TraceFinder Administrator Quick Reference Guide
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1 TraceFinder Administrator Quick Reference Guide This quick reference guide discusses the application configuration tasks assigned to the ITAdmin and LabDirector roles when user security is activated in the Thermo TraceFinder analytical software version 3.0. For detailed descriptions of all procedures described in this quick reference guide, refer to the Using the Application Configuration Mode chapter of the TraceFinder User Guide. Contents Reports Application Defaults Peak Detection Defaults Adducts Optional Features User Administration Trademarks To open the Application Configuration mode Click the Application Configuration icon,, in the upper right corner of any window. IMPORTANT After editing any of the application configuration features, you must apply the changes before they can take effect. To apply the application configuration settings 1. Click Apply. A message prompts you to restart the TraceFinder application to apply your changes. 2. Do one of the following: To restart the TraceFinder application now, click Restart Now. To close the Application Configuration mode and return to the previous mode, click Restart Later. The application preserves the changes until you restart the TraceFinder application. If you want to return the application configuration settings to their original state (when you first opened this mode), click Cancel. Revision A XCALI Thermo Fisher Scientific Inc. All rights reserved.
2 Reports Use the Reports page to configure a list of reports that are available to all users when they generate reports from the Method Development, Analysis, and Acquisition modes. From the Reports page, you can configure standard, custom, ToxID, or target screening reports. To specify which reports are available 1. In the navigation pane for the Application Configuration mode, click Reports. 2. Use the directional arrows to move reports from the Installed Reports pane to the Displayed Reports pane. Tip Use the CTRL or SHIFT keys to select multiple reports. In the Method Development, Analysis, and Acquisition modes, users can access all reports in the Displayed Reports pane. 3. To create a single composite report for an entire batch (rather than a separate report for each sample), select the Batch Level check box for the report. 4. To import new reports, do the following: a. Click Import. b. Browse to a Crystal Reports.dll file or a Custom Reports.xltm file, and click Open. The application saves the imported report to the TraceFinder installation directory and displays the new report in the Installed Reports pane. Application Defaults Peak Detection Defaults Use the Application Defaults page to specify the default laboratory and instrument names, the displayed mass precision, and the chromatogram intensity scale to use for reporting. To specify application defaults 1. In the navigation pane for the Application Configuration mode, click Defaults. 2. Type the name of your laboratory and instrument. The application uses this laboratory name and instrument name in the report headings. 3. In the Display Mass Precision box, set the decimal value for the mass precision to an integer from 2 to 6, inclusive (the default is 2). The TraceFinder application uses this mass precision value to display mass values in reports and spectrum displays. 4. Select Relative or Absolute from the Chromatogram Intensity Scale list. This sets the default display type for both chromatograms displayed in data review and reports. Use the Peak Detection Defaults page to specify detection parameters for the Genesis, ICIS, or Avalon detection algorithm. These parameters are available for quantitation methods only. To specify peak detection defaults 1. In the navigation pane for the Application Configuration mode, click Peak Detection Defaults. 2. In the Detector Type list, select one of the following detector types: MS: Mass spectrometer that ionizes sample molecules and then separates the ions according to their mass-to-charge ratio (m/z). PDA: Photodiode array detector providing a linear array of discrete photodiodes on an integrated circuit chip. It is placed at the image plane of a spectrometer so that a range of wavelengths can be simultaneously detected. Analog: Supplemental detectors (for example, FID, ECD). When you select this detector, any reports that display a QIon value show the value as Analog and any reports that display spectra show the spectra as Not Available. A/D card: If your detector is not under data system control, you can capture the analog signal and convert it to digital using an interface box (for example, SS420X) for storage in the raw data file. UV: A UV spectrophotometer (for variable-wavelength detection) or photometer (for single-wavelength detection) equipped with a low-volume flow cell. This detector detects analytes that readily absorb light at a selected wavelength. 2
3 3. In the Mass Tolerance area, do the following: a. Select the units of measure that you want to use (MMU or PPM). b. In the Value box, specify the number of millimass units or parts per million to use as the upper limit. The application applies this mass tolerance to the extracted chromatograms. The default is 500 MMU. 4. In the Retention Time area, do the following: a. In the Window box, specify the width of the window (in seconds) to indicate how far around the expected retention time the system will look for a peak apex. b. In the View Width box, specify the viewable size (in minutes) of the ion chromatogram display. 5. In the Ion Ratio Parameters area, do the following: a. In the Window Type box, select Absolute or Relative as the calculation approach for determining the acceptable ion ratio range. b. In the Window (+/-%) box, select the acceptable ion ratio range. c. In the Ion Coelution box, select the maximum difference in retention time between a confirming ion peak and the quantification ion peak. 6. In the Peak Detection Parameters area, select one of the detection algorithms: Genesis, ICIS, or Avalon. Each of these detection methods uses specific detection settings. The Genesis peak detection algorithm is provided for backward compatibility with Xcalibur 1.0 studies. The ICIS peak detection algorithm is designed for MS data and has superior peak detection efficiency at low MS signal levels. The Avalon peak detection algorithm is designed for integrating UV/Vis and analog chromatograms. For detailed descriptions of Genesis, ICIS, and Avalon detection parameters, refer to the Using the Application Configuration Mode chapter of the TraceFinder User Guide. Adducts Use the Adducts Configuration page to specify the adducts that will be available for you to use in method development. To add an adduct 1. In the navigation pane for the Application Configuration mode, click Adducts. The Adducts Configuration page opens, displaying the default positive and negative adducts. 2. In the Positive Adducts or Negative Adducts pane, click the Add New Adduct icon,. The application adds an empty row in the Adducts list. 3
4 3. Type the formula for the new adduct ion. The formula syntax is alphanumeric and case sensitive. It can include parentheses and brackets. The formula specifies the difference between the neutral molecule and the charged ion that you expect to see in the results. IMPORTANT When you create an adduct formula, you can type both uppercase and lowercase letters; however, the TraceFinder application interprets all uppercase input as single-letter elements and all lowercase input as two-letter elements. For example, it interprets the string inau as In Au and COSI as C O S I. 4. In the Gain/Loss column, select Gain or Loss. This indicates if the adduct is a loss or gain to the calculated neutral mass. The application calculates the neutral mass value for the adduct. These adducts are available for you to select in the Compound Database view of the Method Development mode when you specify parameter values for target peaks. To remove an adduct 1. In the Positive Adducts or Negative Adducts pane, select the adduct that you want to remove. 2. Click the Delete Selected Adduct icon,. You can delete only adducts that you added to the adducts list. You cannot delete default adducts defined by the TraceFinder installation. 4
5 Optional Features Use the Optional Features page to do any of the following: Activate the features for user security, ToxID, quick acquisition, intelligent sequencing, or multiplexing features. Choose a batch wizard style. Choose between full-sequence and single-sample submission options. Choose a screening library. To open the Optional Features page In the navigation pane for the Application Configuration mode, click Optional Features. The Optional Features page opens. To activate user security Select the User Security check box. When you activate this option, all users must log in to the TraceFinder application to access the modes assigned to their user role. See User Administration on page 7. To activate ToxID Select the ToxID check box. You must have the Thermo ToxID application installed on your computer before you can generate ToxID reports. To activate quick acquisition Select the Quick Acquisition (EnviroLab/ToxLab/QuanLab Forms) check box. Note The Quick Acquisition feature is not available when you activate multiplexing. 5
6 To select a wizard style Select a wizard style from the Batch Wizard Style list. Acquisition Batch Wizard: Adds the Acquisition mode to the navigation pane. When you activate multiplexing, the application automatically activates this wizard style. Batch Template Wizard: This is the default wizard style and is similar to the acquisition wizard in the EnviroLab Forms, ToxLab Forms, and QuanLab Forms applications. Note The Batch Template Wizard option is not available when you activate multiplexing. To activate multiplexing 1. Select the Multiplexing check box. 2. In the channels list, select 2 Channels or 4 Channels. 3. When you select 2 channels, select either the 1 arm or 2 arm autosampler configuration. The 1-arm configuration activates channels 1 and 3; the 2-arm configuration activates channels 2 and 4. When you use a 4-channel configuration, autosampler 1 uses channels 1 and 3 and autosampler 2 uses channels 2 and 4. When you activate multiplexing, the following optional features are not available: Quick Acquisition Batch Template Wizard Single Sample Submission (Intelligent Sequencing) Note The Multiplexing options are available only when you have installed the power modules. Refer to the Using the Application Configuration Mode chapter of the TraceFinder User Guide. To activate intelligent sequencing Select the Intelligent Sequencing check box. Note The Intelligent Sequencing option is not available when you activate multiplexing. The Acquisition Submission Options default to Single Sample Submission. The Full Sequence Submission option is not available when you select the Intelligent Sequencing option. To specify acquisition submission features Select either the Full Sequence Submission or the Single Sample Submission option. Full Sequence Submission: Supports look-ahead features of the autosampler. When the instrument method specifies the look-ahead feature, the Tracefinder application functions like a multiplex driver and submits the next vial position to the autosampler. When you submit a batch, the autosampler begins preparation for all sample injections when the pre-run condition begins. All samples in the batch must be complete before other batches (even higher priority batches) can begin. When you are using Full Sequence Submission, priority batches run immediately after the currently acquiring batch is complete. Single Sample Submission: Supports intelligent-sequencing features. When you submit a batch, the autosampler begins preparation for one sample injection at a time. Higher priority batches can interrupt the sample sequence in the currently acquiring batch. When you are using Single Sample Submission, priority batches run immediately after the currently acquiring sample is complete. Note The Single Sample Submission option is not available when you activate multiplexing. 6
7 User Administration Use the User Administration page to add, remove, or edit user accounts and permissions. To open the User Administration page In the navigation pane for the Application Configuration mode, click User Administration. To add a user 1. In the left pane, click the Add User icon,. 2. Enter a unique name in the Username field. 3. Select a role from the Role list. You must assign each user one of these roles to determine which TraceFinder modes the user can access. User role Method Development Analysis Acquisition Application Configuration LabDirector ITAdmin Supervisor Technician QAQC 4. Enter the user s password. You will not receive a confirmation, so take care to enter the password and communicate it to the user. 5. (Optional) Enter the user s full name, account number, phone number, and address. 6. When all the user information is correct, click the Save Changes icon,. To edit user information 1. In the User Listing table, select a user. The user information populates the parameter fields in the User area of the User Administration page. 2. In the left pane, click the Edit User icon,. The application activates the parameter fields in the User area. 3. Edit any of the parameter values. IMPORTANT If you are the only user in the ITAdmin or LabDirector role, you cannot remove your user name, clear the Enabled check box, or change your role to anything other than ITAdmin or LabDirector. At least one activated user must be assigned to the ITAdmin or LabDirector role so that there is a least one user who can access the User Administration page. 7
8 4. Do one of the following: When all the user information is correct, click the Save Changes icon,. The TraceFinder application adds the new parameter values to the User Listing, and the parameters in the User area are unavailable. or To discard all changes and not save the edits, click the Cancel Changes icon,. All changes are discarded, and the parameters in the User area are unavailable. To remove a user 1. In the User Listing table, select a user. The user information populates the parameter fields in the User area. 2. In the left pane, click the Remove User icon,. If you select your current user name, the Remove User icon is unavailable. You cannot remove yourself. 3. When prompted, confirm that you want to remove this user. If the user is currently logged in to the TraceFinder application, the user s current session is not affected. 4. Click OK. Note Rather than completely removing the user, you can make the user login unavailable without removing all the user information from the system. See To edit user information on page 7. Trademarks TraceFinder and ToxID are trademarks and Xcalibur is a registered trademark of Thermo Fisher Scientific Inc. in the United States. 8
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