install the Oracle client and server software on the appropriate workstations (only when Oracle is used for the auditing database).

Appendix 8, “Installing an Oracle Database.”

Configure the auditing database. “Using the Database Configuration Manager” on page 21.

Confirm that the Finnigan Security Server is set up properly and is running.

“Confirming the Properties of System Services” on page 26.

Restrict access to the registry key for the auditing database. “Configuring Security Settings for the Database Registry Key” on page 40.

Decide how many and what type of user groups you need. “Planning User Groups” on page 46.

Define user groups in the Authorization Manager. “Defining User Groups” on page 47.

Set permission levels for software features for each user group. “Setting Permissions” on page 49.

Save the configuration settings. “Saving the Security Settings” on page 54.


3

Using the Database Configuration Manager

This chapter describes how to use the Database Configuration Manager to configure your compliance database. The compliance database keeps a record of auditable events and changes made to files that Xcalibur either creates or manages. Until you run the Database Configuration manager, all applications run without auditing, and the system is not 21 CFR Part 11 compliant.

Use the Database Configuration manager to configure either a Microsoft Access™ database on your local computer or an Oracle database on a remote computer. To use an Oracle database, confirm that the following tasks have been completed:

• An Oracle database has been installed on an accessible remote server. Consult your Oracle database administrator for more information or see Appendix 8, “Installing an Oracle Database.”

• The Oracle client software has been installed on your local computer. Consult your Oracle database administrator for more information or see Appendix 8, “Installing an Oracle Database.”

• Make sure that you know the User Name, Password, and Oracle Net Service Name of your Oracle database. Obtain this information from your Oracle database administrator.

Note Confirm that no other Xcalibur applications are running when running the Database Configuration manager. Xcalibur cannot audit Xcalibur applications while running the Database Configuration manager.


3 Using the Database Configuration Manager

22

To use the Database Configuration manager to configure your auditing database

1. From the Windows taskbar, choose Start > All Programs > Thermo Foundation 1.0 > Database Configuration. The Auditing Database Configuration Manager dialog box opens (see Figure 1).

Figure 1. Auditing Database Configuration Manager dialog box

2. Select the database type in the Select Database Type area:

• When using a Microsoft Access database, select the Microsoft Access option and go to step 4.

• When using an Oracle database, select the Oracle on Network Server option and go to step 3.

3. To use an Oracle database, specify the Oracle database parameters:

a. Type the database user name in the User Name box.

b. Type the database password in the Password box.

c. Select the Oracle Net Service Name for your database in the Oracle Net Service Name list.

IMPORTANT Be sure to use the Oracle user name and password provided by your Oracle database administrator.



T

4. Click Next. The DatabaseConfigManager dialog box opens (see Figure 2).

Figure 2. DatabaseConfigManager dialog box

5. Confirm that the settings are correct and click OK.

The appearance of the Auditing Database Configuration Manager dialog box is similar to Figure 3.

Figure 3. Auditing Database Configuration Manager dialog box, showing restart settings



24

6. Select a restart option:

• To have the computer restart automatically after you click Finish, select the Restart Computer Now option.

• To restart the computer manually at a later time, select the I Will Restart Later option.

7. Click Finish to save your settings and close the Auditing Database Configuration Manager dialog box.

IMPORTANT The changes you make in the Database Manager do not take effect until you restart the computer.


4

Establishing Secure File Operations

The 21 CFR Part 11 rule requires that record changes cannot obscure previously recorded information. It also requires that records be protected to enable their accurate and ready retrieval. To comply with these requirements, standard operating procedures must be established for precise and systematic record archiving.

This chapter describes how to configure the required operating system security settings to make sure the auditing database, authorization manager, and other security features of Xcalibur 2.0 operate correctly.

Turning Off Fast User Switching for Local WorkstationsSome operating systems let you switch between users without actually logging off from the computer. This feature, called Fast User Switching, can be turned off so that the current user must log off before another user logs on.

To maintain secure file operations, turn off Fast User Switching on all computers that allow it.

• Windows XP Professional operating system allows Fast User Switching on computers that are not members of a network domain.

• Windows Vista operating system allows Fast User Switching on all computers.

To turn off Fast User Switching

1. From the Windows XP taskbar, choose Start > Control Panel to open the Control Panel.

2. Double-click User Accounts.

Contents

• Turning Off Fast User Switching for Local Workstations

• Confirming the Properties of System Services

• Configuring Security Settings for Folders and Files

• Configuring Security Settings for the Database Registry Key

• Removing and Archiving Files


4 Establishing Secure File OperationsConfirming the Properties of System Services

26

3. Under Pick A Task, click Change The Way Users Log On And Off to open the Select Logon And Logoff Options page.

4. Clear the Use Fast User Switching check box.

5. Click Apply Options.

6. Close the User Accounts dialog box.

7. Close the Control Panel.

When a user logs off, the computer automatically shuts down any programs that are running.

Confirming the Properties of System ServicesThe authorization and auditing functions of Xcalibur applications rely on two system services: the Finnigan Security Server and the Finnigan Database Server. These services are installed when the administrator installs the application software. They are configured to start automatically every time the workstation is restarted.

The main function of the Finnigan Security Server is user authentication. If certain events require authentication, the user names and passwords entered are verified by the Finnigan Security Server.

With the Finnigan Database Service, Xcalibur applications can access the auditing database and make auditing entries.

To confirm that the properties of the Finnigan Security Server and Finnigan Database Service are set correctly

1. To open the Services window, choose Start > Settings > Control Panel from your computer taskbar, double-click Administrative Tools, and double-click Services.

2. Confirm properties for the Finnigan Security Server:

a. Right-click Finnigan Security Server and choose Properties from the shortcut menu. The Finnigan Security Server Properties dialog box opens (see Figure 4).

IMPORTANT You must also clear the User Welcome Screen check box.



Figure 4. General page

b. On the General page, in the Startup type list, select Automatic.

c. Confirm that Service status reads Started.

d. Click the Log On tab to display the Log On page (see Figure 5).



28

Figure 5. Log On page

e. Under Log on as, select the Local System account option.

f. Select the Allow service to interact with desktop check box.

g. Click OK to close the dialog box.



3. Confirm properties for Finnigan Database Service:

a. Right-click Database Service and choose Properties from the shortcut menu. The Finnigan Database Service Properties dialog box opens (see Figure 6).

Figure 6. General page

b. On the General page, in the Startup type list, select Automatic.

c. Confirm that Service status reads Started.



30

d. Click the Log On tab to display the Log On page (see Figure 7).

Figure 7. Log On page

e. Under Log on as, select the Local System account option.

f. Clear the Allow service to interact with desktop check box.

g. Click OK to close the dialog box.

4. Close the Services window and close the Administrative Tools window.


4 Establishing Secure File OperationsConfiguring Security Settings for Folders and Files

Configuring Security Settings for Folders and FilesTo confirm the security of your data, restrict access to the folder named security (located by default in C:\Xcalibur\system) that contains the configuration files. Because the Authorization Manager reads the controlled feature information from the configuration files, prohibit access to these files by non-administrators.

Set up specific user group access to folders and files with the NTFS file system (an advanced file system used within the computer operating system). When you set up permissions, specify the level of access for user groups, for example:

• Permit members of one user group to read the contents of a file.

• Permit members of another user group to make changes to the file.

• Prevent members of all other user groups from accessing the file.

New subfolders and files inherit folder permissions automatically. After you set the appropriate permissions, an unauthorized user cannot maliciously or accidentally alter the contents of the folder with utilities such as Windows Explorer.

In the procedures that follow, add an administrative user (or administrative group) and the Everyone group to the Security page Group or user names list. Grant the administrator full access to the security folder and read-only access to everyone else.

Continue with the following procedures:

• Working with Accounts Set up by Xcalibur

• Adding Users

• Removing Users

• Setting Permissions for Xcalibur Folders

Tip When you require more restricted access to folders and files, grant access to only specific user groups. Set up appropriate user groups (see Chapter 5, “Defining Secure User Groups and Adding Users.” Complete the procedures that follow, but use your specific user groups, instead of the Everyone group.



32

Working with Accounts Set up by Xcalibur

To support system security, Xcalibur sets up these files:

If you delete these files, recover them with the following actions:

Adding Users

Before setting permission levels for a folder or registry key, you might need to add users and groups to the Groups or User Names list on the Security page.

To add users and groups

1. Locate the Xcalibur folder in Windows Explorer. (The default path is C:\Xcalibur.)

Xcalibur_System Xcalibur creates this account with administrative privileges. The account name and password are embedded. The account is not interactive. No one ever logs on to this account except Xcalibur itself. Proteomics™ Browser (software included on the BioWorks product CD) requires the installation of IIS to run correctly. Do not delete this file.

IUSR_localPCname

IWAM_localPCname

Installing IIS creates these two accounts. The expression localPCname in the user account name represents the name of your local PC. All accounts appear to interface with Microsoft’s IIS 5.0 for either starting out of process accounts, using anonymous access, or running .NET objects.

ASPNETASPNET.postgres (user account)

Proteomics Browser also creates two additional accounts upon installation:

Might have been installed by a non-Thermo Scientific application. Our layered application Prosite uses the Microsoft asp.net network framework and creates a user account.

ProtUserBioworks 3.2 and later. Created by Proteomics Browser upon installation.

If you deleted this file Action to restore

Xcalibur_System Reinstall the Thermo Xcalibur Foundation software.

IUSR_localPCname

IWAM_localPCname

Reinstall IIS using the instructions in the CD jewel case and the user guide for Bioworks Browser. Apply for the license to be renewed.

ASPNETpostgresProtUser

If installing Prosite installed this file, then reinstall Prosite. If ASPNET was installed by your IT department or another application, then get instructions from the responsible party locally.

Reinstall Proteomics Browser using the instructions in the CD jewel case and the user guide for Bioworks Browser.



2. Right-click the Xcalibur folder and choose Properties from the shortcut menu. The Properties dialog box for the folder opens.

3. Click the Security tab to display the Security page (see Figure 11).

4. Click Add on the Security page of the Properties dialog box. The Select Users or Groups dialog box opens (see Figure 8).

Figure 8. Select Users or Groups dialog box

5. Confirm that the Select this object type box lists the object types that you require (for example, Users, Groups, Built-in security principals).

To change the list, click Object Types. The Object Types dialog box opens. Add or remove object types as needed.

6. Confirm that the From this location box lists the root location that contains your users and groups.

To change where to search, click Locations to open the Locations dialog box and specify a new location.

7. Enter the users or groups in the Enter the object names to select box:

• If the Everyone group was missing from the Group or User Names list on the Security page, type Everyone.

• If the user name of the administrator (or the name of the administrator group) was missing from the Group or User Names list on the Security page, type the appropriate user name or group name.

8. Click Check Names to search for users or groups with the names that you specified in the box. All similar or matching object names that were found appear underlined in the box (see Figure 9).

Tip To enter multiple object names at the same time, separate the names with a semicolon.



34

Figure 9. Select Users Or Groups dialog box, showing the Everyone group

9. Confirm that only the correct object name or names are listed in the box and click OK to close the dialog box and return to the Properties dialog box.

10. Examine the Group or User Names list on the Security page of the Properties dialog box again. The Everyone group and the name of the administrator are now available in the list.

• When additional groups or users appear in the Group or User Names list, go to the next topic, “Removing Users.”

• If no additional groups or users appear, go to “Setting Permissions” on page 35.

Removing Users

To remove users or groups from the Group or User Names list on the Security page

1. Select the name of the user or group.

2. Click Remove to remove the selected user or group.

3. Repeat these steps to remove any other users or groups.

You are now ready to set the permission levels for your users and groups.



Setting Permissions

After the correct users and groups are in the Group or user names list on the Security page of the Properties dialog box, set the permissions as follows:

1. In the Group or user names list, select the administrator (or the administrator group).

2. In the Permissions for Administrators list, select the Allow check box for the Full Control option. All of the other check boxes in the Allow column are automatically selected (see Figure 10).

Figure 10. Security page showing correct administrator settings

Note Groups or users granted Full Control for a folder can delete files and subfolders within that folder regardless of the permissions protecting the files and subfolders.



36

3. In the Group or user names list, select Everyone.

4. In the Permissions for Administrators list, select the Allow check box for the Read option and clear the Allow check box for all other actions in the list.

5. To confirm that the inheritance setting is correct, click Advanced. The Advanced Security Settings dialog box opens.

6. Clear the Inherit from parent the permission entries that apply to child objects check box.

7. Click OK to close the dialog box and return to the Security page of the Properties dialog box.

8. Click OK to close the Properties dialog box and save the permission assignments.

You have configured the security settings for the security folder.

Setting Permissions for Xcalibur Folders

When you configure a system with multiple users who might work with Xcalibur files or folders that they did not create, make sure these users have access with the necessary permissions. If these permissions are not set correctly, users might not be able to open or modify files created by other users.

In the procedure that follows, add the Everyone group to the Security page in the Group or user names list, and grant appropriate access to that group.

To set permissions for Xcalibur folders

1. Locate the Xcalibur folder in Windows Explorer. (The default path is C:\Xcalibur.)

2. Right-click the Xcalibur folder and choose Properties from the shortcut menu. The Properties dialog box for the folder opens.

Note Setting these permissions confirms that none of the files in the folder can be deleted by using Windows Explorer.

Tip When you require more restricted access to folders and files, grant access to only specific user groups. Set up appropriate user groups; see Chapter 5, “Defining Secure User Groups and Adding Users.” Complete the procedures that follow, but use specific user groups instead of the Everyone group.



3. Click the Security tab to display the Security page (see Figure 11).

Figure 11. Security page

4. Click Advanced. The Advanced Security Settings dialog box for the Xcalibur folder opens (see Figure 12).

Figure 12. Permissions page



38

5. Clear the Inherit from parent the permission entries that apply to child objects check box. The Security dialog box opens.

6. Click Copy to copy the inherited permissions to the new folder, and click OK to close the Advanced Security Settings dialog box.

Correct the permission settings later. (See “Setting Permissions” on page 35.)

7. Make sure that the Everyone group appears in the Group or user names list in the Properties dialog box. If it does not appear in the list, add it. (See “Adding Users” on page 32.)

8. Select Everyone in the Group or user names list.

9. Confirm that the Allow check boxes are checked for the following settings:

• Modify

• Read and Execute

• List Folder Contents

• Read

• Write

10. To save the permission assignments, click OK. The Properties dialog box closes.

11. Repeat steps 1 to 10 for any additional folders not in the Xcalibur folder hierarchy that are used to store Xcalibur data.

Sequential User Logon and Automatic Logoff

The Sequential User Logon feature allows a user to log on to a workstation, start data acquisition, and then log off while the system continues to acquire the data. A subsequent user can log on to the workstation and then can queue acquisition sequences and process data while the acquisition that the first user started continues.



To enable or disable Automatic Logoff

1. Choose Start > All Programs > Thermo Foundation 1.0 > AutoLogoff. The AutoLogoff dialog box appears (Figure 13).

Figure 13. Automatic Logoff Setup dialog box

2. Do one of the following:

• To turn on the feature, select the Enable check box. Type a value (1–1000) in the Auto logoff time (minutes) box to specify how long the system waits before logging off the current user.

• To turn off the feature, clear the Enable check box.

3. Click OK.

Note By default, Automatic Logoff is disabled (the Enable check box is cleared.

IMPORTANT If your Xcalibur system is on a computer that has Windows Vista installed, provide the following instruction to your users after you turn on AutoLogoff: Each time a user logs on, Vista asks the user if they permit the system to run AutoLogoff in the background. The user must choose Allow every time. Add this instruction to your standard operating procedures. If this procedure is not acceptable, run Xcalibur on a Windows XP system.

Note If the Windows XP screen saver is set to display on the computer at an earlier time than the Auto Logoff time, the automatic logoff still occurs at the specified time, even though the user cannot see evidence of the logoff because the screen saver is active.


4 Establishing Secure File OperationsConfiguring Security Settings for the Database Registry Key

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Configuring Security Settings for the Database Registry KeyWhen the administrator runs the Database Configuration tool for the first time, the tool creates a registry key for the computer that stores information about the database. To confirm the security of the auditing database, the security settings for this registry key must be set so that only the workstation administrator can make changes to the key.

To configure the security settings for the database registry key

1. From your computer taskbar, choose Start > Run. The Run dialog box opens.

2. Type regedit and click OK. The Registry Editor window opens (see Figure 14).

Figure 14. Registry Editor window, showing CFR_Database key selected

3. Locate the My Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Finnigan\Xcalibur\CFR_Database folder in the left pane of the Registry Editor window.

4. Right-click the CFR_Database folder and choose Permissions from the shortcut menu. The Permissions dialog box for this registry key opens.



5. Click Advanced. The Advanced Security Settings dialog box opens (see Figure 15).

Figure 15. Advanced Security Settings dialog box

6. Clear the Inherit from parent the permission entries that apply to child objects check box. The Security dialog box opens (see Figure 16).

Figure 16. Security dialog box

7. Click Copy to copy the inherited permissions to the CFR_Database registry key and click OK to close the Advanced Security Settings dialog box.



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8. Examine the Group or user name list in the Properties dialog box and note that only the name of the administrator (or the administrator group) and the Everyone group appear in this list.

• If the administrator (or the administrator group) does not appear in the list, add it. (See “Adding Users” on page 32.)

• If the Everyone group does not appear in the list, add it. (See “Adding Users” on page 32.)

• If other users or groups appear in the list, remove them. (See “Removing Users” on page 34.)

9. To set the permissions for the registry key, select the administrator (or the administrator group) in the Group or user name list.

10. Select the Allow check box in the Permissions for Administrators list for the Full Control option. The Read check box in the Allow column is automatically selected (see Figure 17).

Figure 17. Permissions dialog box for CFR_Database, showing permission settings for the Administrators group

11. Select Everyone in the Group or user name list.


4 Establishing Secure File OperationsRemoving and Archiving Files

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12. Select the Allow check box in the Permissions list for the Read option. Clear the Allow check box for all other actions in the list.

13. To save the permission settings, click OK. The Permissions dialog box closes.

14. Choose File > Exit to close the Registry Editor.

Removing and Archiving FilesTo be fully compliant with 21 CFR Part 11, an organization must have proper procedures in place for long-term archiving and retrieving of electronic records, including raw data, processed data, and metadata. There must be a procedure as well for ensuring that retrieval records can be read. Generally, this requires the organization to convert records to a new format or to keep and maintain the tools for reading the records in their current format.

To archive files, use third-party software designed for this purpose. In addition, develop and implement standard operating procedures for archiving files and security procedures to protect the archived data.


5

Defining Secure User Groups and Adding Users

Control access to certain features of the Xcalibur application by defining secure user groups and granting these groups appropriate permission levels. By design, every member of a secure user group holds the same rights and permissions. Use the Xcalibur Authorization Manager to create new groups and define permission levels.

After you define secure user groups and set permission levels, only those users who are in a secure user group can access the application. All others are prohibited access.

Contents

• Planning User Groups

• Using the Authorization Manager


5 Defining Secure User Groups and Adding UsersPlanning User Groups

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Planning User Groups Before you begin, decide how many user groups you require or, if more appropriate, how many levels of access to grant to your users. For example, consider a laboratory in which both scientists and technicians work. The standard operating procedures for this laboratory state that technicians cannot perform certain operations with the software in contrast to scientists who have no restrictions. In this case, the laboratory administrator needs to create at least two user groups—one for technicians and one for scientists.

There is no limit to the number of user groups defined. For simplicity, if all users are to have the same privileges, define a single user group.

A user group can be either a pre-existing Windows domain logon group or a private group:

• The domain administrator must create and manage Windows domain logon groups. For help with domain logon groups, contact your domain administrator.

• The workstation administrator can create and manage private groups. However, before the administrator can add a user to a private group, the user must be a member of a domain group. If an intended user is not a user on the domain, grant a domain account for that person. Contact your domain administrator for help in completing this task.

A single user can belong to more than one user group. If the groups have different permission levels, the most lenient permission level applies to the user.

Using the Authorization ManagerProcedures for using the Authorization Manager follow:

• Defining User Groups

• Editing User Groups

• Setting Permissions

• Specifying Predefined Comments

• Viewing the Authorization Manager History Log

• Printing the Security Settings

• Saving the Security Settings

IMPORTANT As a precaution, define at least one user group. If no user groups are in place, there is no security for the software application.

Note Shut down all Xcalibur applications before running the Authorization Manager. Otherwise, if you make changes to permissions for an application when the application is open, the changes might not take effect until you shut down and restart the program.


5 Defining Secure User Groups and Adding UsersUsing the Authorization Manager

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Defining User Groups

To define user groups

1. From your computer taskbar, choose Start > Programs > Thermo Foundation 1.0 > Authorization Manager. The Xcalibur Authorization Manager opens (see Figure 18).

Figure 18. Xcalibur Authorization Manager

2. Click the appropriate Available Groups option to specify the type of user group:

• To use pre-existing Windows logon groups, select the Domain/Workstation option. Contact your domain administrator to create or change logon groups.

Continue with step 3.

• To use (or to create) a local user group, select the Private option. The administrator of the workstation can create private groups.

Skip to step 4.

3. To define secure domain/workstation logon groups, select a group in the Available Groups box to define as a secure group and click . The group appears in the Secure Groups box.

To define more groups as secure, repeat this process. When you have created all needed groups, go to the next procedure “Editing User Groups” on page 49.



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4. To define secure private groups, click Create in the Secure Groups area. The Create private group dialog box opens (see Figure 19).

Figure 19. Create private group dialog box, showing two users in the new private group, Xcal Users

5. Type a name for the group in the Group Name box.

6. Select a domain in the System group list. Xcalibur displays the domain user accounts in the Users Not In Private Group list.

7. Select a user account and click to add it to the new private group. The user account appears in the Users in private group list.

8. To add users in other domains to the private group, repeat steps 6 and 7. Otherwise, click OK. The new private group appears in the Secure Groups list.

9. To create additional private groups, repeat steps 4 to 8. If you have created all needed private groups, continue with the next procedure.



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Editing User Groups

After defining a secure user group, you can view and (for private groups only) change the members of the group. To do this, right-click the user group in the Secure Groups list and select Members from the shortcut menu.

• If the group is a private group, the Edit user list of private group dialog box opens. Add or remove names from the user group by using the arrow keys.

• If the group is a domain/workstation logon group, the Modify users in group dialog box opens. Because membership in these groups is controlled by the domain administrator, the lists in the Modify users in group dialog box are read-only. (See your domain administrator to make changes to domain/workstation logon groups.)

Setting Permissions

For each secure user group, set the permission levels in the Permission Level area for certain features in the software application. To set up secure reports, see the LCQuan Administrator Guide because this function only supports LCQuan activities.

The available permission levels are listed in Table 2. All new secure user groups, whether domain/workstation groups or private groups, have all features set to Disallowed.

Table 2. Permission levels and descriptions

Permission Level Description

Disallowed Not permitted. Specify whether the user interface control for the disallowed operation is hidden or grayed out.

Signature List To perform the desired action, enter the names and passwords of everyone on the signature list.

A series of dialog boxes (one for each signature) appear when a user attempts to perform this action in the software application.

Supervisor Password To perform the desired action, enter the supervisor name and password.

A dialog box for the supervisor signature opens when a user attempts to perform this action in the software application.

Password To perform the desired action, enter the user password.

A dialog box for the user password opens when a user attempts to perform this action in the software application.

Allowed No restrictions.



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Set permission levels in the following ways:

• Setting the Permission Levels for an Individual Feature

• Setting All Permissions

• Inheriting Permissions

• Exporting and Importing Permissions

Setting the Permission Levels for an Individual Feature

To change the permission level of an individual feature

1. Select a user group in the Secure Groups list.

2. Select the name of your software application from the list in the lower left of the Authorization Manager.

3. Click Expand Tree to show the entire list of controlled features for the application.

4. From the list, select the feature whose permission level you want to change.

5. Select one of the Permission Level options:

• Disallowed

• Signature List

• Supervisor Password

• Password Required

• Allowed

6. If you selected Disallowed, specify the appearance of the user interface control in the Disallowed State area:

• If you do not want the user interface control to appear at all, select the Hidden option.

• To gray out the user interface control, select the Grayed option.

Note You can set permissions only for individual features, not subgroups. After selecting a feature, the Permission Level options are active. If they are unavailable, you probably selected a subgroup, not a feature.

Tip To define the permission level of a feature, right-click the feature and select the permission level from the shortcut menu.



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hermo Scientific Xcalibur System and 21 CFR Part 11 Administrator Guide
7. For Permission Level, if you selected Signature List, use the Signature List Groups area to define the signature list groups:

a. Select a user group in the Available groups list and click . The group appears in the Signature required list.

b. Add other groups to the signature list in the same manner as needed.

c. To require that the current user of the software application be placed on the signature list, select the Current User Must Sign check box.

d. If you must rearrange the order of the groups in the signature list, select a group and click Up or Down in the Move Group area.

8. To permit the user to enter a comment after performing an action, select the Comment check box under Other requirements. (This option is available for all permission settings, except Disallowed.)

After the user enters a comment, it appears in the audit log for the software application.

9. Set the permission levels for any or all of the remaining features:

• To set the permission level of an individual feature, repeat steps 4 to 8.

• To set all of the other features for this application to the same permission level that you just set, select the This application option in the All Features area and click Set To Same.

The Permission Level setting, the Disallowed state setting (if applicable), and the Comment setting are copied to all of the other features for the currently selected application.

• To set all other features for all applications to the permission level that you just set, select the All applications option and click Set To Same.

The software copies the Permission Level setting, the Disallowed state setting (if applicable), and the Comment setting to all other features for all applications.

10. To set the permission levels for other user groups in the Secure Groups list, repeat steps 1 to 9.

Note When you choose a feature in the software application with a permission level of Signature List, a series of password dialog boxes appear, one for each signature (the name and password of every member of the designated group).

The order of the groups shown in the Available groups list defines the order of appearance for the password dialog boxes.

IMPORTANT Permission level settings are retained when you move a user group out of the Secure Groups list and into the Available Groups list. When you move the group back into the Secure Groups list, the permission settings remain intact.

When you delete a user group from the Secure Groups list, however, all permission settings are lost.


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Setting All Permissions

You can set every feature to the same permission level in either of two ways:

• After you set the permission level for one feature, click Set To Same (as described in step 9 of the preceding section).

• Right-click the user group name in the Secure Groups list, and choose Globally Set To > [Permission Level] from the shortcut menu.

Inheriting Permissions

To copy a complete set of permission levels from one secure user group to another secure user group

1. Select the user group in the Secure Groups list that is to receive the set of permission levels.

2. Right-click the selected group and choose Inherit From from the shortcut menu.

The Choose Secure Group dialog box opens and displays a list of the secure groups (minus the current one).

3. Select the group containing the permission levels to copy and click OK.

Both user groups now have the same set of permission levels.

Exporting and Importing Permissions

Importing the permission list that contains the user groups and permissions from a workstation saves time when you have more than one workstation in your lab and plan to provide users access to all stations. Instead of setting up identical user groups on each workstation, copy the permission list from a workstation that has the user groups and access permissions that you require.

To export and import the permission list

1. On the workstation where the correct users and permission levels are set, start the Authorization Manager and click Export. The Save As dialog box opens.

2. Save the permission list in the security folder as a file with the .eperm extension. (The default path for this folder is C:\Xcalibur\system\security; the default file name is permissions.eperm.)

3. Copy the file into the security folder on the new workstation.

IMPORTANT To maintain the security of the permission list, export it to a secure location. The security folder (with proper security settings) on the current workstation is an ideal location.



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4. On the new workstation, start the Authorization Manager and click Import. The Open dialog box opens.

5. Locate the permission list file (.eperm file) and click Open. The user groups and permission levels appear in the Authorization Manager.

6. Confirm that the user groups and permissions are correct and click OK to save the settings and close the Authorization Manager.

Specifying Predefined Comments

As an option, you can require users to select comments from a predefined list rather than typing in comments when they use features that require comment entry. To do this, select the Predefined Comments check box in the Global Security Features area. When predefined comments are active, a dialog box opens whenever a user performs an action that requires a comment. The user must select a comment from a list before proceeding.

To define comments

1. Confirm that the Predefined Comments check box is selected.

2. Click Edit. The Edit Comment List dialog box opens.

3. Click Add New Comment. The New Comment dialog box opens.

4. Type comment text and click OK.

5. Repeat steps 3 and 4 to add each predefined comment.

6. Make any additional changes to the comment list:

• To delete a comment from the list, select the comment and click Remove Comment.

• To move a comment up or down in the list, select it and click Move Up or Move Down.

7. Click OK to save your changes and close the dialog box.


5 Defining Secure User Groups and Adding UsersViewing the Authorization Manager History Log

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Viewing the Authorization Manager History LogThe Authorization Manager automatically maintains a history log to record all changes made to the security settings. The log records the following events:

• The creation of a private group

• The addition or deletion of members from a group

• A change in group permissions

• A switch between private and domain/workstation groups

• The manipulation of the signature list

To display the history log for the Authorization Manager, click History Log.

Each entry in the history log contains the time and date, the user ID and full name, and a description of the event. Sort and filter the entries in the history log by field (for example, sort and filter by date and time) or print the log.

Printing the Security SettingsTo print a report of the security settings for each secure user group, click Print. The report contains a list of the members of the group, the controlled feature information for each application, and the names of any secure folders for each application.

Saving the Security SettingsAfter you have defined your user groups, set the appropriate permission levels, and specified the type of application auditing, click OK to save your settings and exit the Authorization Manager.

The controlled feature information is saved in a configuration file in system\security. (The default path for this file is C:\Xcalibur\system\security.) Prohibit non-administrator access to this folder by properly setting the security for this folder. If you have not already done this, see “Establishing Secure File Operations” on page 25.


6

Using the CRC Validator

The CRC Validator compares the cyclic redundancy check (CRC) value stored in the database for a file with the CRC value computed from the file stored on the hard disk. If the stored CRC value and the computed CRC value do not match, the file might have been corrupted or altered since an Xcalibur application saved it. This chapter describes how to use the CRC Validator to check your files.

Contents

• Checking Files With the CRC Validator

• Selecting Files Using Database Filters

• Selecting Files Using a Pattern

Note Close any open Xcalibur applications before running the CRC Validator.


6 Using the CRC ValidatorChecking Files With the CRC Validator

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Checking Files With the CRC ValidatorTo use the CRC Validator

1. From the Windows taskbar, choose Start > All Programs > Thermo Foundation 1.0 > CRC Validation. The CRC Validator dialog box opens (see Figure 20).

Figure 20. CRC Validator dialog box

2. Select a method for selecting files for validation in the File Selection area:

• To select files that match a database filter, see “Selecting Files Using Database Filters” on page 58.

• To select files that match a pattern, see “Selecting Files Using a Pattern” on page 59.

3. Click Check to check the selected files.

4. Examine the results displayed in the Check Results area. The Status column in the file list indicates the status of each file as described in Table 3.

5. Click Exit to close the CRC Validator dialog box.


6 Using the CRC ValidatorChecking Files With the CRC Validator

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Table 3. Status values for CRC Validation

Status Description

CRCs Match The CRC stored in the database matches the CRC just calculated for the file.

CRCs Do Not Match The CRC stored in the database does not match the CRC just calculated for the file. Most likely, the file has been modified since the tracking record was created.

File Not In Database The file was found on the hard disk, but not in the database. It might not be a tracked file.

File Not On Disk The file was found in the database, but not on the hard disk. The file might have been archived or deleted.


6 Using the CRC ValidatorSelecting Files Using Database Filters

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Selecting Files Using Database FiltersWhen you select files using database filters, select files for validation based on information about those files that is stored in the auditing database. For example, select files created by a particular Xcalibur application or select files created or modified at certain times.

Create two types of filters: non-date filters and date filters. Non-date filters are based on fields from the auditing database. Use them to select files based on characteristics, such as the application used to create the file or the name of the user who created the file. Use date filters to select files based on the date when they were created or last modified.

Combine multiple non-date filters using the AND and OR operators. The default filter is the most recently selected dataset name.

To select files using a database filter

1. Click the Files Matching Database Filter option in the File Selection area.

2. Click Edit filter. The Filters dialog box opens (see Figure 21).

Figure 21. Filters dialog box

3. To add a non-date filter, do the following:

a. Select AND or OR from the first list in the Add Non-Date Filter area.

b. Select the database key to filter on from the second list.

c. Type the value for the database key in the equals box. For example, if you selected Application Name in the second list, you might enter Home Page or Qual Browser in the equals box.

d. Click Add to add this filter to the list of current filters.

e. Repeat steps a through d to add other non-date filters.


6 Using the CRC ValidatorSelecting Files Using a Pattern

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4. To add a date filter, enter the starting date and time for your filter in the Add Date Filter area in the From boxes and enter the ending date and time for your filter in the To boxes. Click Add to add this filter to the list of current filters.

5. To remove unwanted filters from the filter list, click the filter name in the list and click Remove Filter.

6. When you have made all needed changes, click OK to save your changes and close the dialog box.

Selecting Files Using a PatternWhen selecting files that use a pattern, specify the folder containing the files and the format type of the files (for example, a .raw file).

To select files using a pattern

1. Select the Files Matching Pattern option in the File Selection area.

2. In the File Path list, select the path to the folder containing the files to check or click Browse to find the folder.

3. Select the file extension of the files to check in the File Name list.

4. Select the Include Subfolders check box to have the CRC Validator check files in subfolders of the selected folder.

5. Click OK to save your changes and close the dialog box.


7

Auditing

Using the Audit Viewer utility, you can perform these auditing functions:

• Display all auditable events and changes made to files created or managed by LCquan™.

• View a history of what has been done during data acquisition and data processing to produce results.

• Get information about all events that have occurred within LCquan.

Accessing the Auditing DatabasesLCquan writes to the Global Auditing database and maintains the LCquan workbook databases to ensure compliance with 21 CFR Part 11. The Global Auditing database stores LCquan start and stop events. All other LCquan events are stored in the LCquan workbook databases.

You can access either of the following types of databases using Audit Viewer:

• Global Auditing database: Keeps a log of auditable events for all the Xcalibur-related data files and applications it recognizes. The Xcalibur-related data files include the raw files that you acquire in LCquan.

Contents

• Accessing the Auditing Databases

• Viewing Audit Viewer Pages

• Filtering Audit Viewer Entries

• Sorting Audit Viewer Entries

• Printing the Audit Viewer Entries

IMPORTANT You must configure the database in the Auditing Database Configuration Manager before you can access the Global Auditing database. See “Using the Database Configuration Manager” on page 21.


7 AuditingAccessing the Auditing Databases

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• LCquan workbook database: Keeps a log of auditable events associated with the current workbook, including the entries that have not been saved to the database. Each workbook database also includes a log about the raw files that are acquired as part of the workbook.

Accessing the Global Auditing Database

You can access the Global Auditing database when you start Audit Viewer from the Windows desktop.

To start Audit Viewer from your Windows taskbar

Choose Start > All Programs > Thermo Foundation 1.0 > Audit Viewer. The Audit Viewer window opens.

Figure 22. Audit Viewer window displaying entries for the Global Auditing database


7 AuditingAccessing the Auditing Databases

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Accessing an LCquan Workbook Database

Each LCquan workbook has its own database. When you start Audit Viewer from an LCquan workbook, Audit Viewer displays the saved and unsaved entries for the current workbook. The unsaved entries are highlighted in yellow in the Audit Viewer window.

To access the auditing database for a workbook

1. Open the LCquan workbook.

2. In the LCquan Workbook window, choose File > Audit Trail. The Audit Viewer window opens and displays the entries for the open workbook (Figure 23). Yellow highlights indicate any unsaved entries.

To access the auditing database for a different workbook, repeat steps 1 and 2. A second instance of Audit Viewer starts and displays the entries for that workbook.

Figure 23. The Audit Viewer window for an LCquan workbook

Note The Audit Viewer entries can also include unsaved changes from another workbook, if the changes are still in memory.


7 AuditingViewing Audit Viewer Pages

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Viewing Audit Viewer PagesThe Audit Viewer window contains the following pages, each of which has a different function:

• The All page (Figure 23) provides a summary of all entries for the current database.

To display the Audit Viewer page associated with an entry on the All page, double-click the entry on the All page.

• The History page provides a chronological listing of all the changes made to method files and result lists.

• The Event page lists all user-initiated auditable software events. All events that are subject to authorization control are auditable.

• The File Tracking page provides the following types of information:

− Global Auditing database: Lists the changes that are made by any program to the Xcalibur-created files.

− LCquan workbook database: Lists the changes made within LCquan to any LCquan-owned files in the workbook, including the workbook file (.lqn), processing method (.pmd), instrument method (.meth), sequence (.sld), and any imported sample data files (.raw). The File Tracking page does not include the data files (.raw) acquired from within the LCquan workbook that are tracked in the Global Auditing database.

− If any of the workbook files are modified outside of LCquan, LCquan displays a file-tracking error message.

• The Instrument Error page lists significant events that occur to instruments that Xcalibur creates or manages.

Note Entries are not saved to the database until you save the workbook. Unsaved entries are highlighted in yellow in the Audit Viewer.


7 AuditingFiltering Audit Viewer Entries

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Filtering Audit Viewer Entries By applying a filter, you can display a subset of the entries in the Audit Viewer window. You can set up two types of filters: filters based on dates and filters not based on dates (non-date filters). You can use a combination of the two types of filters.

To set up a non-date filter

1. In the Audit Viewer window, click Filter. The Filter Entries Dialog Box opens.

Figure 24. Filter Entries dialog box

2. In the Add Non-Date Filter area, select AND or OR from the first list.

3. In the list to the right, select a column on which to filter.

4. In the equals box, type the text string that you want the filter to match and click Add. The filter statement appears in the box.

5. Repeat steps 2 to 4 to add additional filters.

6. When you have defined all your filters, click OK. The Audit Viewer window displays the results.

Note The non-date filter accepts partial matches. For example, if you have a user name of john.doe, then a filter string of john or doe would match entries for that user name.


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To set up a date filter

1. Under Add Date Filter, enter the beginning date and time in the From box.

2. Enter the ending date and time in the To box.

3. Click Add and click OK to apply the filter. The Audit Viewer window displays the results.

To remove a filter

1. In the Filter Entries dialog box, select the filter statement.

2. Click Remove Filter.

3. Click OK. The Audit Viewer window displays the results.

Sorting Audit Viewer EntriesYou can sort the entries by column headings on each of the Audit Viewer pages.

To sort the entries on an Audit Viewer page

1. In the Audit Viewer window, click the tab of the page you want to view.

2. Click Sort. The Sort Entries dialog box opens.

Figure 25. Sort Entries dialog box using all three sort fields

3. In the 1st Sort Field list, select the column heading and select Ascending or Descending.

Repeat this step for the 2nd Sort Field and 3rd Sort Field.

4. Click OK. The Audit Viewer page displays the entries in the specified sorting order.


7 AuditingPrinting the Audit Viewer Entries

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Printing the Audit Viewer EntriesThe printing options vary depending on whether you are printing the audit trail for the Global Auditing Database or a workbook database.

• Printing the Audit Trail for the Global Auditing Database

• Printing the Audit Trail for an LCquan Workbook Database

Printing the Audit Trail for the Global Auditing Database

To print the audit trail for the Global Auditing database

1. From the Windows desktop, choose Start > All Programs > Thermo Foundation 1.0 > Audit Viewer.

2. In the Audit Viewer window, click the tab of the page you want to print.

3. Click Print.

4. In the Print Options dialog box, select printing options, and then click OK.

Printing the Audit Trail for an LCquan Workbook Database

You can print the entries only when you save all displayed records on the Audit Viewer page.

To print the audit trail for an LCquan workbook database

1. In the LCquan Workbook window, choose File > Audit Trail.

If the workbook already contains saved entries, go to step 3.

If the workbook contains any unsaved entries, Xcalibur displays a View Audit Trail message asking if you want to save the workbook before continuing.

2. In the View Audit Trail dialog box, do one of the following:

• Click Yes to save the workbook entries. Xcalibur logs the automatic save in the audit trail and starts Audit Viewer.

• Click No to start Audit Viewer without saving the workbook.

3. In the Audit Viewer window, click the tab of the page that you want to print.

Note If you select the Don't tell me about this again check box, Xcalibur automatically applies the last requested behavior (Save or Not Save) each time you start Audit Viewer when the LCquan workbook contains unsaved entries. To restore the message, choose Options > Enable Warnings.


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4. Make sure the displayed page contains only saved entries. Yellow highlights appear on the rows of any unsaved entries.

If you have a mix of saved and unsaved entries, you can do one of the following:

• In the LCquan Workbook window, choose File > Save to save the LCquan workbook. In the Audit Viewer window, click Refresh.

• In the Audit Viewer window, click Filter, and then add filter rules so that only the saved records appear on the page you want to print. See “Filtering Audit Viewer Entries” on page 65 for details.

5. Click Print.

6. In the Print Options dialog box, select printing options, and then click OK.


8

Installing an Oracle Database

This appendix describes the procedure used by Thermo Fisher Scientific to install the Oracle Server and Client software. Consult your Oracle database administrator for advice and instructions on how to install this software for your application.

The installation information in this chapter supplements the documentation that Oracle provides and does not replace it. Refer to your Oracle manuals for installation and configuration details.

Note The procedures contained in this chapter describe how to install the Oracle9i Database. The installation procedures for other versions or releases of the database might differ from those described here.

Contents

• Installing the Oracle Server

• Installing the Oracle Client


8 Installing an Oracle DatabaseInstalling the Oracle Server

70

Installing the Oracle ServerTo install the Oracle Server

1. Insert the Oracle Database compact disc. The Autorun installation program starts automatically. If the installation program does not start automatically, find and double-click the setup.exe file.

2. Click Install/Deinstall Products in the installation program. The Welcome page opens (see Figure 26).

Figure 26. Welcome page

IMPORTANT Do not install the Oracle Server in an existing Oracle environment with a previous version of the software already installed. Remove previous versions before installing the new version. If you have data in the other database, back it up and use the Oracle Data Migration Assistant to migrate it to the new database during or after the installation. Refer to your Oracle documentation for more information.



3. To remove a previous version of Oracle software before proceeding with this installation, click Deinstall Products. The Inventory dialog box opens. Select the previous version from the list and click Remove.

4. Click Next on the Welcome page. The File Locations page opens (see Figure 27).

Figure 27. File Locations page

5. In the Name box under Destination, type or select a name for the Oracle Home.

6. In the Path box, type or select the location for the Oracle components. Or click Browse to search for a different location.

IMPORTANT The Source Path box automatically fills with the location of the installation files. Do not change the path.



72

7. Click Next. The Available Products page opens (see Figure 28).

Figure 28. Available Products page

8. Select the product to install.

9. Click Next. The Installation Types page opens (see Figure 29).

Figure 29. Installation Types page



10. Select the type of installation.

11. Click Next. The Database Configuration page opens (see Figure 30).

Figure 30. Database Configuration page

12. Select a database.



74

13. Click Next. The Database Identification page opens (see Figure 31).

Figure 31. Database Identification page

14. Type the global database name for the database and enter the Oracle System Identifier (SID) in the fields provided.



15. Click Next. The Database File Location page opens (see Figure 32).

Figure 32. Database File Location page

16. Enter the directory location for the database files. The directory location must be a mapped drive.



76

17. Click Next. The Database Character Set page opens (see Figure 33).

Figure 33. Database Character Set page

18. Select the character set to use in your database.

19. Click Next. The Summary page opens (see Figure 34).

Figure 34. Summary page



20. Review the space requirements on the Summary page to confirm that you have enough disk space.

21. Click Install to start the installation.

When the installation is complete, the Configuration Tools page opens and a series of tools starts automatically creating and configuring your database and Oracle Net Services environments.The Configuration Tools page displays the results of running these tools (see Figure 35).

Figure 35. Configuration Tools page

• If the Oracle Database Configuration Assistant tool runs, continue with step 22.

• If the Oracle Database Configuration Assistant tool does not run, go to step 27 on page 78.



78

22. If the Oracle Database Configuration Assistant tool runs, wait for it to complete. The Oracle Database Configuration Assistant dialog box opens (see Figure 36). Make note of the database information that is listed in this dialog box.

Figure 36. Oracle Database Configuration Assistant dialog box

23. Click Password Management. The Password Management dialog box opens (see Figure 37).

Figure 37. Password Management dialog box

24. Change the default passwords.

25. Lock or unlock the database user accounts as necessary.

26. Click OK to save the changes and close the dialog box.

27. When all of the tools on the Configuration Tools page have finished, click Next. The End Of Installation page opens.

28. Click Exit to exit from the Oracle Universal Installer. The database is installed.


8 Installing an Oracle DatabaseInstalling the Oracle Client

Installing the Oracle ClientTo install the Oracle Client software

1. Insert the Oracle Database Client compact disc. The Autorun installation program starts automatically. If it does not, find and double-click the setup.exe file.

2. Click Install/Deinstall Products in the installation program. The Welcome page opens.

3. To remove a previous version of Oracle software before proceeding with this installation, click Deinstall Products. The Inventory dialog box opens. Select the previous version from the list, and click Remove.

4. Click Next on the Welcome page. The File Locations page opens (see Figure 38).

Figure 38. File Locations page

5. In the Name box under Destination, type or select a name for the Oracle Home.

6. In the Path box, type or select the location for the Oracle components. Or click Browse to search for a different location.

7. Click Next. The Installation Types page opens (see Figure 39).

IMPORTANT Do not install the Oracle Server in an existing Oracle environment with a previous version of the software already installed. Remove previous versions before installing the new version. Refer to your Oracle documentation for more information.

IMPORTANT The Source Path box automatically fills with the location of the installation files. Do not change the path.



80

Figure 39. Installation Types page

8. Select the type of installation.

9. Click Next. The Summary page opens (see Figure 40).

Figure 40. Summary page



10. Review the space requirements on the Summary page to confirm that your system has enough disk space.

11. Click Install to start the installation.

When the installation is complete, the Configuration Tools page opens. A series of tools automatically starts creating and configuring your database and Oracle Net Services environments. The Configuration Tools page displays the results of running these tools (see Figure 41).

Figure 41. Configuration Tools page



82

• If the Oracle Net Configuration Assistant runs (see Figure 42), continue with step 12.

Figure 42. Welcome page

• If the Oracle Net Configuration Assistant does not run, go to step 25 on page 85.

12. Select the No, I will create net service names myself option.

13. Click Next. The Net Service Name Configuration, Database Version page opens (see Figure 43).

Figure 43. Net Service Name Configuration, Database Version page

14. Select the Oracle 8i or later database or service option.



15. Click Next. The Net Service Name Configuration, Service Name page opens (see Figure 44).

Figure 44. Net Service Name Configuration, Service Name page

16. Enter the global database name.

17. Click Next. The Net Service Name Configuration, Select Protocols page opens (see Figure 45).

Figure 45. Net Service Name Configuration, Select Protocols page

18. Select the protocol used for the database.



84

19. Click Next. The next page that opens depends on what protocol you selected.

For example, if you selected the TCP protocol, the Net Service Name Configuration, TCP/IP Protocol page opens (see Figure 46).

20. Based on your choice of protocol, the software requests protocol parameter information. Complete the specification for the selected protocol and click Next.

For example, on the Net Service Name Configuration, TCP/IP Protocol page, type the host name for the computer where the database is located and click the Use the standard port number of 1521 option (see Figure 46).

Figure 46. Net Service Name Configuration, TCP/IP Protocol page

The Net Service Name Configuration test page opens.

21. On the Net Service Name Configuration, Test page, select the Yes, perform a test option and click Next. The Net Service Name Configuration, Connecting page opens and a connection test is performed.

• If the test is successful, click Next. The Net Service Name Configuration, Net Service Name page opens (see Figure 47).

• If the test fails, click Back to review the information that you entered. Make any necessary changes and try the test again.



Figure 47. Net Service Name Configuration, Net Service Name page

22. On the Net Service Name Configuration, Net Service Name page, accept the default net service name or type another net service name that is unique to the client.

23. Click Next. The Net Service Name Configuration, Another Net Service Name? page opens.

24. On the Net Service Name Configuration, Another Net Service Name? page, specify whether or not to configure another net service name for this client.

• When you select Yes and click Next, the Oracle Net Configuration Assistant leads you through the process of configuring another net service name.

• When you select No and click Next, the Net Service Name Configuration Done page opens. Click Next again and click Finish to complete the Oracle Net Configuration Assistant. You are returned to the Configuration Tools page (Figure 41).

25. On the Configuration Tools page, click Next. The installation is complete.



86

9

Reference Tools

Read this chapter for information about specific tools that work with Xcalibur.

Command Line ArgumentsUse command line arguments to open a file, create a new file, or print a file automatically from a script or command line. You can do these functions from command lines in the following locations:

• From the Microsoft Windows Run application (choose Start > Run from the Windows taskbar).

• From the Sequence Setup view of the Home Page window, choose Actions > Run This Sample or Actions > Run Sequence. When the Run Sequence dialog box opens, use the Pre Acquisition or Post Acquisition command line boxes.

• From the Programs view of the Processing Setup window, by using the Program or Macro Name column.

• From the Microsoft Windows Command Prompt (choose Start > Programs > Accessories > Command Prompt from the Windows taskbar).

Contents

• Command Line Arguments

• ExcelExp.exe

• Command Line Format

• XConvert.exe


9 Reference ToolsCommand Line Arguments

88

The following is standard syntax for these command lines:

Where:

path is the absolute pathname.

new filename is the name that you would like to apply to your new file.

filename is the name of an existing file.

application is the application name. The possible applications are:

• HomePage - Home Page window and Sequence Setup view

• InstSetup - Instrument Setup window

• ProcSetup - Processing Setup window

• QuanBrowser - Quan Browser window

• QualBrowser - Qual Browser window

For example, use this syntax to print the file drugx_01.raw:

C:\Xcalibur\system\programs\QualBrowser /p C:\Xcalibur\examples\data\drugx_01.raw

You can omit the application path (path) if you are running the command line from within Xcalibur. For example, to print the file drugx_01.raw, use:

QualBrowser /p C:\Xcalibur\examples\data\drugx_01.raw

If you are running the command line from the Processing Setup window, the program warns you when you type an invalid program name or path.

To open an application:

path application

To create a new file in an application:

path application path new filename

To print a file from an application:

path application /p path filename


9 Reference ToolsCommand Line Arguments

T 89
hermo Scientific Xcalibur System and 21 CFR Part 11 Administrator Guide
The following table lists the possible command lines. If you have installed Xcalibur to the default location, the path before the application is C:\Xcalibur\system\programs\.

Table 4.

File Type Example parameters and results

.raw pathQuanBrowser pathfile.raw

Opens the file in the Quan Browser window.

pathQuanBrowser /p pathfile.raw

Opens the file in the Quan Browser window, prints the spectrum and chromatogram, and then closes the Qual Browser window.

pathQualBrowser pathfile.raw

Opens the file in the Qual Browser window.

path\QualBrowser /p pathfile.raw

Opens the file in the Qual Browser window, prints the spectrum and chromatogram, and then closes the Qual Browser window.

.sld pathHomePage pathfile.sld

Opens the file in the Home Page window - Sequence Setup view.

pathHomePage /p pathfile.sld

Opens the file in the Sequence Setup view, and displays the Print Selection dialog box. After you click OK, the sequence is printed.

.pmd pathProcSetup pathfile.pmd

Opens the file in the Processing Setup window.

path\ProcSetup /p pathfile.pmd

Opens the file in the Processing Setup window, and displays the Print dialog box. After you click Print, the processing method is printed.

.meth pathInstSetup pathfile.meth

Opens the file in the Instrument Setup window.

9 Reference ToolsExcelExp.exe

90

ExcelExp.exeYou can create and export summary reports and results file exports that can be opened directly in Microsoft Excel using the ExcelExp program [ExcelExp.exe].

Command Line Format

The command line for this program has three fields: Export Type, Data Source Path Name, and Export File Type. Xcalibur names the output file name based on the data source file name and places it in the same directory as the data source file.

ExcelExp.exe /Eexport type /data source path /Texport file type

/E - Set export type

/F - Path name of file to summarize/export

/T - Set export file format

Export Types (/E):

SUMMARY (for example, /ESUMMARY)

RESULT (for example, /ERESULT)

.rst pathQuanBrowser pathfile.rst

Opens the file in the Quan Browser window.

pathQualBrowser pathfile.rst

Opens the file in the Qual Browser window.

pathQualBrowser /p pathfile.rst

Opens the file in the Qual Browser window, prints the spectrum and chromatogram, and then closes the Qual Browser window.

Table 4.

File Type Example parameters and results

Note ExcelExp.exe has no user interface and can only be accessed through its command line.


9 Reference ToolsExcelExp.exe

Path Names (/F)

For SUMMARY, this must be the path name of a sequence file (.sld).

For RESULT, this must be the path name of a results file (.rst).

Export File Formats (/T)

XLS (for example, /TXLS)

TXT (for example, /TTXT)

CSV (for example, /TCSV)

Use the XLS format whenever possible.

Command Prompt Examples

Choose Start > Run to open the Run dialog box, or choose Start > Programs > Accessories > Command Prompt to open the Command Prompt dialog box.

• To create a summary report for the steroids sample data set:

c:\xcalibur\system\programs\ExcelExp.exe /ESUMMARY /Fc:\xcalibur\examples\methods\steroid.sld /TXLS

• To create a result file dump of the steroids15 results file from the Xcalibur xcalibur\examples\data folder:

c:\xcalibur\system\programs\ExcelExp.exe /ERESULT /Fc:\xcalibur\examples\data\steroids15.rst /TXLS

Note For RESULT exports, the export file will have a .crf extension. You can open this file directly in Microsoft Excel.


9 Reference ToolsXConvert.exe

92

Processing Setup Example

To create a processing setup

1. From the Road Map view of the Home Page window, choose GoTo > Processing Setup. The Processing Setup window opens.

2. Click the Programs button in the View bar. The Programs view opens. Select the Enable check box to activate a row.

3. Double-click the Program or Macro Name box and browse to ExcelExp.exe (see path in the next step).

4. Type program parameters in the Parameters box.

Program or Macro Name box:

c:\xcalibur\system\programs\ExcelExp.exe

Parameters box:

/ERESULT /F%F /TXLS

XConvert.exeThis Xcalibur utility program converts source files of one data format to destination files having a different data format:

Note If you use ExcelExp.exe as a Programs entry in a processing method, use the place holder %F. At the time the program is run, the %F is replaced with the current results file name. In addition, avoid running /ESUMMARY from ExcelExp.exe. It is better to create summary reports by batch processing from the Sequence Setup window by choosing Actions > Batch Reprocess. Select the Print Summary Reports check box to print a summary report for all of the samples in the current sequence.

Source Files Extension

Xcalibur (*.raw)

ICIS (*.dat)

GCQ (*.ms)

Magnum (*.ms)

ANDI (*.cdf )

Mass Lab 2 (*.raw)

Lasermat (*.*)

Destination files Extension


9 Reference ToolsXConvert.exe

T

Execution

From the Road Map view of the Home Page window, choose Tools > File Converter. The File Converter Dialog Box opens. This is the same dialog box that opens if you double-click XConvert.exe located in the Xcalibur > System > Programs directory.

You can also run XConvert.exe from the following command lines:

From the Sequence Setup view of the Home Page window, choose Actions > Run This Sample or Actions > Run Sequence. When the Run Sequence dialog box opens, use the Pre Acquisition or Post Acquisition command line boxes.

From the Programs view of the Processing Setup window, use the Program or Macro Name command line box.

Xcalibur (*.raw)

ICIS (*.dat)

ANDI (*.cdf )

Text files (*.txt)

Note Xcalibur does not currently support all interconversion combinations and posts a message whenever an unsupported conversion is requested.


Automatic File Conversion

You can automatically convert and store files as they are created in Xcalibur using the Xcalibur Convert.exe application and by selecting Run Program in the Action list.

The command line format is:

Path\XConvert /SSource Type /DDestination Type Source Path/File /O Destination Directory.

where /SSource Type, /DDestination Type, and Source Path/File are mandatory. If you are using this command line in the Programs column of the Processing Setup window, you can omit the path to XConvert.

These are the currently supported source and destination types:

Source Type: Xcalibur (.raw) file [L], ICIS (.dat) file [I], ANDI (.cdf ) file [A]

Destination Type: Xcalibur (.raw) file [L], ICIS (.dat) file [I], ANDI (.cdf ) file [A], Text (.txt) file [T]

Examples:

• To convert a file (myfile.raw), located in the last specified source directory, from Xcalibur (.raw) file format to ICIS (.dat) file format, use the following command line:

C:\Xcalibur\system\programs\XConvert %R /SL /DI, where %R is the current raw file in the path.

• To convert a file (myfile.raw) located in C:\Xcalibur\data from Xcalibur (.raw) file format to ANDI (.cdf ) file format, use the following command line:

C:\Xcalibur\system\programs\XConvert /DA /SL %R, where %R is the current raw file in the path.

• To convert a file (myfile.raw) located in C:\Xcalibur\data from ICIS (.dat) file format to Xcalibur (.raw) file format with the resulting .raw file being stored in C:\temp, use the following command line:

C:\Xcalibur\system\programs\XConvert /SI /DL C:\Xcalibur\data\myfile.dat /O C:\temp

D

System Administration Reference

This appendix provides reference information to configure and manage the system and to support compliance with the Electronic Records and Electronic Signatures Rule, published by the United States Food and Drug Administration as 21 CFR Part 11.

Xcalibur System Administration• Configuring Xcalibur

• Configuring the System

• Configuring Instruments

• Instrument Setup

Contents

• Xcalibur System Administration

• Xcalibur Administrator Utilities for Compliance with 21 CRF Part 11


D System Administration ReferenceXcalibur System Administration

664

Configuring Xcalibur

On the pages of the Xcalibur Configuration dialog box, enter configuration information for the Xcalibur data system.

Xcalibur Configuration Dialog Box

The Xcalibur Configuration dialog box has these pages:

• Customer Info Page

• Dataset List Page

• Folders Page

• Fonts Page

• Intelligent Shutdown (Error Handling) Page

• Labeling And Scaling Page

• Mass Options Page

• Peak Detection Page

Customer Info Page

Use the Customer Information page of the Xcalibur Configuration dialog box to confirm and update the following Xcalibur software license information.

Table 222.

Parameter Description

User Name View or change the name assigned to the Xcalibur license agreement. To change the user name, log on to your computer as an administrator.

Organization View or change the organization assigned to the Xcalibur license agreement. To change the organization, log on to your computer as an administrator.

Address View the address assigned to the Xcalibur license agreement. Commas separate the sections of the address, for example: City, State, and Country.

Voice Phone View the voice telephone number assigned to the Xcalibur license agreement.

Fax View the fax telephone number assigned to the Xcalibur license agreement.

Email View the e-mail address assigned to the Xcalibur license agreement.

Print User Info Print a report that lists the current user name, organization, address 1, address 2, voice phone number, and fax telephone number.



Dataset List Page

Use the Dataset List page of the Xcalibur Configuration dialog box to define or edit the list of dataset names available to the user when choosing a dataset. Only the administrator can access this feature.

Note The names of several parameters on this page change when you select a new Display Name (see below). The default Display Name is Dataset. When you change the Display Name, the following four parameters are renamed: Dataset List, Add New Dataset Name, Remove Selected Dataset Name, and Blank Dataset Name Is A Valid Selection. For example, if you change the Display Name from Dataset to Study, the parameter Dataset List changes to Study List.

Table 223.


Dataset List View or change the list dataset names that have been entered. The names are stored in the registry. To add a new dataset name to the list, click Add New Dataset Name.

Display Name View or change the name that Xcalibur uses for a dataset. You can type in a new name or you can select a new name from the list. The options are Dataset, Study, and Job.

When you change the Display Name, the parameters on this page and elsewhere are renamed to reflect the change. For example, if you change the Display Name from Dataset to Study, the parameter Dataset List changes to Study List.

Add New Dataset Name Enter a new dataset name. The new dataset name is added to the Dataset List and stored in the registry.

Remove Selected Dataset Name

Remove the currently selected name from the Dataset List and from the registry. This action does not remove the name from the database if the name has already been used.

Blank Dataset name is a valid selection

Set to allow a user to select a blank name when asked to select a dataset.

Clear to require the user to select a valid dataset.

Selection restricted to entered names

Select to list only the names listed in the Dataset List in the Dataset Name Selector dialog box.

Clear to show the names listed in the Dataset List as well as a those obtained from the database in the Dataset Name Selector dialog box.

Maximum number of names to display

View or change the maximum number of dataset names that are shown in the Dataset Name Selector dialog box.

In the Dataset Name Selector dialog box, the dataset names from the Dataset List are shown first. Then, if allowed, the most recent dataset names stored in the database are used to fill the list until the maximum number of entries is shown.



666

Folders Page

Use the Folders page of the Xcalibur Configuration dialog box to specify the default location of your Xcalibur data, methods, and report templates.

Fonts Page

Use the Fonts page of the Xcalibur Configuration dialog box to change the appearance of fonts in Xcalibur.

Table 224.


Default Folders

Data View or change the current default path to the folder that contains your Xcalibur data. To change the path, click Browse and select the folder to hold your data. When you click OK, Xcalibur changes the default path in the Data box to the new path.

Methods View or change the current default path to the folder that contains your Xcalibur methods. To change the path, click Browse and select the folder to hold your data. When you click OK, Xcalibur changes the default path in the Methods box to the new path.

Report Templates View or change the current default path to the folder that contains your Xcalibur report templates. To change the path, click Browse and select the folder to hold your report templates. When you click OK, Xcalibur changes the default path in the Report Templates box to the new path.

Note If Xcalibur displays the elemental composition values in light gray, close Qual Browser and choose Xcalibur Roadmap > Tools > Configuration to display the Configuration page. Select the Fonts tab and set all font sizes to a minimum of 10 points.

Table 225.


Fixed Pitch Font

Font View or change the fixed pitch (non-proportional) font that Xcalibur currently uses; the name appears in the topmost Font box. The default fixed pitch font is Courier New. The Fixed Pitch Font list displays all of the fixed pitch fonts that are currently available on your data system. Fixed pitch fonts have characters whose width is constant. To change the font, select a font in the Font list. Xcalibur displays the selected font in the topmost box and displays an example in the associated Preview area. When you click OK, Xcalibur implements this font throughout all Xcalibur programs wherever fixed pitch fonts are used.



Min View or change the minimum fixed pitch font size that Xcalibur currently uses; the number appears in the topmost Min box. The default minimum fixed pitch font size is 7 points. To change this value, select another font size in the list. Xcalibur displays the selected font size in the topmost box and displays both the current font and the selected font size in the top row of the associated Preview area.

Max View or change the maximum fixed pitch font size that Xcalibur currently uses; the number appears in the topmost Max box. The default maximum fixed pitch font size is 12 points. To change this value, select another font size in the list. Xcalibur displays the selected font size in the topmost box and displays both the current font and the selected font size in the bottom row of the associated Preview area.

Fixed Pitch Font Preview

Preview View the following examples:

Example text with fixed pitch font at minimum size.

Example text with fixed pitch font at maximum size.

Proportional Pitch Font

Font View or change the proportional pitch font that Xcalibur currently uses; the name appears in the topmost Font box. The default proportional pitch font for Xcalibur is Arial. The Proportional Pitch Font list displays all of the proportional pitch fonts that are currently available on your data system. Proportional pitch fonts have characters that vary in width. For example, the widest character is W. To change the font, select a font in the Font list. Xcalibur displays the selected font in the topmost box and displays an example in the associated Preview area. When you click OK, Xcalibur implements this font throughout all Xcalibur programs wherever proportional pitch fonts are used.

Min View or change the minimum proportional pitch font size that Xcalibur currently uses; the number appears in the topmost Min box. The default minimum proportional pitch font size is 7 points. To change this value, select another font size in the list. Xcalibur displays the selected font size in the topmost box and displays both the current font and the selected font size in the top row of the associated Preview area.

Max View or change the maximum proportional pitch font size that Xcalibur currently uses; the number appears in the topmost Max box. The default maximum proportional pitch font size is 12 points. To change this value, select another font size in the list. Xcalibur displays the selected font size in the topmost box and displays both the current font and the selected font size in the bottom row of the associated Preview area.

Proportional Pitch Font Preview

Preview View the following examples:

• Example text with fixed pitch font at minimum size.

• Example text with fixed pitch font at maximum size.

Table 225.




668

Intelligent Shutdown (Error Handling) Page

Use the Intelligent Shutdown page of the Xcalibur Configuration dialog box to specify the response Xcalibur makes when an error occurs during data acquisition.

Labeling And Scaling Page

Use the Labeling and Scaling page of the Xcalibur Configuration dialog box to enter default values for labels and scales used to display data in the chromatogram and spectrum views.

Table 226.


No Action When an error occurs during data acquisition, set Xcalibur to take no action and try to continue to the next sample.

Attempt to stop the devices and pause the sequence

When an error occurs during data acquisition, set Xcalibur to send a stop command to all devices and pause the acquisition sequence before the next injection.

Attempt to turn off the devices and pause the sequence

When an error occurs during data acquisition, set Xcalibur to send a Turn off device command to all devices and pause the acquisition sequence before the next injection.

Table 227.


Default Chromatogram and Spectrum Scaling

Labeling options

Select default values for labeling and scaling in the displays of spectrum and chromatogram data. The values you specify as defaults are applied throughout Xcalibur only if no other value is available in the currently open method or raw file.

In Processing Setup and Quan Browser, for example, Xcalibur uses the default values for labeling and scaling when you change the value for Detector Type. In Qual Browser, however, Xcalibur uses the default values when you display a new spectrum, chromatogram, or map plot, or if the layout file (.lyt) in Qual Browser is unavailable.

Label For MS Data Specify the default source of labels for the Y-axis of MS data. Specify either custom (user-defined) labels or labels from the detector.

If you select custom labels, use the adjacent box to specify the label; for example, specify Intensity as a label.

Label For PDA/UV Data Specify the default source of labels for the Y-axis of PDA/UV data. Specify either custom (user-defined) labels or labels from the detector.

If you select custom labels, use the adjacent box to specify the label. For example, specify uAU as a label.



Mass Options Page

Use the Mass Options page of the Xcalibur Configuration dialog box to select default values for Mass Tolerance, Mass Units, and Mass Precision. If you select the check box labeled Use user defined, you can specify the default values for the parameters in the Default Mass Tolerance area. Xcalibur uses these defaults throughout to acquire and display your data. If you do not select the Use user defined check box, then Xcalibur uses the values for mass options that are stored in the open raw file in Xcalibur.

(Use the Masses dialog box in Processing Setup, Qual Browser, and Quan Browser to change the default settings for tolerance and precision in those applications.)

Label For Other Data Types Specify in this list the default source of labels for the Y-axis of data types other than MS and PDA/UV. Specify either custom (user-defined) labels or labels from the detector.

If you select custom labels, use the adjacent box to specify the label. For example, specify mVolts as a label.

Use absolute scale

Specify absolute scaling as the default for displays of spectrum and chromatogram data. The values you select are applied throughout Xcalibur only if no other value is available in the currently open method or raw file.

MS Data Specify that the default (global) settings use absolute scaling with MS data.

PDA/UV Data Specify that the default (global) settings use absolute scaling with PDA/UV data.

Other Data Specify the default (global) settings for data types other than MS and PDA/UV.

Retention time precision

Decimals Specify the number of decimal places to include when reporting retention times. The value can be from 1 to 5.

Table 227.


Table 228.


Default mass tolerance

Use user defined Activate the user-defined default settings for mass tolerance and mass units.



670

Mass tolerance Specify the user-defined default setting for mass tolerance. To activate the user-defined settings, select the Use user defined check box. Then, enter a value from 0.1 to 50000.

Xcalibur uses the default mass tolerance value only when you create a new method. It does not modify any existing methods (for example, processing methods or Qual Browser layout files). Qual Browser does not use the default mass tolerance value unless you delete the default layout file. Xcalibur then creates a new default layout file with this mass tolerance value.

Units Specify the default units that are used in processing mass spectral data. To activate the user-defined settings, select the Use user defined check box. Then, select either the mmu option or the ppm option.

Default mass precision

Decimals Specify the default number of decimals places (places after the decimal point) that Xcalibur uses to process mass spectral data. Specify from 0 to 5 decimal places. The number of decimal places applies throughout Xcalibur.

Xcalibur uses the default mass precision value only when you create a new method. It does not modify any existing methods (for example, processing methods or Qual Browser layout files). Qual Browser does not use the default mass precision value unless you delete the default layout file. Xcalibur then creates a new default layout file with this mass precision value.

Default mass defect

View or change the parameters used in library searches so that you can correct for the differences between the actual masses and the nominal integer masses of the atoms in a molecule. Assign a larger value (in millimass units) for mass defect to larger molecules because, in general, they are composed of more atoms than smaller molecules; larger molecules need a larger correction factor to approximate the linear function that Xcalibur uses to calculate masses. The values you specify for the default mass defect are applied throughout Xcalibur if no other value is available in the currently open method or raw file.

Defect Specify default values (in millimass units) for mass defect. Specify a smaller value for lower mass ranges in the first box, and specify a larger value for higher mass ranges in the second box.

at mass (amu) Specify the default masses at which Xcalibur applies specified mass defect values to calculations of mass. Specify a smaller mass value in the first box, and specify a larger mass value in the second box.

Table 228.




71
Peak Detection Page

Use the Peak Detection page of the Xcalibur Configuration dialog box to select which peak detection algorithm to use as the default for different data types. All new processing setup methods are created using the currently selected Xcalibur default peak detection algorithm. You can return to the Peak Detection page at any time to change the Xcalibur default peak detection algorithm. Specify a default algorithm to use for different data types in the Default Peak Detection Algorithm area.

Configuring the System

Xcalibur provides the following system configuration boxes:

• Add Programs To Tool Menu Dialog Box

• Add Tool Dialog Box

• Comment Dialog Box

• Customize Toolbar Dialog Box

• Dataset Name Selector Dialog Box

• File Converter Dialog Box

• File Save - Audit Trail Dialog Box

• File Summary Information Dialog Box

• Password Dialog Box

• Print Selection Dialog Box

• Select Directory/Select Data Directory Dialog Box

• Supervisor Permission Dialog Box

• View Audit Trail Dialog Box

Table 229.


Default Peak Detection Algorithm

Default Peak Detection Algorithm For MS Data

Select ICIS, Genesis, or Avalon as the default peak detection algorithm for MS data.

Default Peak Detection Algorithm For PDA/UV Data

Select ICIS, Genesis, or Avalon as the default peak detection algorithm for PDA/UV data.

Default Peak Detection Algorithm For Other Data Types(Data types other than MS and PDA/UV)

Select ICIS, Genesis, or Avalon as the default peak detection algorithm for data types other than MS, PDA, or UV data.


672

Add Programs To Tool Menu Dialog Box

Use the Add Programs To Tool Menu dialog box to add and to remove application programs from the Tool menu and to adjust the sequence of the menu.

Add Tool Dialog Box

Use the Add Tool dialog box to specify the path to the program that you want to add to the Tools menu.

Table 230.


Menu Contents View the names of the current list of tools (programs) that have been added to the Tool menu. These names appear when you choose the Tools menu. You can use the Add button, Remove button, Move Up button, and Move Down button in the Add Programs to Tool Menu dialog box to edit the current list of programs.

Menu Text View or change the name of the tool (program) selected in the Menu Contents box. To change the name, type the new name in the Menu Text box.

Program Type the path and file name of the tool (program) that you want to add to the Tools menu, or click Browse to select the path and file name.

Arguments Add command line arguments.

Initial Directory View or change the path that Xcalibur uses to find the tool (program) selected in the Menu Contents box. To change the path, type the new path in the Initial Directory box.

Close Save all changes and close the current page or dialog box.

Add Add a tool (program) to the Tools menu.

Remove Remove the name of the tool (program) selected in the Menu Contents box from the list of tools.

Move Up Select a tool and move it up in the current sequence of tools (programs) in the Menu Contents box. This is the sequence displayed when you choose the Tools menu.

Move Down Select a tool and move it down in the current sequence of tools (programs) in the Menu Contents box. This is the sequence displayed when you choose the Tools menu.

Table 231.


Program Type the path and file name of the tool (program) that you want to add to the Tools menu or click Browse to select the path and file name.

Browse Find an existing file.



Comment Dialog Box

The Comment dialog box opens when you try to perform an action or access a feature that requires a comment before continuing.

Customize Toolbar Dialog Box

Use the Customize Toolbar dialog box to modify the toolbar. You can add buttons for many menu commands, remove buttons, or change the order of the buttons.

Table 232.


Your Comment Enter your comment in this box. The comment appears in the Audit Log.

Note This feature is only available in Sequence Setup, Qual Browser, and Quan Browser. In Qual Browser, you cannot customize the Amplify toolbar.

Table 233.


Categories View the menu categories available on the toolbar. Select a menu category to view the Commands list and buttons (if available on the toolbar) for that category.

Commands View the commands associated with each menu category and the associated buttons on the toolbar if available.

Buttons

Close Save all changes and close the current page or dialog box.

Reset Return the setting for the current selection to the value that was displayed when you selected the setting. The Reset command button only works on boxes.



674

Dataset Name Selector Dialog Box

Use the Dataset Name Selector dialog box to select a dataset from a predefined list of names. All database entries are then grouped into this dataset. Each application displays the dataset name in the title bar. The format for display is Dataset: Name, where Dataset is the name defined by the administrator and Name is the selected name. Examples are Dataset: Pharmco or Study: Pharmco.

The title of this dialog box might be different if the administrator chooses to use another name for a dataset. For example, it might be titled Study Name Selector or Job Name Selector.

File Converter Dialog Box

Use the File Converter dialog box to convert one data file type to another data file type.

Table 234.


Dataset Name List Displays the list of predefined dataset names. When the dialog box opens, the list of predefined dataset names appears in this order:

1. The last dataset name used appears at the top of the list.

2. The dataset names from the Dataset List page of the Configuration dialog box appears.

3. If the system settings permit, the most recent dataset names stored in the database fill the list until it reaches the maximum number of entries.

4. If a blank name is permitted, the time [Blank] appears in the list.

Button

New Enter a name for a new dataset and save the name in the database for future use. The new dataset name appears in the Dataset Name List.

Note

• Xcalibur does not currently support all interconversion combinations and posts a message whenever an unsupported conversion is requested.

• Not all formats have the same data fields. Xcalibur can only convert matching data fields and does not typically convert instrument method information.

• You can also convert files by running XConvert.exe from two locations: the Pre Acquisition or Post Acquisition run line of the Run Sequence dialog box located in the Sequence Setup view of the Home Page window, or from the Program or Macro Name run line of the Run Sequence dialog box located in the Programs view of the Processing Setup window.



Xcalibur provides file interconversions for the following file types:

To convert a file

1. Select the source and destination directories, and the conversion type in the File Converter Dialog Box.

2. Click Convert. Xcalibur automatically performs the file conversion and creates a new file. The Status page displays the conversion status of each job.

Table 235.

File Type File Extension

Xcalibur *.raw

ICIS *.dat

GCQ *.ms

Magnum *.ms

ANDI *.cdf

AutoMass *.spa

MassLab2 *.raw

LaserMAT *.*

Table 236.


Conversion source

Source data type View the data type of the file that you want to convert into another data type. All of the files in the Folder list in the Conversion source area are displayed in the Conversion source table. You can select the following data types from the Source data type list for conversion into another data type:

• Xcalibur Files (*.raw)

• ICIS Files (*.dat)

• GCQ Files (*.ms)

• Magnum Files (*.ms)

• ANDI Files (*.cdf )

• Automass Files (*.spa)

• Mass Lab 2 Files (*.raw)

• Lasermat Files (*.*)

The source data type is selected from the Destination data type list.



676

Folder View or change the path to the source file that you want to convert to another data type. The list contains all the paths that you have recently selected. Click Browse in the Conversion source area to select another path to source files.

Conversion source table View the file name, type, size, and date of the files located in the directory specified in the Folder list and of the type specified in the Source data type list.

Browse Select the folder that contains the files that you want to convert to another data type and click OK. Xcalibur displays the path to the folder in the Folder list and the previous path remains in the folder list.

If the selected folder has no file of the type specified in the Source data type list, no entries appear in the Conversion source table.

Select All Select all of the files that appear in the Conversion source table. Xcalibur highlights all of the files.

Clear Selection Clear the currently selected files.

This button is only active when you select one or more files in the Conversion source table.

Add Job(s) Add the specified conversion job to the Jobs page of the Conversion destination area. Each file conversion is considered a separate job.

The following is an example of a job displayed on the Jobs page for the conversion of an Xcalibur file of type .raw to an ANDI file of type .cdf:

C:\Xcalibur\examples\data\drugx_06.raw

C:\Xcalibur\examples\data\drugx_06.cdf

The Add Job(s) button is only active when one or more files have been selected on the Jobs page. You can only add a job if you have selected a valid data type in the Destination data type list and have selected a valid destination from the Folder list in the Conversion destination area.

Conversion destination

Destination data type View the data type that you want the source data files converted to. The following data types can be selected from the Destination data type list:

• ICIS Files (*.dat)

• ANDI Files (*.cdf )

• Text Files (*.txt)

The software selects the data type that a source data type file can be converted from in the Source Data Type list.

Table 236.




Folder View the path to the destination folder to hold your converted file. The list contains all the paths that you have recently selected. To select another folder to store your converted files, click Browse in the Conversion destination area.

Browse Select the folder to hold your converted files and click OK. Xcalibur displays the path to the folder and the previous path remains in the Folder list.

Jobs page This page in the Conversion destination area displays the jobs that have been selected for conversion. The job display format is as follows:

C:\Xcalibur\examples\data\drugx_06.raw

C:\Xcalibur\examples\data\drugx_06.cdf

To remove a job prior to running the conversion, select the job and click Remove Job(s).

Remove Job(s) Removes jobs that are selected for removal from the Jobs page. You must remove a job prior to converting it.

Status page This page in the Conversion destination area displays the status of jobs that have been converted. The format is as follows:

Successfully converted C:\Xcalibur\examples\data\drugx_06.raw to C:\Xcalibur\examples\data\drugx_06.cdf

This page also displays the status of unsuccessful conversions.

Other buttons

Convert Starts conversion of all jobs displayed on the Jobs page in the Conversion destination area. Xcalibur stores the converted files in the displayed folder. The status of all converted files appears on the Status page. This page in the Conversion destination area displays the status of jobs that have been converted. The format is as follows:

Successfully converted C:\Xcalibur\examples\data\drugx_06.raw to C:\Xcalibur\examples\data\drugx_06.cdf

This page also displays the status of unsuccessful conversions.

Table 236.




678

File Save - Audit Trail Dialog Box

The File Save - Audit Trail dialog box requires that you enter information about the current file changes before you save the file.

When you have entered the above audit information, click Continue to save the file.

If you have not entered the audit trail information, a dialog box opens with the following message:

***Please enter your user name and a description into the audit log.***

You must enter this information before you can save the file.

File Summary Information Dialog Box

Use the File Summary Information dialog box to obtain information and provide reference information about the current file.

Password Dialog Box

The Password dialog box opens when you try to perform an action or access a feature for which the administrator has required that you enter your user name and password.

Table 237.


User Enter a string of up to 24 alphanumeric characters that identify the operator. To include reference text that identifies the operator, type the text in the User box.

Comment View and enter useful information about the active file.

What Changed View Xcalibur-generated information about changes to the active file. This information is part of the Xcalibur audit system.

Table 238.


Header The header information includes the date and time that the file was created, the date and time that the file was last modified (if applicable), the user name of the person who last saved the file, and the number of times that the file has been saved.

Comment View or change a description of the active file and any comments that have been entered. You can edit the text directly in the box.

Table 239.


Name Enter your user name in this box.

Enter Password Enter your password in this box.



Print Selection Dialog Box

Select Directory/Select Data Directory Dialog Box

Use the Select Directory dialog box or the Select Data Directory dialog box to select a directory on the Xcalibur computer hard drive. If you are connected to another computer over a network, you can also select a directory on another computer that you have access to. Xcalibur displays the current path below the text: Directory selected. An example of a directory for an Xcalibur method is c:\Xcalibur\system\methods.

The title text that appears in the title bar of this dialog box varies depending upon what you are doing when you activate the dialog box.

Your Comment Enter your comment in this box. The comment will appear in the Audit Log.

The Your Comment field appears only if the administrator has required that you enter a comment to perform this action.

Table 239.


Table 240.


Select The Printing Output

Vial Position List Print a sequentially numbered vial position list from the active sequence. The vial position list summarizes the sequence settings for each vial. A vial position list is useful when you are setting up the autosampler tray vial sequence.

All Columns Print selected rows in a sequence.

Displayed Columns Only Print the currently displayed columns of the active sequence.

To change the sequence columns displayed, choose Change > Column Arrangement.

Table 241.


Directory selected View named groups of files called subdirectories and folders. Select the directory that contains the file you want to open.

Drives View the letter designations of all of the hard drives that your computer currently has access to. You can gain access to additional drives by connecting to a network.

Disk Space/No Chart View the amount of disk space available on the default path disk drive.

Network Connect your computer to any drive on a network that you have access to.



680

Supervisor Permission Dialog Box

The Supervisor Permission dialog box opens when you try to perform an action or access a feature that first requires the supervisor to enter his or her user name and password.

View Audit Trail Dialog Box

Spectrum Ranges Dialog Box

Use the Spectrum Ranges dialog box to view and edit the mass range, time, and other properties of a spectrum plot:

• In Qual Browser, for all plots in the active spectrum view.

• On the Home Page, for the active spectrum plot in Real Time Plot mode.

You can also apply automatic processing options such as smoothing and background subtraction. The dialog box consists of two pages:

• Ranges Page, Spectrum Ranges dialog box

• Automatic Processing Page, Spectrum Ranges dialog box

Table 242.


Name Enter your user name in this box as supervisor.

Enter Password Enter your password in this box as supervisor.

Your Comment Enter a comment in this box. The comment appears in the Audit Log.

The Your Comment field appears only if the administrator has required that you enter a comment to perform this action.

Table 243.


Date/Time View the month/day/year and time that the active file was changed. This information is used for the Xcalibur audit system.

User ID View the user identification number of the current user. This information is part of the Xcalibur audit system.

Logon ID View the Logon identification of the current user. This information is part of the Xcalibur audit system.

What Changed View Xcalibur-generated information about changes to the active file. This information is part of the Xcalibur audit system.

User Comment View comments made by the user describing the modification to the active file. This information is part of the Xcalibur audit system.



Configuring Instruments

Use these dialog boxes to configure your instruments.

• Instrument Configuration Dialog Box

• Out Of Date Instrument Drivers Detected Dialog Box

Instrument Configuration Dialog Box

Use the Instrument Configuration dialog box to review all available devices and configure the devices that you want to install using the following controls:

Table 244.


Device Types

View or change the category of device types currently displayed in the Available Devices area. The default option is All. The other options allow you to select a subset of all of the devices as follows:

All: Displays all configurable Xcalibur devices.

AS: Displays all configurable Xcalibur autosampler devices.

Detector: Displays all configurable detector devices.

GC: Displays all configurable Xcalibur gas chromatograph devices.

LC: Displays all configurable Xcalibur liquid chromatograph devices.

MS: Displays all configurable Xcalibur mass spectrometer devices.

Other: Displays all other Xcalibur configurable devices.

Available Devices

This area displays buttons for all available devices of the type selected in the Device Types list. For example if All is displayed in the Device Types list, this area displays all Xcalibur configurable devices.

Available Device View available instruments. Each button displayed in the Available Devices area represents an instrument that can be configured as an Xcalibur device. The buttons that are displayed depend upon the selection in the Device Types list. To select an Xcalibur device for configuration, click the button corresponding to the device to be configured and click Add.



682

Add Add the device you have selected in the Available Devices area to the Configured Devices area.

A device must be present in the Configured Devices area to begin the process of configuring the device.

Configured Devices

View all of the devices that have been added from the devices listed in the Available Devices group box.

A device must be present in the Configured Devices area to begin the process of configuring the device.

Remove Remove the device you have selected from the Configured Devices area.

Each button displayed in the Configured Devices area represents an instrument that has been selected for configuration as an Xcalibur device but might or might not have been configured. To configure a device listed in the Configured Devices area, click the button of the device to be configured, and then click Configure to open the appropriate configuration dialog box.

Configure Open the appropriate configuration dialog box for the device you have selected in the Configured Devices area. For example, to configure an LCQ MS detector, click LCQ in the Configured Devices area, and then click Configure. The LCQ Configuration dialog box opens.

Other Controls

Done Close the Xcalibur Hardware Configuration dialog box after you have configured Xcalibur devices.

Table 244.




Out Of Date Instrument Drivers Detected Dialog Box

This dialog box opens only when you select Start > Programs > Thermo Foundation 1.0 >Instrument Configuration. The Instrument Configuration view opens. If your Xcalibur software is out of date, Xcalibur displays the following message:

The device drivers for the following instruments are not compatible with the installed version of Xcalibur. You must install the current drivers before you can use these instruments.

If this message appears, install the latest software for the instruments listed. This software is located on an Xcalibur CD-ROM. Run the appropriate setup file to load the new software. Run Setup.exe from the appropriate instrument directory on the CD-ROM.

Note The Xcalibur Data system and inlets are shipped on a separate CD-ROM from the Xcalibur software used for the MS detectors and mass spectrometers. When a new version of Xcalibur is released, usually you must update the software for both the Data system and inlets software as well as the MS detectors and mass spectrometers for all configured instruments.

Table 245.


Instrument View currently installed instruments with out-of-date software. Installed in this context indicates that the Setup.exe files for the listed instruments have been previously run from the appropriate directory of an Xcalibur CD-ROM.

In Use View the status of the instrument displayed in the Instrument list: In Use (Yes) or Not In Use (blank). In Use devices appear in the Configured Devices area of the Instrument Configuration view.

Version View the current version of the instrument that is displayed in the same row of the Instrument list. Make sure the version to be installed is more recent than the current version.



684

Instrument Setup

After selecting which instruments you want Xcalibur to control using the Instrument Configuration program, use Instrument Setup to specify your instrument settings.

• File Menu for the Instrument Setup Window

• Instrument menu for the Instrument Setup Window

• Help Menu for the Instrument Setup Window

• Instrument Setup Window Toolbar

The Instrument Setup window displays the setup parameters required for each instrument that you select on the View bar. These might include your autosampler, chromatograph, MS detector or mass spectrometer, divert valve, syringe pump, contact closure timing sequence, and/or all other Xcalibur supported instruments that you have configured.

You can create new methods, modify existing methods, and save method files. You can import previously collected data files to help you set up time segments and scan events based upon the data acquired.

You can also enter a method summary that appears in the Open dialog box and on all method printouts. All changes are audited by logon ID and user self-identification so that you can describe why you changed a method.

The Instrument Setup window displays the icons of all of the Xcalibur instruments you have selected using the Instrument Configuration dialog box. (See the View bar on the left side of the window.) If you have configured more instruments than can be displayed on your screen, a vertical scroll bar appears in the View bar so that you can access all the instruments.

To enter the setup parameters for a particular instrument, click the icon for that instrument. Xcalibur displays one or more pages of parameters to be set for the one you selected.

View Bar

The View bar is a vertical bar on the left of the Instrument Setup window. It contains an icon for each of the instruments that you have selected using the Instrument Configuration program.

Note Before you use the Instrument Setup window, use the Instrument Configuration program to select the instruments for your experiment.



Menus

Instrument Setup contains the following menus:

• File Menu for the Instrument Setup Window

Instrument

• Instrument menu for the Instrument Setup Window

The Instrument menu changes when you use the View bar to select an instrument. Each instrument-specific menu contains instrument-specific menu commands.

• Help Menu for the Instrument Setup Window

Toolbar

Instrument Setup toolbar



686

File Menu for the Instrument Setup Window

Table 246.

Command Description

New Create a new file having the appropriate extension.

Open Find and open a file that already exists.

Save Open the File Save - Audit Trail dialog box if the file has been saved before so that you can enter audit information about the active file.

Save As Edit user and description information, as well as view header information about the active file.

When you click OK, Xcalibur opens the File Save - Audit Trail Dialog Box, so you can enter audit information about the active file. When you click Continue, Xcalibur saves the file.

Summary Information Edit user and description information, as well as view header information about the active file.

Change Dataset Name Select a dataset from a predefined list of names.

The text of this menu item might be different if the administrator chose to use another name for a dataset. For example, this menu item might be Change Job Name.

Audit Trail View all auditable events and changes made to data files in the current application.

Print Print your method.

Print Preview View your page setup so that you can see what it looks like before printing it.

Print Setup Select the following printing options: printer, form, orientation, and one- or two-sided printing.

Most Recently Used Files View the paths and names of the last four files used. These are located above the Exit command. Both open and closed files are displayed. Click a displayed file to load it. If the selected file was closed, it is opened.

Exit Close the active window. If you exit before clicking OK from an active dialog box, Xcalibur asks if you want to save your changes.



Instrument menu for the Instrument Setup Window

Xcalibur groups commands that deal with instrument-specific controls in the [Instrument] menu. You can activate [Instrument] commands from either the mouse or keyboard.

Help Menu for the Instrument Setup Window

Table 247.

Command Description

[Instrument] Help Open the Configuration and Setup Help for the selected instrument.

Instrument Setup Help Open Xcalibur Help and display Help for the Instrument Setup window.

Help On Current Item View Help for the Instrument Setup page that is currently displayed.

[Instrument] Contents and Index

View the Contents, Index, and Find Help pages for the selected instrument.

Xcalibur Help Open Xcalibur Help.

Glossary Open the glossary.

How To Use Help Open Help that describes how to use the Help viewer.

About Instrument Setup View the installed version number of the Instrument Setup program and the Thermo Fisher Scientific copyright notice.



688

Instrument Setup Window Toolbar

Table 248.

Button Description

New Create a new instrument method.

Open Find and open an existing file.

Save Enter audit information about the active file if your method has been saved before and click Continue to save the file.

If your method has not been saved before, clicking Save opens the Save As dialog box. Select the name and location for your instrument method. When you click Save, the File Summary Information Dialog Box opens. Enter header information for your instrument method. When you click OK, the File Save - Audit Trail Dialog Box opens. Enter audit information about the active file and click Continue to save the file.

Print Print the parameters in your instrument method.

Home Page View the Home Page window - Roadmap view.

Help View Help for the Instrument Setup page that is currently displayed.


D System Administration ReferenceXcalibur Administrator Utilities for Compliance with 21 CRF Part 11

T

Xcalibur Administrator Utilities for Compliance with 21 CRF Part 11The Xcalibur Administrator Utilities assist an organization in becoming compliant with the Electronic Records and Electronic Signatures Rule, published by the United States Food and Drug Administration as 21 CRF Part 11. These tools help to set up and maintain the security features and functions of Xcalibur. These include detailed audit logs, the ability to allow authorization to be made before specific actions are allowed, and file tracking.

Explore these Xcalibur Administrator Utilities:

• Audit Viewer

• Auditing Database Configuration Manager

• Xcalibur Authorization Manager

• CRC Validator

In addition, the Authorization Manager contains the following dialog boxes:

• Sort Entries Dialog Box

• Create Private Group and Edit User List Of Private Group Dialog Boxes

• Edit Comment List Dialog Box

• Users In Group Dialog Box



690

Audit Viewer

The Audit Viewer displays all auditable events and changes made to files created or managed by Xcalibur.

The Audit Viewer has the following pages:

• All Page, Audit Viewer

• History Page, Audit Viewer

• Event Page, Audit Viewer

• File Tracking Page, Audit Viewer

• Instrument Error Page, Audit Viewer

When you double-click a log item on the All page, the Audit Viewer displays the page associated with the log item and highlights the item on that page. The History page provides a chronological listing of all of the changes made to method files and/or result lists. The Event page lists auditable software application events that the user initiated. The File Tracking page lists all changes made to data files.

The Audit Viewer has slightly different capabilities when run as a stand-alone application than when run from within an Xcalibur application.

• When you run the Audit Viewer as a stand-alone application (by choosing Start > All Programs > Thermo Foundation 1.0 > Audit Viewer), the Audit Viewer displays all items in the database (excluding any uncommitted items or unsaved changes), and the data can be printed.

• When you open the Audit Viewer from within most applications (by choosing File > Audit Trail), the Audit Viewer displays only the items associated with the current application, including uncommitted items. However, you cannot print the data.

• When you open Audit Viewer from within LCquan (by choosing File > Audit Trail), Audit Viewer displays both committed and uncommitted items and you can print the committed items.

In addition, the Audit Viewer contains the following dialog boxes:


• Print Options Dialog Box

• Filter Entries Dialog Box



T

All Page, Audit Viewer

The All page of the Audit Viewer displays all auditable events and changes made to files created by or managed by Xcalibur. When you double-click a log item on the All page, the Audit Viewer displays the page associated with the log item and highlights the item on that page.

The Audit Viewer has slightly different capabilities when run as a stand-alone application than when run from within an Xcalibur application. When you run the Audit Viewer as a stand-alone application (by choosing Start > All Programs > Thermo Foundation 1.0 > Audit Viewer), Audit Viewer displays all items in the database (excluding any uncommitted items or unsaved changes), and you can print the data. When you open the Audit Viewer from within an application (by choosing File > Audit Trail), the Audit Viewer displays only the items associated with the current application, including uncommitted items. However, you cannot print the data.

Table 249:


Date/Time View when the log entry occurred.

Dataset Name View the dataset that contains the affected files.

Computer Name View the name of the workstation where the item change originated.

User Name View the logon name of the user who changed the item. The administrator of the network assigns logon names for each user.

Full Name View the descriptive name of the user who changed the item. Often, this is the first and last name of the user. The administrator of the network assigns a full name to the logon name for each user.

Application Name View the name of the software application that is associated with the log entry.

Table Name View the type of record: History, Event, or File Tracking. The log entry is found on this page of the Audit Viewer.

Buttons

Sort Specify how you want to sort the entries in the Audit Viewer.

Filter Specify how you want to filter the entries in the Audit Viewer.

Auto Width Expand the grid columns to display the longest entry in that column.

Print Print an active file or document.

Refresh Update the log.



692

History Page, Audit Viewer

The History page of the Audit Viewer provides a chronological listing of all of the parameter changes made to method files or result lists.


Table 250:




Computer Name View the name of the workstation where the item change originated.

User Name View the logon name of the user who changed the item that is listed in the Item Changed field. The administrator of the network assigns logon names for each user.

Full Name View the full name of the user who changed the item that is listed in the Item Changed field. Often, this is the first and last name of the user. The administrator of the network assigns a full name to the logon name for each user.

Application Name View the name of the software application that is associated with the log entry.

Filename View the name of the affected file. The file name is not case-sensitive.

Path View the route through the file system to the affected file.

Old Row View the pre-change row number of the item if the change resulted in a change of row number.

New Row View the post-change row number of the item if the change resulted in a change of row number.

Change Type View the type of operation (edit, delete, and so on) that changed the item.

Item Changed View the setting that was changed.

Old Value View the old value of the item that is listed in the Item Changed field (if applicable).

New Value View the new value of the item that is listed in the Item Changed field.

User Data 1 View custom user data, if supported by the application. The user data is unique for each application.



http://searchwin2000.techtarget.com/sDefinition/0,,sid1_gci212118,00.html


T

Event Page, Audit Viewer

The Event page of the Audit Viewer lists auditable application events that were initiated by the user. Events can include starting an Xcalibur application, printing a file from within an Xcalibur application, and importing a file from within an Xcalibur application.





Buttons






Table 250:


Table 251:


Date/Time View when the event occurred.


Computer Name View the name of the workstation initiating the event.

User Name View the logon name of the user who initiated the event. The administrator of the network assigns logon names for each user.

Full Name View the descriptive name of the user who initiated the event. Often, this is the first and last name of the user. The administrator of the network assigns a full name to the logon name for each user.



694

File Tracking Page, Audit Viewer

The File Tracking page of the Audit Viewer lists significant events that occur to files that Xcalibur creates or manages. File tracking helps to make sure the data on the hard disk are not tampered with.

The Audit Viewer has slightly different capabilities when run as a stand-alone application than when run from within an Xcalibur application. When you run the Audit Viewer as a stand-alone application (by choosing Start > All Programs > Thermo Foundation 1.0 > Audit Viewer), you can view and print all items in the database (excluding any uncommitted items or unsaved changes). When you open the Audit Viewer from within an application (by choosing File > Audit Trail), the Audit Viewer displays only the items associated with the current application, including uncommitted items. However, you cannot print the data.

Application Name View the name of the software application that is associated with the event.

Event View what occurred. Typical events include importing and exporting data files, methods, and sequences.

Response View the action taken by the user (if any) in response to the event.

Comment View the comment associated with the event.

Buttons






Table 251:


Table 252:




Computer Name View the name of the workstation performing the file change.

User Name View the logon name of the user who changed the file. The administrator of the network assigns logon names for each user.

Full Name View the descriptive name of the user who changed the file. Often, this is the first and last name of the user. The administrator of the network assigns a full name to the logon name for each user.

Application Name View the name of the software application that was used to change the file.



T

Instrument Error Page, Audit Viewer The Instrument Error page of the Audit Viewer lists error codes from instruments.

The Audit Viewer has slightly different capabilities when run as a stand-alone application than when run from within an Xcalibur application. When you run the Audit Viewer as a stand-alone application (by choosing Start > All Programs > Thermo Foundation 1.0 > Audit Viewer), you can view and print all items in the database (excluding any uncommitted items or unsaved changes). When you open the Audit Viewer from within an application (by choosing File > Audit Trail), the Audit Viewer displays only the items associated with the current application, including uncommitted items. However, you cannot print the data.

File name View the name of the affected file. The file name is not case-sensitive.

Path View the route through the file system to the affected file.

File Status View the operation or action that caused the entry to be made in the log.

File is createdFile was copiedFile was movedFile was deletedFile was modifiedFile was renamedResult of renameOld folder nameNew folder nameResult of file move

Comment View the comment associated with the log entry.

Buttons



Auto Width View the longest entry in that column.



Table 252:


Table 253:





696

Computer Name View the name of the workstation performing the change.

User Name View the logon name of the user who made the change causing the error notification. The administrator of the network assigns logon names for each user.

Full Name View the descriptive name of the user who made the change causing the error notification. Often, this is the first and last name of the user. The administrator of the network assigns a full name to the logon name for each user.

Application Name View the name of the software application that was used to change the instrument.

Dataset Name View the dataset that contains the affected instrument.

Instrument Error Code View the code Xcalibur produced when Xcalibur received information about the instrument error.

Instrument ErrorSeverity

View the severity error level for the incident.

Instrument ErrorString View the instrument error string produced.

Device VI State View the device status state at the time the log event occurred.

Time Offset If an acquisition was in progress when the log event occurred, view the acquisition time. If no acquisition was in progress, this field will be zero.

Buttons



Auto Width View the longest entry in that column.



Table 253:




T

Sort Entries Dialog Box

Use the Sort Entries dialog box to specify how to sort the entries in the Audit Viewer. Each page in the Audit Viewer has a unique set of fields that can be sorted.

Print Options Dialog Box

Use the Print Options dialog box to choose document properties for printing the log.

Table 254:


1st Sort Field Specify the first field in the log that is sorted.

2nd Sort Field Specify the second field in the log that is sorted. You cannot specify a second sort field if the 1st Sort is not already defined.

3rd Sort Field Specify the third field in the log that is sorted. You cannot specify a third sort field if the 2nd Sort is not already defined.

Ascending Sort fields in ascending order.

Descending Sort fields in descending (reverse) order.

Table 255:


Printer Options

Orientation: Portrait Print the log vertically.

Orientation: Landscape Print the log horizontally.

Font Size: Small Print the log in 8-point font.

Font Size: Medium Print the log in 10-point font.

Font Size: Large Print the log in 12-point font.



698

Filter Entries Dialog Box

Use the Filter Entries dialog box to specify how you want to filter the entries in the Audit Viewer or in the CRC Validator. By applying a filter, you can display a subset of the entries in the Audit Viewer or a subset of the entries to be validated in the CRC Validator.

Table 256:


Add Non-Date Filter

Operator View or change the operator (AND or OR) used in the filter.

Field View or change the field to filter, for example, Application Name.

Equals String View or change the field value to filter, for example, Authorization Manager.

Add Add the new filter to the Filter Entry box.

Add Date Filter

From Date/Time View or change the earliest date and time for the time/date range for the filter.

To Date/Time View or change the latest date and time for the time/date range for the filter.

Add Add the new filter to the Filter Entry box.

Filter Entry box View or change the filters that Xcalibur uses to filter the audit records.

You can click the filters to select them. When a filter is selected, the Remove Filter button becomes active.

Button

Remove Filter Delete the selected filter in the Filter Entry box.



T

Auditing Database Configuration Manager

Use the Auditing Database Configuration Manager to select and configure the auditing database. Follow the instructions in the box in the top of the Auditing Database Configuration Manager. You must reboot your computer to make the changes effective. For more information on setting up your database, see Chapter 3, “Using the Database Configuration Manager.” Not all of the parameters are displayed at every step in the configuration process.

Note If you are using Oracle as the database backend, install at least one relational database on an accessible server and install the Oracle client on the system computer before using the Auditing Database Configuration Manager.

Table 257:


Database Name View the currently configured database.

This line does not appear if this is the first time that you are running the Auditing Database Configuration Manager.

Database Type View the database type. The database must be an Oracle database on a remote server or a Microsoft Access database on a local computer.


Database Is Installed On Host

View where the Oracle database is installed on the host computer. (When using a Microsoft Access database, this line is blank.)


Database Service Name View the Oracle database service name. (When using a Microsoft Access database, this line is blank.)


User Name View the logon name for the Oracle database. (When using a Microsoft Access database, this line is blank.)


Select Database Type

Oracle On Network Server Select to use a remote server running the Oracle database. You must enter a valid user name and password to access the database.

Microsoft Access Select to use a local database based on Microsoft Access.



700

User Name View the Oracle database logon name.

(When using a Microsoft Access database, this box is grayed out.)

Password View the Oracle database password.

(When using a Microsoft Access database, this box is grayed out.)

Oracle Net Service Name View the name of the Oracle Net Service that the database administrator set up during the Oracle Client configuration that provides database connection information. All available names appear in the list.

(When using a Microsoft Access database, this list does not appear.)

Restart Computer Now Restart the computer automatically when you click Finish.

You must reboot your computer to make the changes effective.

I Will Restart Later End the database configuration without restarting the computer when you click Finish.

You must reboot your computer to make the changes effective.

Button

Finish Close the Auditing Database Configuration Manager.

If you selected the Restart Computer Now option, save and close all other applications before clicking this button.

Table 257:




T

Xcalibur Authorization Manager

In addition to using the security features of your computer operating system, use the Xcalibur Authorization Manager to define user groups and to set permission levels for those groups. Setting permission levels makes sure that specific Xcalibur applications that generate electronic records can be accessed only by individuals who have some level of responsibility towards those records. You must be logged on as administrator to set these permissions. For more information about using the Xcalibur Authorization Manager to define user groups and set permission levels, see Chapter 5, “Defining Secure User Groups and Adding Users.”

Table 258:


Available Groups

Domain/Workstation Use pre-existing Windows logon groups. Contact your network administrator to create or change logon groups.

Private Use or create a private (local) user group. The administrator of the workstation can create private groups.

Available Groups View the available Windows logon groups (Domain/Workstation option) or private (local) groups (Private option).

To move a group into the Secure Groups list, select the group in the Available Groups list and click >>. To move a group out of the Secure Groups list, select the group in the Secure Groups list and click <<, or double-click the group.

Secure Groups

Create Create private groups.

Select the Private (Available Groups) option to enable the Create button.

Delete Select a private group in the Secure Groups list and click Delete to delete the group.



702

Secure Groups View the Windows logon groups (Domain/Workstation option) or private (local) groups (Private option) for which you have set permission levels.

To move a group into the Secure Groups list, select the group in the Available Groups list and click >>. To move a group out of the Secure Groups list, select the group in the Secure Groups list and click <<, or double-click the group. To delete a secure group, select the group in the Secure Groups list and click Delete. Right-click a group in the Secure Groups list to display a shortcut menu.

Members: Opens the Edit User List Of Private Group dialog box (for private groups) or the Users In Group dialog box (for domain groups).

Globally Set To: Sets all software features in all applications to the same permission level: Disallowed, Signature List, Supervisor Password, Password, or Allowed.

Inherit From: Opens the Choose Secure Group dialog box.

Create Group: Opens the Create Private Group dialog box. (Only for private groups)

Global Security Features

Predefined Comments Require the user to select from a list of predefined comments instead of typing in a comment for features that require comments.

When you select this check box, the Edit button becomes active. Click Edit to open the Edit Comment List dialog box and define a list of comments.

Table 258:




T

Edit Define a list of comments from which a user must choose for certain features that require them.

Permission Level Pane

Permission Level pane View permission levels for software applications.

To display the Permission Level pane, select a group in the Secure Groups list.

To display the group’s permission levels for an application, select the application in the Permission Level pane and click Expand Tree. To change a permission level, select a permission for a feature in the Permission Level pane to activate the Permission Level area. Select the new permission level in the Permission Level area.

When you log in after restarting a session, wait a few moments before opening LCQuan so that the system recognizes your permission levels.

Expand/ Collapse Tree View the permissions for an application after you select the application in the Permission Level pane.

Secure Folders

Table 258:




704

Secure folders View the folders whose root folder can be changed. You must define a list of secure folders if you set the feature Allow Change of Root Folder in the Permission Levels pane to a permission level other than Disallowed. For more information about creating a list of secure folders, see Chapter 4, “Establishing Secure File Operations.”

Secure folders are used only in LCquan. This box is grayed out unless LCQuan is selected in the Permission Level pane.

Add Locate the folder that you want to add to the Secure Folders list.

Secure folders are used only in LCQuan. This button is grayed out unless LCQuan is selected in the Permission Level pane.

Delete Select and remove a folder from the Secure Folders list.

Secure folders are used only in LCQuan. This button is grayed out unless LCQuan is selected in the Permission Level pane.

Permission Level

Disallowed To refuse access to the procedure that you selected, set the permission level of the procedure in the Permission Levels pane to Disallowed. By default, all new secure user groups have all features set to Disallowed.

If Disallowed and Allowed are the only options available (all of the other options are grayed out), then these options do not indicate permission levels, but instead indicate configuration settings. Disallowed means that the selection in the Permission Levels pane is not displayed by the application and Allowed means that the selection is displayed.

For example, if you select Xcalibur Configuration | Allow To Access | Dataset List page in the Permission Levels pane, only the Disallowed and Allowed settings are available. If you select Disallowed, the Dataset List page is not displayed in the Xcalibur Configuration dialog box. If you select Allowed, the Dataset List page is displayed in the Xcalibur Configuration dialog box.

Signature List Require that the names and passwords of everyone on the signature list be entered to perform the action that you selected in the Permission Levels pane. When an action with a permission level of Signature List is chosen, a series of password dialog boxes appear, one for each signature (name and password of a member of a designated signature group). The order of the groups shown in the Signature List Groups: Signature Required list defines the order in which the password dialog boxes appear.

Supervisor Password Require that the name and password of the supervisor be entered to perform the action that you selected in the Permission Levels pane. In this context, a supervisor is any person who has permission to do this operation—that is, the person’s permission level for this operation is either Allowed or Password Required.

Table 258:




T

Password Required Require that the password of the user be entered to perform the action that you selected in the Permission Levels pane.

Allowed No restrictions. Allows the user to perform the action that you selected in the Permission Levels pane without restriction.

If Disallowed and Allowed are the only options available (all of the other options are grayed out), then these options do not indicate permission levels, but instead indicate configuration settings. Disallowed means that the selection in the Permission Levels pane is not displayed by the application and Allowed means that the selection is displayed.

For example, if you select Xcalibur Configuration | Allow To Access | Dataset List page in the Permission Levels pane, only the Disallowed and Allowed settings are available. If you select Disallowed, the Dataset List page is not displayed in the Xcalibur Configuration dialog box. If you select Allowed, the Dataset List page is displayed in the Xcalibur Configuration dialog box.

Disallowed State

Hidden Hide the disallowed action that you selected in the Permission Levels pane.

Grayed Gray out the disallowed action that you selected in the Permission Levels pane.

Signature List Groups

Available Groups View the groups from which you can require signatures.

To move a group into the Signature Required list, select the group in the Available Groups list and click >>. To move a group from the Signature Required list, select the group in the Signature Required list and click << or double-click the group. The only groups that can be in the Signature Required list are those groups that have permission (Allowed or Password Required) to do the operation.

Select Permission Level: Signature List to activate the Available Groups list.

Signature Required Require a signature from a specified group. When an action with a permission level of Signature List is chosen, a series of password dialog boxes appear, one for each signature (name and password of a member of a designated signature group). The order of the groups shown in the Signatures Required list defines the order in which the password dialog boxes appear.

To move a group into the Signature Required list, select the group in the Available Groups list and click >>. To move a group from the Signature Required list, select the group in the Signature Required list and click <<. The only groups that can be in the Signature Required list are those groups that have permission (Allowed or Password Required) to do the operation.

Select Permission Level: Signature List to activate the Signatures Required list.

Table 258:




706

Use the Authorization Manager to set permissions for Xcalibur features. You can set them for individuals or for groups. Certain permission level settings override other settings.

Current User Must Sign Add the current user to the Signatures Required list.

Select Permission Level: Signature List to activate the Current User Must Sign check box.

Move Group Up Move the group that you selected in the Signatures Required list up one spot in the list.

Select Permission Level: Signature List to activate the Move Group Up button.

Move Group Down Move the group that you selected in the Signatures Required list down one spot in the list.

Select Permission Level: Signature List to activate the Move Group Down button.

Other Requirements

Comment Require the user to enter a comment that will appear in the Audit Log when performing an action.

All Features

All Applications Sets the software features in all applications to the same permission level that you just set.

This Application Sets all of the other software features in the selected application to the same permission level that you just set.

Set To Same Set all the other software features (for all applications or for just this application) to the same permission level that you just set.

Buttons

History Log Open the Audit Viewer. The Audit Viewer is a record of all changes made to the security settings. The following events are logged:

• The creation of a private group

• A change in group permissions

• A switch between private and domain/workstation groups

• Changes to the Signature List

Print Print a report of Authorization Manager settings for each secure group. The reports include listings of group members, secure folders, and applications and their permissions.

Export Save the Authorization Manager settings in a permissions file.

Import Import previously saved Authorization Manager settings. You save Authorization Manager settings in a permissions file.

Table 258:




T

The following table lists the Xcalibur features that you can configure in the Authorization Manager.

Table 259.

Features Description

CRC Validator

Run Application If you set this feature to Disallow, then the user cannot open the software application. In this case, Xcalibur ignores the permission level settings for other Features.

If a user whose permission is set to Disallow tries to access the system, an entry is made in the Global Auditing Database history log.

Home Page

Run Application If you set this feature to Disallow, then the user cannot open the software application. In this case, Xcalibur ignores the permission level settings for other features.


Dataset Selection Dataset Selection Displayed at Startup: Set this feature to Disallow to hide access to the Dataset Selection feature at startup.

Dataset Selection Allowed in Menu: Set this feature to Disallow to hide access to the Dataset Selection menu item.

Allow New Dataset: Set this feature to Disallow to hide access to the New Dataset feature.

Analysis Start Analysis: Set this feature to Disallow to hide access to the Start Analysis feature.

Stop Analysis: Set this feature to Disallow to hide access to the Stop Analysis feature.

Pause Analysis: Set this feature to Disallow to hide access to the Pause Analysis feature.

Devices Devices On: Set this feature to Disallow to hide access to the Devices On feature.

Devices Standby: Set this feature to Disallow to hide access to the Devices Standby feature.

Devices Off: Set this feature to Disallow to hide access to the Devices Off feature.

Automatic Devices On: Set this feature to Disallow to hide access to the Automatic Devices On feature.



708

Sequence Operations Run Sequence: Set this feature to Disallow to hide access to the Run Sequence feature.

Batch Sequence: Set this feature to Disallow to hide access to the Batch Sequence feature.

Import Sequence: Set this feature to Disallow to hide access to the Import Sequence feature.

Export Sequence: Set this feature to Disallow to hide access to the Export Sequence feature.

Run This Sample: Set this feature to Disallow to hide access to the Run This Sample feature.

File Saving Files: Set this feature to Disallow to hide access to the File Save feature.

Print Print Sequence: Set this feature to Disallow to hide access to the Print Sequence feature.

Instrument Setup



Dataset Application Dataset Selection Displayed at Startup: Set this feature to Disallow to hide access to the Dataset Selection feature at startup.




Print Print Sequence: Set this feature to Disallow to hide access to the Print Instrument Method feature.

Library Manager



Table 259.




T



Manage Libraries Add: Set this feature to Disallow to hide access to the Add Library feature.

Delete: Set this feature to Disallow to hide access to the Delete Library feature.

Archive: Set this feature to Disallow to hide access to the Archive Library feature.

Convert Libraries Convert: Set this feature to Disallow to hide access to the Convert Library feature.

Processing Setup







Print Print Sequence: Set this feature to Disallow to hide access to the Print Processing Method feature.

Options Chromatography Type Change: Set this feature to Disallow to hide access to the Change Chromatography Type feature.

Calibration Options: Set this feature to Disallow to hide access to Calibration Options features.

Delete Selected Component: Set this feature to Disallow to hide access to the Delete Selected Component feature.

Table 259.




710

Programs Accept Program Changes: Set this feature to Disallow to hide access to the Program Changes feature.

Qual Browser






Layout Usage Apply: Set this feature to Disallow to hide access to the Apply Layout feature.

Apply Default: Set this feature to Disallow to hide access to the Apply Default Layout feature.

Saving Files: Set this feature to Disallow to hide access to the Save Layout feature.

Save as Default: Set this feature to Disallow to hide access to the Save Layout as Default feature.

Restore Factory Default: Set this feature to Disallow to hide access to the Restore Factory Default feature.

Tools Add Tools: Set this feature to Disallow to hide access to the Add Tools feature.

Table 259.




T

Edit Copy View to Clipboard: Set this feature to Disallow to hide access to the Copy View to Clipboard feature.

Copy Special to Clipboard: Set this feature to Disallow to hide access to the Copy Special to Clipboard feature.

Copy Cell to Clipboard: Set this feature to Disallow to hide access to the Copy Cell to Clipboard feature.

Print Print Cells: Set this feature to Disallow to hide access to the Print Cells feature.

Quan Browser






Export Export Processing Method: Set this feature to Disallow to hide access to the Export Processing Method feature.

Export Data to Excel Export Short Excel Report: Set this feature to Disallow to hide access to the Export Short Excel Report feature.

Export Long Excel Report: Set this feature to Disallow to hide access to the Export Long Excel Report feature.

View All Samples Show All Samples: Set this feature to Disallow to hide access to the Show All Samples feature.

Show Standard and QC Sample Types: Set this feature to Disallow to hide access to the Show Standard and QC Sample Types feature.

Options Delete Selected Component: Set this feature to Disallow to hide access to the Delete Selected Component feature.

Table 259.




712

Results Grid Delete Selected Samples: Set this feature to Disallow to hide access to the Delete Selected Samples feature.

Add Samples: Set this feature to Disallow to hide access to the Add Samples feature.

Copy Row: Set this feature to Disallow to hide access to the Copy Row feature.


Save All Saving All Result Files: Set this feature to Disallow to hide access to the Save All Result Files feature.

Print Print Reports: Set this feature to Disallow to hide access to the Print Reports feature.

Queue Manager






Queue Pause: Set this feature to Disallow to hide access to the Pause Queue feature.

Resume: Set this feature to Disallow to hide access to the Resume Queue feature.

Purge Queue: Set this feature to Disallow to hide access to the Purge Queue feature.

Analysis Remove From Queue: Set this feature to Disallow to hide access to the Remove From Queue feature.

Subtract Background



Table 259.




T



Operation Proceed: Set this feature to Disallow to hide access to the Proceed feature.

Xcalibur Configuration



Customer Info Print User Info: Set this feature to Disallow to hide access to the Print User Info feature.

Allow Access to Tabs Folders: Set this feature to Disallow to hide access to the Folders feature.

Customer Info: Set this feature to Disallow to hide access to the Customer Info feature.

Fonts: Set this feature to Disallow to hide access to the Fonts feature.

Peak Detection: Set this feature to Disallow to hide access to the Peak Detections feature.

Mass Options: Set this feature to Disallow to hide access to the Mass Options feature.

Labeling and Scaling: Set this feature to Disallow to hide access to the Labeling and Scaling features.

Intelligent Shutdown: Set this feature to Disallow to hide access to the Intelligent Shutdown feature.

Dataset List: Set this feature to Disallow to hide access to the Dataset list feature.

Reset Reset Allowed: Set this feature to Disallow to hide access to the Reset Allowed feature.

Instrument Configuration



Table 259.




714

In addition, the Authorization Manager contains the following dialog boxes:


• Create Private Group and Edit User List Of Private Group Dialog Boxes

• Edit Comment List Dialog Box

• Users In Group Dialog Box

Instrument Operations Add: Set this feature to Disallow to hide access to the Add Instrument feature.

Remove: Set this feature to Disallow to hide access to the Remove Instrument feature.

Configure: Set this feature to Disallow to hide access to the Configure Instrument feature.

File Converter





Convert Button Convert Button Check: Set this feature to Disallow to hide access to the Convert Button Check feature.

XReport



Table 259.




T

Choose Secure Group Dialog Box

Use the Choose Secure Group dialog box to select a secure user group so you can copy the complete set of permission levels to another group.

Create Private Group and Edit User List Of Private Group Dialog Boxes

Use the Create Private Group dialog box to create a new private (local) group and to add users to the group. After you create a private group, use the Edit User List Of Private Group dialog box to add or remove users from the group.

Table 260:


Secure Group View the list of secure user groups. When you select a group and click OK, the complete set of permission levels for the group is copied to the group selected in the Secure Groups list in the Authorization Manager.

Table 261:


System Group Select a domain name.

Users In System Group View the user accounts in the selected domain.

Group Name View the name of the new private group.

Users in Private Group View users in the new private group.

Buttons

Add Add the currently selected user in the Users In System Group list to the new private group.

Delete Remove the currently selected user in the Users in Private Group list.



716

Edit Comment List Dialog Box

Use the Edit Comment List dialog box to define a list of comments that a user must select from for features that require entering a comment.

Users In Group Dialog Box

Use the Users In Group dialog box to view the users in a domain or workstation logon group. Because membership in these groups is controlled by the domain administrator, the lists in this dialog box are read-only. See your domain administrator to make changes to domain or workstation logon groups.

New Comment Dialog Box

Use the New Comment dialog box to add comments to the list of predefined comments.

Table 262:


Comment View the predefined comments in the order that they appear to the user.

Buttons

Add New Comment Define a new comment.

Remove Comment Delete the currently selected comment in the Comment list.

Move Up Move the selected comment up one position in the Comment list.

Move Down Move the selected comment down one position in the Comment list.

Table 263:


Users In Group Users who are currently in the domain logon group.

Users Not In Group Users who are not currently in the domain logon group.

Table 264:


Enter A New Comment Enter a new comment to be added to the Comments list.



T

CRC Validator

Use the CRC Validator to compare the CRC (cyclic redundancy check) value stored in the database with the one calculated for the current file or files on the hard disk.

Table 265:


File Selection

Files Matching Database Filter

Select files by using the filter shown in the Database Filter box.

Edit Filter Specify how you want to filter the entries in the Audit Viewer or in the CRC Validator.

Database Filter View the current database filter. This box is read-only.

The default filter is the last selected dataset name. To change the filter, click Edit Filter.

Files Matching Pattern Select files matching the file pattern listed in the File Path and File Name lists.

File Path The path to files to be checked. You can enter the path manually or click Browse to select the path.

File Name The name of the file to check. You can use a wildcard character to represent one or more characters in the file name. Use an asterisk (*) as a substitute for zero or more characters. Use a question mark (?) as a substitute for a single character in the file name. You can also select a common file extension from the list.

Include Subfolders To include all subfolders in the search for matching files.

Check Results

View the results of the comparison of the CRC value for each selected file. The table includes the name of the file tested, the status of the check, and the full path to the file.

File Name View the name of the file tested, including the extension.

Status View the status of the check. The status value is one of the following:

CRCs Match: The CRC stored in the database matches the CRC just calculated for the file.

CRCs Do Not Match: The CRC stored in the database does not match the CRC just calculated for the file. Most likely, the file has been modified since the tracking record was created.

File Not In Database: The file was found on the hard disk but was not found in the database. It might not be a tracked file.

File Not On Disk: The file was found in the database but was not found on the hard drive. The file might have been deleted or archived.

Folder Name View the full path to the file.

Files Tested View the total number of files tested.



718

The CRC Validator also contains the “Filter Entries Dialog Box” on page 698.

Not In Database View the number of files that were not found in the database.

Not On Disc View the number of files that are in the database but could not be found on the disk.

CRCs Match View the number of files where the CRC value stored in the database matches the CRC just calculated for the file.

CRCs Differ View the number of files where the CRC value stored in the database does not match the CRC just calculated for the file.

Buttons

Check Start the comparison of the CRC value stored in the database with the one calculated for the specified file or files on the hard disk.

Print Print the CRC validation report. The report contains the filter or file mask used and the time and date that the report was produced.

Table 265:



I

Index
Numerics21 CFR Part 11
protecting records and 25requirements of 14Xcalibur software and compliance with 17

Aaccess

restricting to folders and files 31unauthorized

definition 15prevention of, overview 18

Add Programs to Tool Menu dialog box 104allowed (permission level), definition 49archiving files 43audit log, requiring comments for 51audit trail, definition 18Audit Viewer

filtering entries 65Instrument Error Page 127printing entries 67sorting entries 66starting from LCquan workbook 63starting from Windows desktop 62tabs 64use for auditing 61

Auditing Database Configuration Manager dialog box, showing restart settings 23auditing databases, accessing 61– 63auditing databases, configuring 22Authorization Manager

figure 47history log for 54printing security settings in 54saving controlled feature settings in 54using 46

Automatic Logoff feature 38Automatic Logoff Setup dialog box 39

Ccommand line arguments 89Comment dialog box 105comments, requiring 51configuration file 54configuring software applications

checklist (table) 19overview of 17

configuring the auditing database 22controlling user access

overview of 18through secure user groups 47

CRCsSee cyclic redundancy checks

Create private group dialog box, using 48Cyclic redundancy checks (CRCs)

CRC Validator 18, 56checking files with 56

definition 18

Ddata

falsification, prevention of 14reconstruction 14

database filters, selecting files using 58database, configuring 22DatabaseConfigManager dialog box 23databases

Global Auditing database, accessing 61– 63workbook database, accessing 61– 63

disallowed (permission level), definition 49disallowed state, changing appearance of 50domain logon groups

defining as secure 47definition 46


2

Index: E

Eevent log, definition 18Event page, Audit Viewer 64ExcelExp.exe 90exporting permissions 52

FFile Tracking page, Audit Viewer 64files

configuring security settings for 31removing and archiving 43tracking 18

Filter Entries dialog box 65filters, selecting files using 58Finnigan Security Server

confirming properties of 26functions 26

Finnigan Security Server Properties dialog boxGeneral page 27Log On page 28

foldersconfiguring security settings for 31permissions, inheriting 31

GGlobal Auditing database 61– 62

Hhistory log

for Authorization Manager 54for software applications 18

History page, Audit Viewer 64

Iimporting permissions 52inheriting permissions 52Instrument Error page, Audit Viewer 64, 127Instrument menu - Instrument Setup 119

Llogging on and off 38

Mmulti-user logon 38

OOut Of Date Instrument Drivers Detected dialog box 115

Ppassword (permission level), definition 49Password dialog box 110patterns, using to select files 59permission levels

Allowed, definition 49definition (table) 49Disallowed, definition 49exporting 52importing 52inheriting 52lost when user group deleted 51Password, definition 49retained when user group moved 51setting 49setting all 52setting all features to same 51Signature list, definition 49Supervisor password, definition 49

permissions, for folders and filessetting 35settings for administrators 35

printing security settings 54private groups

creating 48defining as secure 48definition 46editing 49

protecting records, overview of 17


Index: R

Rrecords, protecting 17removing files 43

Ssaving controlled feature settings 54security features, within software applications 18security folder, configuration file and 54security server

See Finnigan Security Serversecurity settings

folders and files 31printing from Authorization Manager 54

selecting filesusing a pattern 59

selecting files using database filters 58Sequential User Logon feature 38Set To Same button 51signature list

definition 51order of password dialog boxes and 51

signature list (permission level), definition 49Sort Entries dialog box 66Status values for CRC Validation 57Supervisor Password (permission level), definition 49Supervisor Permission dialog box 112system security 15

Ttracking, files 18

Uunauthorized access

definition 15preventing, overview 18

user access, controlling 18user authentication 26user groups

defining 47definition 46editing 49planning 46single user belonging to multiple 46

Wworkbook databases 63workbooks, auditing databases 62

XXConvert.exe 93
