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Xcalibur 3.0 XReport User Guide Version A

1. 82 Select Plot Details Paces renea Fede ped E bet edited 84 Select Enhance Details Page 225522 Sol cued oes giae a DARE QS 86 Select Chromatogram Style Page i i ee abides a ore EX toe Rage yea 87 Select the Peak Labeling Page oo sees ede eese ecce uiae dads 88 Select How the Chromatogram Axes Will Be Configured Page 91 Configure Normalization for the Chromatogram Page 92 Finishing the Chromatogram Wizard 0 0000s cece eee ee 93 Configuring a Component Calibration Curve vires pde aap CR 93 Configuring 4 Spectr ni aeajr bath acta Rosa e a a etna e a 95 Gotifigut ODHUOBS ters inieris ii naati are statutes oe Enara i eyele Saioa 96 Configure Plot Types 12d 40 chin ces edocet DEOR eee ed 96 Enhance Speotia uaa aan a alow tid adios ud acest oed Aa keds anota 97 Confipure Spectrum Style xu os eese acer A Ea weet 98 Configure Peak Labels au Y eto re ebd oratione Ae mies dites 99 COHDBUEG Aes oet cotes orale g tet kate ee East eet dirait iocus 100 Select Normalization Options sx Gn e x eel oie rere tuc d 101 Specify Mui cT 102 Configuring Columns 1559 rex ae ee bebe eae eae stim sad 103 Set Sample Repeat Options n us Aera ade etai uc opa bc cR a ates 104 Set Summary Repeat Options 0 eee ee eee 105 Sample XReport Template Files 0 0c cece eee eee eee eee 107 Types of Report Objects 00 c cece cece cece cette tent e ee eeeee 109 Text Object D
2. Signature infomation order C Signed By first 2 To display the Created By signature block before the Signed By signature block select the Created by first option in the Signature Information Order area or to display the Signed By block before the Created By block select the Signed by first option 3 Click OK Thermo Scientific XReport User Guide 69 4 Configuring Objects and Sections Configuring a Bitmap Object Configuring a Bitmap Object To configure the bitmap object 1 Right click the bitmap object and choose Properties from the shortcut menu The Bitmap Properties dialog box opens see Figure 46 Figure 46 Bitmap Properties dialog box Bitmap Properties Bitmap file If the bitmap needs to be changed the new bitmap file name should be entered here or click on the browse button to browse for the file Bitmap file Reset to original size Press OK or Apply to see the effect 2 Enter the name of the image file Choose one of the following file formats bmp dib gif jpg or ico 3 To set the size of the bitmap image to the size of the original file click Reset to original size 4 Click OK 70 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Chromatogram Object Configuring a Chromatogram Object To configure a chromatogram report object 1 Right click the object and choose Properties from the shortcut menu The Chromatogram Properties di
3. Double click the Report Name column to select an XReport template xrt file to use for this report 4 Save the processing method Thermo Scientific XReport User Guide 33 3 Generating a Report Creating a Report from the Xcalibur Data System Generating Reports when Running a Sequence You must create a sequence to run either a single sample or multiple samples from the Sequence Setup window When you click the Run Sample icon in the Sequence Editor toolbar the data system automatically selects the first row of the sequence When you click the Run Sequence icon the data system automatically selects the entire sequence if you have not already selected a subset of sequence rows t v 1 34 XReport User Guide To generate reports when running a sequence Set up the report options in a processing method as described in Setting Report Options in a Processing Method In the Xcalibur Sequence Setup window open the sequence that you want to run Specify the processing method that includes all of the report options in the Proc Meth column To run a subset of the sequence select the sequence rows that you want to run Choose Actions Run This Sequence or Actions Run This Sample The Run Sequence see Figure 13 dialog box opens The Run Rows box lists the row selection Figure 13 Run Sequence dialog box Run Sequence Acquisition Options User Instrument Start Instrument Mass Spectro
4. Area End RT Found RT Height e Start RT User Columns 1 to 5 The Spectrum List table displays the text equivalent of the spectrum graphic object This table provides information for each peak with each sample There is a separate row for each sample peak combination The rows are grouped so that all peaks in a sample are shown together Required data file rst raw Section placement Nonrepeating section The Spectrum List table has the following possible fields miz Intensity Relative e Wavelength User Columns 1 to 5 Thermo Scientific D XReport Reference Report Objects Text Objects Text objects contain text labels and associated text fields These fields can be deleted cut copied and pasted anywhere in the report template for example a header The text object fields are replaced with textual information when a report template is resolved with Xcalibur data These text objects are available in XReport Annotation Processing Method General Component IdentDetectCal Settings Processing Method Qual Component ISTD Settings Summary Quan ISTD Peak Summary Component Settings Summary Quan Peak Summary Component Sys Suit Flags Settings Report Info Instrument Method Sample Header Annotation Use the Annotation object to insert static text into your report To enter the text right click the object and choose Properties from the shortcut menu The Annotation Properties dialog box opens Type your text in the bo
5. UsetLabel2 UserVal2 UsetLabel3 UserVal3 UsetLabel4 UserVal4 UsetLabel5 UserVal5 m Objects pane Section End CompName ISTDName Expected ExpRetTime a e N 89 9 8 Retention RetTimeWin Time dow View Width Retention RetTimeRef Relative Abundance Genesis GenMinPea Minimum 4 2 2013 4 05 57 PM Template pane Template outline pane The Sections pane lists the available sections for the selected application for example Xcalibur To add a section to a report drag it from the Sections pane to the Template pane The Objects pane lists the objects that are available for the currently selected section To add an object to a report drag it from the Objects pane to the currently selected section in the Template pane 2 XReport User Guide Thermo Scientific 1 Introduction to XReport Report Templates Overview Use the Template pane to configure a report layout by dragging and arranging objects To configure a report object right click it and choose Properties from the shortcut menu To configure a repeating section right click the QL or QN icon in the left margin of the page at the top of the sections pane and choose Properties from the shortcut menu The size of the page in this pane corresponds to the size of a standard 8 5 x 11 in piece of paper in either portrait or landscape mode Adjust the height of sections by dragging the
6. Expand the Home Page entry In the directory tree expand the Sequence Operations entry in the permission level pane Select Batch Reprocess from the list of operations below Sequence Operations Select Signature List in the Permission Level area In the Signature List Groups area select a group from the Available groups list and click gt gt to move it to the Signatures Reqd list The members of this group must type their log on names and passwords to electronically sign the report when it is generated Repeat this step for each group that you want to add to the Signatures Reqd list Note If you do not have any groups available or if the groups do not contain the correct members refer to the Foundation Administrator Guide or the Foundation Help for information on how to create and modify groups To require a signature from the current user when the report is generated select the Current User Must Sign check box Thermo Scientific 3 Generating a Report Creating a Report from the Xcalibur Data System At this point the settings should be similar to the settings in Figure 17 Figure 17 Sequence Setup settings for producing signed reports Authorization Manager r Available Groups C DomainAworkstation Private Expand Tree CRC Validator s Home Page m Run Application Dataset Selection Analysis Devices m Sequence Operations v Run Sequence 7 Batch Reprocess v Import
7. Reporting Tool for the Xcalibur and LCquan Data Systems User Guide Software Version 3 0 XCALI 97554 Revision A June 2013 DOCUMENTATION 2013 Thermo Fisher Scientific Inc All rights reserved Xcalibur is a registered trademark and LCquan is a trademark of Thermo Fisher Scientific Inc in the United States Microsoft Windows and Excel are registered trademarks of Microsoft Corporation in the United States and other countries Adobe Acrobat and Reader are registered trademarks of Adobe Systems Incorporated in the United States and other countries The following are registered trademarks in the United States and possibly other countries Oracle is a registered trademark of Oracle Corporation and or its affiliates All other trademarks are the property of Thermo Fisher Scientific Inc and its subsidiaries Thermo Fisher Scientific Inc provides this document to its customers with a product purchase to use in the product operation This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited except with the written authorization of Thermo Fisher Scientific Inc 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 represent
8. on page 46 Topics in this section Adding Deleting or Reordering Sections Resizing Sections Configuring a Qual or Quan Repeating Section o Qo o Adding Deleting or Reordering Sections To add a section to the report drag it from the Sections pane upper left to the Template pane center Add only one section to the template at a time To delete a section from the report click it in the Report Template Outline pane far right and press DELETE The system prompts you to confirm the deletion You cannot delete the header or footer sections When the Report Template Outline pane is not visible choose View gt Report Template Outline or right click a section and choose Delete Section from the shortcut menu To change the order of the sections in the template drag them in the Report Template Outline pane Header and footer sections must remain at the top and bottom of the list respectively Resizing Sections To automatically remove the extra space at the top and bottom of a section select the section and choose Layout gt Shrink Wrap To automatically add a half page of extra space at the bottom of a section select the section and choose Layout gt Expand To manually add or remove extra space at the bottom of a section drag the bottom border of a section up or down 16 XReport User Guide Thermo Scientific 2 Creating a Template Adding Ordering and Configuring Sections Configuring a Qual or Quan Repeati
9. 1 39533 BB 1 519 methyltestosterone Expected Retention Time min Retention Time Window sec View Width min Retention Time Reference Genesis Minimum Peak Height S N Genesis Smoothing Points 7 Detector Type MS Valley Detection Enabled Genesis Constrain Peak Width Enabled No 2 0 30 00000 1 00000 Yes 3 00 No Relative Abundance 100 90 80 70 60 50 40 30 20 10 0 Calculated Amount Signal To Noise Area cts sec RT 1 49 2 49 SM 7G 1 99 NL 9 60E4 m z 266 6 267 6 284 7 285 7 F c Full ms2 303 30 i 100 00 310 00 MS Genesis steroids02 H I 1 5 2 0 Time min 5 10841 148 23 1040530 60245 Thermo Scientific Peak Integration Report Page 4 Peak Integration Report progesterone methyltestosterone Expected RT 2 67 3 67 SM 7G ee Expected RT 1 49 2 49 SM 7G Retention Retention i Time min 32 90 Time min 2 0 i Retention 80 Retention 80 Time Window Time Window sec 30 00000 a sec 30 00000 M View Width ES View Width i f min 1 00000 3 50 min 1 00000 2 5 Retention 2 Retention Time g Time Reference No se Reference Yes i Genesis 20 Genesis 20 Minimum Peak Minimum Peak 40 Height S N 3 00 25 i Height S N 3 00 Genesis 7748s a0 32 c4 as Genesis is ao Smoothing Time min Smoothing Tite m Points 7 Points 7 Detector Type MS Detector Type MS Valley Valley Detection
10. Always save and close the report template in XReport before using it to generate a report from the Xcalibur data system Sample Reports and Summary Reports To set up reporting options in the data system in Processing Setup or Quan Browser select two types of reports Sample reports to print reports that give information about individual samples Summary reports to print reports that give summary information about an entire sequence or set of samples The example template files included with XReport indicate the specific templates to use to generate sample reports or summary reports For descriptions of sample files see Sample XReport Template Files on page 107 Generating a Report From Sequence Setup To generate reports from the Sequence Setup window create a processing method that includes the necessary report options on the Reports page of the method Use the Sequence Setup window to generate reports when running a sample or sequence or batch processing a sequence See these topics for more information Setting Report Options in a Processing Method Generating Reports when Running a Sequence Generating Reports when Batch Processing a Sequence 32 XReport User Guide Thermo Scientific 3 Generating a Report Creating a Report from the Xcalibur Data System Setting Report Options in a Processing Method To automated reporting set up the appropriate report templates in your processing methods To set up reports
11. Calculated Amount Actual Ion Ratio Ion Ratio Passed Target Range Qualifier Ion User Columns 1 to 5 Library Search Graphics Table 178 The Library Search Graphics table displays the graphical results from a library search on a Qual peak Required data file rst raw Section placement Nonrepeating section This table has the following possible fields XReport User Guide Hit Spectrum Delta Compound Structure Thermo Scientific Library Search Results Table Thermo Scientific The Library Search Results table displays the results of a library search on a Qual peak Required data file rst raw Section placement Nonrepeating section This table has the following possible fields SI RSI Compound Name Cas Probability Area Area Library Molecular Formula Molecular Weight RT Scan User Columns 1 to 5 D XReport Reference Report Objects XReport User Guide 179 D XReport Reference Report Objects Processing Method Programs Table 180 XReport User Guide The Processing Method Programs table displays a list of programs to be run by the data system after the sample has been analyzed and the data has been processed The application runs programs in the order listed Required data file pmd Section placement Nonrepeating section This table has the following possible fields Num Enable Std QC Unk Action Other Parameters Program or Macro Name Sync
12. Peak Area Peak Height BL Data File Name Sample ID S N Area Peak Width Saturated User Column 1 to 5 Thermo Scientific Quan Summary Table Thermo Scientific D XReport Reference Report Objects The Quan Summary table displays information specific to component peaks detected by quantitative analysis for all samples in a sequence Note To display component peak information for a single sample only use the Quan Peak Table object Required data file sld pmd rst Section placement Nonrepeating section The Quan Summary table has the following possible fields Component Name RT Calculated Amount Response BL Diff Area Area Area Ratio Calibration Flags Component Found Component Type Data File Name Data Flags Expected RT Height Height Ratio Ion Ratio Status ISTD Area ISTD Height ISTD Name ISTD Response Keys Peak Purity Peak Status Response Ratio S N Sample ID Sample Type Saturated Specified Amount System Suitability Units Width User Columns 1 to 5 XReport User Guide 185 D XReport Reference Report Objects Sample Table 186 XReport User Guide The Sample table displays system suitability and flag processing results for each component in a sample and repeats this information for every sample in a sequence This table provides information for each peak with each sample There is a separate row for each sample peak combination The rows are grouped
13. Table 65 Preview window parameters Parameter Print Save Next Page Prev Page First Page Last Page Description Print your report preview This option is available only for resolved reports not for simulated reports Save your report in the following formats available only for resolved reports not simulated reports Microsoft word document doc Microsoft Excel workbook xls Web page htm or html Plain text txt Rich text format rtf Adobe PDF pdf Scroll the preview to the next or previous page in the report Scroll the preview to the first or last page in the report Page Xof Y View X the current page and Y the total number of pages in the report Type in a new value for X to scroll to that page Two Page View the preview two pages at a time Zoom In Zoom Out Increase or decrease the size of the report in the preview window Close Close the preview window and go to XReport Help View XReport Help Save As Dialog Box 164 XReport User Guide Use the Save As dialog box to save your report template The Save As dialog box is the standard Microsoft Save dialog box with the addition of a Lock Template check box If you select this check box the template cannot be saved with the same name again It can however be opened edited and resolved with data To save an edited version save it as a different filename Thermo Scientific D XRe
14. User Columns 1 to 5 Thermo Scientific D XReport Reference Report Objects Processing Method Sample Reports Settings Table The Processing Method Sample Reports Settings table displays sample report information for each sample in a sequence including the template name and the report file name Specify the sample type in the processing method Required data file pmd Section placement Nonrepeating section This table has the following possible fields Num Enable Std QC Unk Other Report Template Name Save As User Columns 1 to 5 Processing Method Summary Reports Settings Table The Processing Method Summary Reports Settings table displays summary reports to be issued after processing the samples in a bracketed or non bracketed sequence Required data file pmd Section placement Nonrepeating section This table has the following possible fields Num Enable Save As Report Template Name e User Column 1 to 5 Thermo Scientific XReport User Guide 181 D XReport Reference Report Objects Qual Peak Table 182 XReport User Guide The Qual Peak table displays information specific to chromatogram peaks detected by qualitative analysis for a single sample Note To display information on chromatogram peaks for an entire sequence use the Qual Summary Table Required data file rst Section placement Nonrepeating section This table has the following possible fields RT Pea
15. XReport Templates Save in o Templates amp ak EJ 3E calibrationFile xrt B IonRatioConfirmation xrt 3E compCalReport xrt il IonRatioConfirmationGraphical x 3E CompCalReport Avalon xrt Sl lonRatioConfirmationGraphicalSir 3EllCompCalReport Genesis xrt 3SElTenRatioConfirmationaraphicalSt Sl CompCalReport ICIS xrt 3ElubrarysearchReport xrt SE CustLibrsearRept xrt SElPeakintegration xrt C emm E File name Save as type XReport Template xt xl Cancel Help Lock template 2 Give the report template an appropriate name and save it in the Xcalibur templates folder with the templates that ship with the Xcalibur software 3 Select the Lock Template check box and click Save XReport User Guide 27 p Generating a Report To generate an Xcalibur report resolved document combine a report template with one or more Xcalibur data source files pmd raw rst sld xcal files There are two ways to generate reports Use the XReport Data Source Browser to automatically search for the required data source files and combine the data with a template to generate a report This method generates a single report Associate the data you produced in the Xcalibur data system with a report template and combine the data with the template to generate a report This method generates multiple reports from the data system Contents Creating a Report Within XReport Creating a Report
16. b Select a processing method file c Choose a component in the Use the Select Component dialog box d Click OK to return to the wizard The Next button is active only after you have entered a component 3 Select the Use Quan peak s associated Internal Standard check box of the Quan peak to use the selected the associated internal standard of the Quan peak instead of the Quan peak Note Select a valid peak for XReport to resolve the report correctly If the file used to resolve the report does not contain the specified peak the Xcalibur data system removes the chromatogram from the resolved report 4 Click Next to go to the next page of the wizard Select the Qual Peak Page Use the Select the Qual Peak page to explicitly specify the Qual peak for a Qual Results Based chromatogram report object To specify a Qual peak 1 To specify the Qual peak in the Qual Peak to Display area type the appropriate retention time in the Retention time box see Figure 55 The Next button is active only after you have selected a component in the Retention time box Set the retention time to any time within the start and end peak boundaries Note Select a valid retention time for XReport to resolve the report correctly If the file used to resolve the report does not contain the specified retention time the chromatogram is removed from the resolved report 80 XReport User Guide Thermo Scientific 4 Configuring Objects and S
17. choose Layout Preferences The Preferences dialog box opens see Figure 6 Set the spacing between grid lines and whether to snap objects to the grid as they are added to the Template pane Figure 6 Preferences dialog box Preferences Grid spacing DK Width 5 Units CAES Height 5 Units Help Actions V Snap to arid Show page end Show template configuration 20 XReport User Guide Thermo Scientific 2 Creating a Template Adding and Configuring Report Objects Using Columns Add columns to arrange other reporting objects so that they appear in columns To add a column to the template drag the column object from the Objects pane to the Template pane After adding a column object to the template you can resize reposition and configure it To configure a column object 1 Right click the column object 2 Choose Properties from the shortcut menu The Column Properties dialog box opens see Figure 7 To learn how to configure columns and how columns work with different repeat types see Configuring Columns on page 103 Figure 7 Column Properties dialog box Column Properties Number of columns 2 9 Repeat type Sample repeat Summary repeat G C MN Cancel Help You can resize the entire column object select it and drag the corner handles but the columns within the column object remain equal in size After you have finished configuring the columns drag objects to the co
18. select the Base Peak check box The data system displays BP before the label To label peaks with the signal to noise ratio at the peak maximum select the Signal to Noise check box The data system displays SN before the label To label peaks with flags providing supplemental information about the peak data select the Flags check box When a peak is saturated the data system displays an S above the peak Thermo Scientific 4 Configuring Objects and Sections Configuring a Chromatogram Object 6 To label peaks with the integrated area of the peaks select the Area check box The data system displays AA before the label when detected automatically or MA when detected manually 7 To label peaks with the apex height select the Height check box The data system displays AH before the label when detected automatically or MH when detected manually 8 To offset a label from its normal position to avoid conflict with another label select the Offset check box in the Label Styles area Type the number for the offset for the number of characters in the Size box 9 To use vertical rather than horizontal labels select the Rotated check box 10 To place a rectangular outline around each peak label select the Boxed check box 11 To limit the labeling of peaks to those exceeding the specified percentage of the base peak set the Label threshold box to a percent value between 100 and 0 12 Click Next to go to the next page o
19. select the Use demo file check box Figure 52 Figure 52 Selecting a Quan result based chromatogram Select Demo File demo file can be associated with a chromatogram control This demo file allows the control to show how the current settings for the chromatogram will look when applied to real data v Use demo file m Demo File c calibur examples data drugx_01 rst d When using result data for the chromatogram demo you must explicitly specify the peak to demo m Demo Peak Quan component D4 E coc Heo 2 To search for the required demo file raw file click the browse button in the Demo File area The Select Raw Data File dialog box opens 3 Select a demo file and click Open 4 To specify the peak to demo click the browse button in the Demo Peak area The Select a Peak dialog box opens 5 Select a peak from the list located in the result file 6 Click OK to apply the selection and return to the wizard 7 Click Next to go to the next page of the wizard Thermo Scientific XReport User Guide TI 4 Configuring Objects and Sections Configuring a Chromatogram Object Qual Result Based Chromatogram Explicit Peak When configuring a chromatogram report object based on Qual Results with an explicit Peak Type required use this procedure to select a file To select a demo file for a Qual based chromatogram 1 Select the Use demo file check box to associate a demo file with the chromatogram
20. selecting one of the following options Auto zero Optimize the y axis automatically for each chromatogram Intensity range Set the range manually Type the minimum and maximum intensity required for the y axis The valid range is 200 00 to 200 00 Figure 65 Configure Normalization for the Chromatogram page Configure Normalization For The Chromatogram Configure how the chromatogram display will be normalized The normalization method will be applied to each trace in the chromatogram individually RT 1 48 2 48 SM 7G Normalize method 400 RT 1 99 C uto zero 80 60 Normalize each plot to 40 Largest peak in subsection v o c m D i ci a TX v m w c 20 Largest peak in selected time range C Largest peak in all times 1 5 2 0 Time min a ae 92 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Component Calibration Curve 2 Define a peak to use for normalization in the Normalize each plot area by selecting one of the following options Largest peak in subsection Normalize each split time range to the largest peak in the division Largest peak in selected time range Normalize the spectrum to the largest peak in the displayed time range Largest peak in all times Normalize the spectrum to the largest peak in the entire chromatogram The Normalize each plot area is active when you select a raw based chromatogram and yo
21. Chrom Spec Chrom 1 Spec 1 Chrom 2 Spec 2 Lus Sample 1 Chrom 3 Spec 3 Chrom 4 Spec 4 Chrom 1 Spec 1 Chrom 2 Spec 2 SS Sample 2 Chrom 3 Spec 3 Chrom 4 Spec 4 Text If you click the New Sample New Row option data for a new sample always starts on a new row Thermo Scientific XReport User Guide 161 D XReport Reference XReport Dialog Boxes Configure Component Calibration Curve Dialog Box Set parameters in the Configure Component Calibration Curve dialog box to specify the component name that a nonrepeating Component Calibration Curve report object is plotted for in your report Table 61 Configure Component Calibration Curve dialog box parameters Parameter Description Component Name Specify the name of the component to display in your component calibration curve Click the Browse button to open a dialog box and select a processing method file After you select a processing method file XReport provides a list of the components to choose from in that file After you select a component XReport returns to the Configure Component Calibration Curve Dialog Box and adds the selected component to the Component Name box Data Sources Dialog Box Select data files to apply to the current report in the Data Sources dialog box Table 62 Data Sources dialog box parameters Parameter Description Calibration File Select the calibration xcal file to apply to the current report Processing Method File Select the process
22. File Connect a demo file with the chromatogram report object Demo File Specify the path to the demo file Demo Peak Quan Component Specify the Quan peak to use in the demo file Click the Browse button The Select A Peak Dialog Box opens This box appears only if you are configuring a Quan based chromatogram Qual Peak RT Specify the Qual peak to use in the demo file Click the Browse button The Select A Peak Dialog Box opens This box appears only if you are configuring a Qual based chromatogram and not showing all Qual peaks Select these options on the Select Chromatogram Type page 136 XReport User Guide Thermo Scientific D XReport Reference XReport Dialog Boxes Select Enhance Details Set parameters on the Select Enhance Details page to enhance a chromatogram plot by applying smoothing Table 26 Select Enhance Details page parameters Parameter Enable Smoothing Description Apply smoothing to the chromatogram Smoothing Details Type Define the type of smoothing algorithm applied to the chromatogram either Boxcar or Gaussian Points Specify the number of smoothing points to use in the smoothing algorithm Select How the Chromatogram Axes Will Be Configured Set chromatogram axes labels and display parameters on the Select How The Chromatogram Axes Will Be Configured page Table 27 Select How the Chromatogram Axes Will Be Configured page parameters Parameter Description X axi
23. Flags provide supplemental information about the peak data For example when a peak is saturated the Xcalibur data system displays an S above the peak 3 To specify that other spectrum peaks are labeled relative to that value type a value in the Relative to box 4 Type the number of decimal places to be used in the labels in the Decimals box Thermo Scientific XReport User Guide 99 4 Configuring Objects and Sections Configuring a Spectrum 5 To move a label from its normal position to avoid conflict with another label select the Offset check box in the Label Styles area Choose the number for the offset for the number of characters in the Size box 6 To use vertical rather than horizontal labels select the Rotated check box 7 To place a rectangular outline around each peak label select the Boxed check box This option does not apply to flags 8 To limit the labeling of peaks to those exceeding the specified percentage of the base peak type a percent in the Label Threshold box Configure Axes To set spectrum axis labels and display options use the Axis Page To configure axis options 1 Type the x axis name in the Name box in the X Axis area see Figure 73 Figure 73 Axis page in the Spectrum Properties dialog box Spectrum Properties Options Plot type Enhance Style Labels Axis Normalization Peak X Aris Name Offset m z r Split mass range Division 2 Relative Abun
24. Generates a Quan sample report containing peak integration data generated using Genesis Thermo Scientific XReport User Guide 107 A Sample XReport Template Files Table 2 Sample XReport template files Sheet 2 of 2 Report template file name Data source files ProcessingMethod xrt pmd ProcessingMethod Avalon xrt ProcessingMethod_Genesis xrt ProcessingMethod_ICIS xrt Description Use Generates processing method sample reports Use from Processing Method Setup in the Xcalibur data system QualPeakReport xrt Ist raw Generates a simple Qual sample report Use for data from Batch Processing in the Xcalibur data system QuanPeakResults_ESTD xrt Ist raw pmd Generates Quan sample reports Can QuanPeakResults ISTD xrt QuanResults xrt QuanSimple xrt QuantifySampleReport xrt sld pmd rst raw be used from Batch Processing or Quan Browser in the Xcalibur data system Generates a Quan summary report containing chromatograms and a Quan summary table SequenceReport xrt sld Generates a summary report showing the sequence being processed Use for batch processing in the Xcalibur data system Refer to the section Processing a Batch of Samples in Chapter 5 of the Xcalibur Data Acquisition and Processing User Guide SpectrumCandidates xrt ISt raw 108 XReport User Guide Generates a Quan summary report only applicable to GC MS Use from batch processing or Quan Browser in the Xcalib
25. Height Genesis Identify By Avalon Peak Genesis Minimum Integration Detection Peak Height Avalon Smoothing Points Other Blank Line and User Text Data Items Thermo Scientific Component Settings Summary Table 68 Component Settings Summary object fields headings D XReport Reference Report Objects The Component Settings Summary object displays a short list of peak detection and integration parameters for a specified component Required data file pmd Section placement Quan repeating section repeats on component peak For this object s possible fields and headings see Table 68 Component Name Detector Type Filter Trace Mass Range Wavelength Range 1 Wavelength Range 2 Thermo Scientific Expected Retention Time Retention Time Window View Width Retention Time Reference Component Type ISTD Standard Dilution Base Amount Peak Detection Algorithm Genesis Peak ICIS Peak Integration Detection Integration Detection Genesis Smoothing CIS Smoothing Points Points CIS Constrain Peak Valley Detection Width Enabled CIS Identify By Genesis Constrain Peak a e ICIC Minimum Peak Width Height Genesis Identify By Avalon Peak Genesis Minimum Integration Detection Peak Height Avalon Smoothing Points Other Blank Line and User Text Data Items XReport User Guide 191 D XReport Reference Report Objects Component Sys Suit Flags S
26. Parameter Description Title View the custom title of the selected object Include The Title In Include the custom title in the final report The Resolved Report Available Columns View columns that are available for the selected table A user column is a column that you can configure to display what you want on a later page of the wizard Add Add one or more columns to the table Select one or more columns from the Available Columns list and click Add to add them to the table Add All Add all of the available columns to the table Remove Remove one or more columns from the table Select one or more columns from the Selected list and click Remove to remove them from the table Remove All Remove all of the columns from the selected list Selected View the columns that are currently selected to be included in the table The columns are listed in the order that they appear in the table Column Header View the heading for the currently selected column 148 XReport User Guide Thermo Scientific D XReport Reference XReport Dialog Boxes Table 44 Select Table Fields page parameters Sheet 2 of 2 Parameter Decimal Setting Description View or change the number of digits displayed after the decimal point for values displayed in this column This parameter is only available for some table fields Move Up Move a column up in the Selected list Select a column in the Selected list and click Move Up to move th
27. Set Table Font page Avalon Qual Events Table Set Table Font To define the font for a specific element 1 Click the appropriate button The Font dialog box opens see Figure 37 Figure 37 Font dialog box 2 Select font options and click OK Repeat the process as needed for other table elements 62 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Table Object Setting Additional Table Properties After completing the Table wizard additional Properties dialog boxes appear for the following table objects Library Search Graphics Table Properties Library Search Results Table Properties Sample Table Properties Spectrum List Table Properties Electronic Signature Table Properties Library Search Graphics Table Properties Thermo Scientific To set Library Search Graphics Table properties right click the table and choose Properties from the shortcut menu The Table Properties wizard opens When you complete the wizard and click Finish the Library Search Graphics Table Properties dialog box opens see Figure 38 Click Cancel to close the dialog box Figure 38 Library Search Graphics Table Properties dialog box Library Search Graphics Table Properties Max of hits to display 5 V Display Column Labels Show Peak Spectrum OK Cancel Help ok To set the parameters in the Library Search Graphics Table Properties dialog box 1 Type the total nu
28. Table Electronic Signature Ion Ratio Confirmation Results Table IRC Settings Table IRC Summary Table Lib Search Graph Table Lib Search Results Table Proc Method Programs Table Proc Method Sample Reports Settings Table Proc Method Summary Reports Settings Table Qual Peak Table Qual Summary Table Quan Peak Table Quan Summary Table Sample Table Quan Results Sequence Table Spectrum Candidate Results Table Spectrum List Table When XReport combines a report template with data it replaces graphic objects with graphical information Configure or change the properties of a graphic object to customize its output See Graphic and Formatting Objects on page 170 for more information The following graphic objects are available in XReport Bitmap e Chromatogram Component Cal Calibration Curve Spectrum XReport User Guide 7 1 Introduction to XReport Report Templates Overview Formatting Objects These objects which only format the report are available in XReport Columns Page Break Data Source Files Data source files are files that contain acquired data For example there are five types of Xcalibur data source files Processing method pmd Raw raw Result rst Sequence sld Calibration xcal Report Generate a report or resolved document using a report template In an Xcalibur report the software combines the report objects in the report templa
29. There are several ways to contact Thermo Fisher Scientific for the information you need To contact Technical Support Phone 800 532 4752 Fax 561 688 8736 E mail us techsupport analyze thermofisher com Knowledge base www thermokb com Find software updates and utilities to download at mssupport thermo com To contact Customer Service for ordering information Phone 800 532 4752 Fax 561 688 8731 E mail us customer support analyze thermofisher com Web site www thermo com ms To copy manuals from the Internet Go to mssupport thermo com agree to the Terms and Conditions and then 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 http www surveymonkey com s PQM6P62 Send an e mail message to the Technical Publications Editor at techpubs lcms thermofisher com Thermo Scientific XReport User Guide ix Introduction to XReport XReport is the custom reports feature of the Xcalibur data system Use XReport to create customized reports containing all of the results and important information produced with the application In addition use XReport to format a report to a style print the report and save the report in text txt file Microsoft Word document doc file Microsoft Excel workbook xls file rich text rtf file portable display pdf file or Web page htm or html file formats Use these options to
30. U Quantitation limit Indicates that the quantitation threshold for the concentration of the quantified peak is outside the specified tolerance Y Linearity limit Indicates that the linearity threshold for the concentration of the quantified peak is outside the specified tolerance XReport User Guide 199 D XReport Reference Report Templates Report Templates An XReport template is an XReport document xrt file that defines the content layout and style of an Xcalibur report You can include sections and report objects in the report template An Xcalibur report is generated when a report template is resolved combined with Xcalibur data data source files XReport comes with several example Xcalibur 2 0 report templates for you to use These templates described below are located in the Xcalibur Templates folder Table 80 XReport templates Sheet 1 of 2 Report names Description Files needed CalibrationFile For reporting calibration data raw xcal CompCalReport Generates summary reports showing processing method rst raw pmd Avalon Genesis ICIS details calibration curve and sample table Quan results Use this report with results from Xcalibur batch processing and Quan Browser sld CustLibrSearRept Generates Qual sample reports that display Qual peaks and ISt raw LibrarySearchReport library search details Use this report with results from Xcalibur batch processing IonRatio Gene
31. Width E nabled nabled 30 Relative Abundance Relative Abundance 0 20 Time min Component Name hydrocortisone Actual RT Calculated Amount 4956 Response 1892943 Base Line Signal To Noise 703 56 YoDiff 0 38 Area Ratio Area 1892943 Specified Amount 5 000 Page 2 num 5 18 2004 2 43 13 PM 2 Click Save to save the report in the following file formats Microsoft Word doc Microsoft Excel xls Web page htm or html rich text rtf PDF pdf or text txt 3 To print the report click Print 4 To return to the XReport window click Close Thermo Scientific XReport User Guide 31 3 Generating a Report Creating a Report from the Xcalibur Data System Creating a Report from the Xcalibur Data System When generating a report the data system combines the data that you produced in the data system with a report template You can generate multiple reports from the data system To proceed you must have a basic understanding of the Xcalibur data system Refer to the Xcalibur Getting Started Guide for more information Generate a report from the following areas of the application See Generating a Report From Sequence Setup when running a sample or sequence and batch processing See Generating a Report From Quan Browser when using the Reports dialog box In addition when generating reports from the Xcalibur data system create reports containing electronic signature information
32. Xcalibur data system hides the baselines peak tracing and full peak annotation Set Custom Window Width Override the default value of the peak window width the default is peak width plus one min manually This option is always available for Qual peaks and is sometimes available for Quan peaks Custom Width min Define the Custom window width The default value is 0 75 min Configure Normalization For The Chromatogram Set parameters on the Configure Normalization For The Chromatogram page to select the normalization y axis scaling method used for the chromatogram Table 20 Configure Normalization for the Chromatogram page parameters Parameter Description Normalize Method Auto Zero Optimize the y axis automatically for each chromatogram Intensity Range Set the range manually Type the minimum and maximum intensity required for the y axis The value can be from 200 0 to 200 0 Normalize Each Plot To Largest Peak In Subsection Normalize each split time range to the largest peak in the division Largest Peak In Selected Time Range Normalize the chromatogram to the largest peak in the displayed time range Largest Peak In All Times Thermo Scientific Normalize the chromatogram to the largest peak in the entire chromatogram XReport User Guide 133 D XReport Reference XReport Dialog Boxes Select A Peak Dialog Box Use the Select A Peak dialog box to select a peak in a demo file
33. a heading or annotation To add a custom text field 1 On the Data page select User Text in the Available Items list and click Add see Figure 24 Figure 24 Adding a custom text field Component Sys Suit Flags Settings Resolution Parameters Resolution Threshold Blank line S ummetru Parameters C M E 2 Select lt User Text gt in the Selected list Thermo Scientific XReport User Guide 51 4 Configuring Objects and Sections Configuring a Text Object 3 Type the text in the text area and press ENTER see Figure 25 Figure 25 Customizing a text field Component Sys Suit Flags Settings lt User text gt Your Text Your Text Herd C e am on 4 Click OK to save your changes 52 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Text Object Configuring Text Attributes Thermo Scientific To configure text attributes right click a text object in the template and choose Properties from the shortcut menu A dialog box opens Click the Attributes tab see Figure 26 Figure 26 Attributes page in the Sample Header Properties dialog box Sample Header Properties Data Attributes Font Number of columns 6 1 C2 C 3 Horizontal spacing IV Include data label v Include spacing between data label and its data gt Vertical spacing Single 1 5lines C Double To configure attributes 1 To format the tex
34. bottom border of the section downward A selected section has a bright blue border around it The Report Template Outline pane lists the sections that are in the current report You can move or delete sections from this pane as well as un dock reposition or close it To un dock the pane drag the top gray portion away from the pane To redisplay the pane choose View gt Report Template Outline pane To delete a section from a template click it in the Report Template Outline pane and press DELETE To move a section drag it up or down in the Report Template Outline pane list You cannot move the header and footer sections To select and scroll to a section double click it Report Templates Overview Report Template Thermo Scientific This section defines the basic terminology used throughout the software and this manual for new users of XReport and the Xcalibur data system This section defines the following key terms Report Template Sections Report Objects for more information see Appendix B Types of Report Objects Data Source Files pmd raw rst sld xcal Report An XReport template is an XReport document xrt file that defines the content layout and style of a report Use the template to include sections and report objects for example graphs tables annotation text or graphics in a report template The software generates an Xcalibur report after combining a report template with Xcali
35. dde 19 Centering CODIGOS uocis DU dapi Dace ape S ai EO a VE DU a aq 20 Using the Report Template Grid isso dA Ferr ERE V ER PERPE AE 20 Using Colitis ocossat ar ears uos he wis Ea bl fea it EA ale ae dos 21 Usine Page Bfeaksoeeso wean oun qux a Red rete Wat mate aout 21 Configuring Objects ecuador eG ern heen RU eA p NO Dura ades 22 Adding User Text to a Text Object ss ait Lecce mea orar e 22 Adding a hotinnlato a lable via d ep et eaters ie Rae Pul 23 Changing Font Settings suus ois Selita tl aba ata datas dedos 24 Changing Page Layout o Louie datae dre aereo dn fosa ames ye RCM De skits 25 Previewing and Saving the Template 54e isse e boxe oca ted 25 Generating a Report 00 cece eee cece eee IR 29 Creating a Report Within XReport i oid erbe Edo d oats eas 29 Choosing Data Sources fora Template 0 44 ive seed cass vod ae panes 29 Generating Saving and Printing a Report 0 00200 31 Creating a Report from the Xcalibur Data System 0000000006 32 Sample Reports and Summary Reports i5 ve 2adobui ha e iter wr Rte d re 32 Generating a Report From Sequence Setup 0 0 0 liess 32 Generating a Report From Quan Browser 00 cee cee eee 37 Creating a Signed Report ierat uelP aoa P aren aie PU xao ees 40 Configuring Objects and Sections Luuuuusuuueueeusss 45 Configuring a Repeating Section rustico eb que obot eatis eth oto ed 46 Configuring a Text Object t cu
36. for the plot in minutes to one decimal place Separate entries by a dash with no spaces The default setting is which means to display the entire time range for the plot Fixed Scale Set the y axis maximum to a specific value Clear this check box to activate the Normalize To area on the Configure Normalization For The Chromatogram page Autofilter Repopulate a chromatogram view with Thermo Scientific A plot showing the chromatogram without any scan filters Plots for each scan filter applied to the chromatogram XReport User Guide 139 D XReport Reference XReport Dialog Boxes Select the Peak Labeling Set parameters on the Select the Peak Labeling page to choose the type and style of peak labels Table 30 Select the Peak Labeling page parameters Parameter Label With Description Retention Time Label the peaks with the time in minutes prefixed by RT Scan Number Label the peaks with number of mass scans at peak maximum prefixed by S Base Peak Label the base peak in the mass spectrum of the chromatogram peak prefixed by BP Signal To Noise Label the peaks with the signal to noise ratio at the peak maximum prefixed by SN Flags Label the peaks with flags providing supplemental information about the peak data For example if a peak is saturated the data system displays an S above the peak Area Label the peaks with the integrated area of the peaks pre
37. from the Xcalibur Data System Creating a Report Within XReport To create a report within XReport use these procedures Choosing Data Sources for a Template Generating Saving and Printing a Report Choosing Data Sources for a Template The process of generating a report from an XReport template involves using the Data Sources Dialog Box to search for the required data source files The data source files required to generate a report depend on the content sections and report objects of the report template To learn which data files are needed for each type of report object see Appendix B Types of Report Objects Thermo Scientific XReport User Guide 29 3 Generating a Report Creating a Report Within XReport 1 To resolve a template with data mmn To open the template xrt file choose File Open in XReport The XReport Templates dialog box opens 2 Select the template and click Open 3 Choose Report Data Sources The Data Sources dialog box opens see Figure 11 Figure 11 Data Sources dialog box Data Sources Calibration File Cancel Processing Method File Apply c MX caliburexamples methods steroid pmd p Help Default Raw Data File C Xcalbur examples data steroids02 raw e Result File C Xcalibur examples data steroids02 RST i Sequence List File C Xcalibur examples methods steroid sid m In each box enter or search for a data file If you specify an
38. function if they wish to use this facility Zero is Help substituted for numeric operation on strings Refer to the Report documentation for full details Formula AVERAGE B RROWw Functions Add Function Function AVERAGE Syntax AVERAGE x1 x2 xN Description returns the average of a list of values For the selected column edit a formula for the user column and configure valid fields and associated functions Below the functions list is a brief description of each function at the bottom of the dialog box To enter a formula in the Formula box select a function from the Functions list and click Add Function or type directly in the box When you click Add Function a configuration dialog box opens for that function For example for the Average function choose the column to average To return to the Configure User Column Parameters page click OK Click Next to go to the next page of the wizard Thermo Scientific 4 Configuring Objects and Sections Configuring a Table Object Specifying Table Sort Order Use the Set Table Sort Filter page of the Table wizard to define a method for sorting table data when you generate a report see Figure 35 Figure 35 Set Table Sort Filter page Component QC Level Table Set Table Sort Filter The generated table data can be ordered on any of the selected columns Up to three columns can be used for ordering with the first order taking precedence o
39. greater than the resolution threshold specified in the System Suitability page of Quan View in Processing Setup W Peak Width A peak passes this test if its width falls between the minimum and maximum values specified in the System Suitability page of Quan View in Processing Setup T Tailing A peak passes this test if its calculated tailing falls below the threshold specified in the System Suitability page of Quan View in Processing Setup O Column Overload A peak passes this test if its calculated overloading falls below the threshold specified in the System Suitability page of Quan View in Processing Setup B Baseline Clipping A peak passes this test if baseline clipping is not detected Signal to Noise Ratio A peak passes this test if its signal to noise ratio falls above the threshold specified in the System Suitability page of Quan View in Processing Setup C Concave A peak passes this test if it does not exhibit a concave depression due to noise D Saturation A peak passes this test if the detector did not saturate during data acquisition Thermo Scientific XReport User Guide 197 D XReport Reference Report Objects 198 XReport User Guide lt Blank Line gt and lt User Text gt Data Items All text objects except for the Annotation object and Instrument Method object have two special data items lt Blank Line gt and lt Text gt These data items appear in the Available Items list of the Data Pa
40. own label for the y axis Name Specify the name for the y axis if you selected Custom label above Offset Move the axis label away from the spectrum Units Absolute Use absolute units on the y axis Relative Use relative units on the y axis Enhance Page Specify spectrum enhancement details on the Enhance page Note Clear the Use Processing Method Properties For Plot Type And Enhancement Info check box on the Options Page to modify the Enhance page parameters Table 36 Enhance page parameters Sheet 1 of 2 Parameter Description Smoothing Enable Turn on spectrum smoothing Type Specify the type of smoothing algorithm to apply to the spectrum Choose from Boxcar or Gaussian Points Specify the number of points for spectrum smoothing This must be an odd number from 3 minimum smoothing to 15 maximum smoothing Refine Enable Turn on refine spectrum enhancement Thermo Scientific XReport User Guide 143 D XReport Reference XReport Dialog Boxes Table 36 Enhance page parameters Sheet 2 of 2 Parameter Description Window Define an area for drawing a peak by specifying the number of seconds on either side of the specified point A reasonable initial value is the peak width in seconds Noise Threshold Specify the cutoff point for peaks Type 0 to show all peaks in the spectrum and slowly increase the value until the noise peaks are eliminated Use this setting to eliminate peaks generated from
41. placed in a nonrepeating section See Report Objects on page 170 for information on how a report object functions when it is placed inside or outside a repeating section XReport User Guide 165 D XReport Reference Report Sections Nonrepeating Section 166 XReport User Guide A nonrepeating section is any portion of a report template that is not classified as a repeating section A nonrepeating section usually displays static details associated with either data or methods that apply once and globally within the system A nonrepeating section can have these objects Formatting Objects Page Break Columns Graphic Objects Electronic Signature Table Bitmap Chromatogram Component Cal Curve Spectrum Table Objects Avalon Qual Events Table Calibration File Table Component Cal Level Table Dilution Factor Table IRC Summary Table Processing Method Programs Table Processing Method Sample Reports Settings Table Processing Method Summary Reports Settings Table Qual Peak Table Quan Peak Table Sequence Table Spectrum Candidate Results Table Thermo Scientific D XReport Reference Report Sections Text Objects Annotation nstrument Method Processing Method General Processing Method Qual Sample Table Thermo Scientific XReport User Guide 167 D XReport Reference Report Sections Report Header and Footer The report header and footer sections contain data to be repeated at the top a
42. program you select Open Find and open xrt files ay B Save Save the current template as an xrt file This option is not available if you are using a locked template In this case choose File Save As and save the template with a different name X Cut Remove the currently selected objects and place them on the clipboard Copy Copy the currently selected objects to the clipboard e Paste Insert the contents of the clipboard in the currently selected section Align Left Align the left edges of the currently selected objects to the left edge of the first 2 selected object To select more than one object click and drag a selection box around the objects or hold down the SHIFT key and click each object Align Right Align the right edges of the currently selected objects to the right edge of the first selected object To select more than one object click and drag a selection box around the objects or hold down the SHIFT key and click each object Align Top Align the top edges of the currently selected objects to the top edge of the first selected object To select more than one object click and drag a selection box around the objects or hold down the SHIFT key and click each object Align Bottom Align the bottom edges of the currently selected objects to the bottom edge of the first selected object To select more than one object click and drag a selection box around the objects or hold down the SHIFT key and click each obj
43. rst file that references a raw file and that raw file does not exist or is in the wrong folder XReport sends an error message Make sure the raw file is in the correct folder 5 Click OK 30 XReport User Guide Thermo Scientific 3 Generating a Report Creating a Report Within XReport Generating Saving and Printing a Report To create a report using selected data sources 1 Choose Report gt Resolve Report in XReport The Preview window opens see Figure 12 The Preview window shows a report combined with chosen data sources Figure 12 Preview window ion PeakIntegration xrt 2 Print Save First Page Prev Page Pagef of 5 Next Page Last Page Two Page Zeon in Peak Integration Report Component Name hydrocortisone ISTD Name methyltestosterone Expected Reten 0 64 RT 0 18 1 18 SM 76 Expected Reten 2 01 RT 1 40 24B SM 76 tion Time min 100 RT 0 68 tion Time min RT 1 99 Retention Time 30 00 Retention Time 30 00 Window sec 80 Window sec View Width m 1 00 70 View Width m 1 00 LN 60 D Retention Time No Retention Time Yes Reference 50 Reference Genesis Minim 3 00 40 Genesis Minimu 3 00 um Peak Heigh m Peak Height t SIN SIN Genesis Smooth 7 20 Genesis Smooth 7 ing Points 40 ing Points Detector Type MS Detector Type MS Valley Detectio No 05 10 Valley Detectio No n Enabled Time min n Enabled Genesis Constra No Genesis Constra No in Peak Width E in Peak
44. that opens in the report preview Table 21 Select a Peak dialog box parameters Parameter Description Result File Select the name of the result file to be the demo file Peak Type Define the peak type Quan or Qual in the result file Peak List View the list of peaks that are in the result file Select Chromatogram Style Use the Select Chromatogram Style page to determine the appearance of the chromatogram Table 22 Select Chromatogram Style page parameters Parameter Description Plotting Point to Point Display point to point peak profiles see Figure 60 Stick Display the chromatogram as vertical lines Arrangement Stack 2D Stack plots vertically same x axis with no overlap one y axis for each plot Overlay 3D Move plots vertically same x axis with an optional horizontal skew y axis time offset When selected the 3D display options are turned on Use the 3D arrangement if you selected Multiple Quan Traces on the Select Mass Spectrum Quan Traces to Display page 3D Elevation Set the elevation angle amount of overlay from 0 to 60 degrees for the 3D plot style Skew Set the skew angle time offset from 0 to 45 degrees for the 3D plot style Draw Backdrop Add a drawn perspective backdrop to 3D plots 134 XReport User Guide Thermo Scientific D XReport Reference XReport Dialog Boxes Select Chromatogram Type Set the chromatogram type for the chromatogram report object
45. the Selected list Add AII Add all of the items in the Available Items list to the Selected list Remove Remove the currently highlighted item from the Selected list Remove All Remove all of the items from the Selected list Selected This box lists the items that are already selected to be displayed in the text object Move Up Move Down Rearrange the order of the items in the Selected list by moving the currently highlighted item up or down in the list Thermo Scientific XReport User Guide 157 D XReport Reference XReport Dialog Boxes Table 56 Data page parameters Sheet 2 of 2 Parameter Description Data Label Show the data label or heading text for the currently highlighted data label or heading in the Selected list Edit the data labels or headings by typing in this box Decimal Setting Specify the number of digits displayed after the decimal point for values displayed with the selected data label This parameter is only available for some data labels Attributes Page Format the currently selected text object on the Attributes page Table 57 Attributes page parameters Parameter Description Number of Columns 1 2 0 3 Display the data in 1 2 or 3 columns Horizontal Spacing Include Data Label Show or hide the data labels adjacent to the data Include Spacing Between Data Label and Its Add space between data labels and the data so that all data values are Data aligned Vertical Spacing
46. the second row of column B and displays the result in the second row of the User Column c The data system continues this process until all rows of the table have been completed Figure 33 Configure User Column Parameters page Avalon Qual Events Table Configure User Column Parameters User Colum x Each User Column in a Report Table allows a Formula to be entered by a user that can be inserted into columns in a Table on a report generated using Xcalibur This facility allows manipulation of the other data items in the same row in the T able User Columns Dx User Column Title nn User Column Formula Edit Formula HET The data system displays the User Columns you have selected for the table in the User Columns list Thermo Scientific XReport User Guide 59 4 Configuring Objects and Sections Configuring a Table Object 60 XReport User Guide To define each user column Select a user column in the User Columns list Type a title for the user column in the User Column Title area Click Edit Formula in the User Column Formula area The Edit Formula dialog box opens see Figure 34 Figure 34 Edit Formula For dialog box Edit Formula For User Column 1 Some help will be provided here to enable configuration of valid Formula fields and associated functions This is a free text field and no syntax checking is Cancel performed It is the responsibility of the user to enter a valid
47. the box Formulas obey the following syntax rules The formula must begin with an equals sign Each table column is represented by an alphabetic letter identifier A B C and so on displayed beneath the column title in the Table object Type simple mathematical expressions A B A B A B and A B as well as any of the functions listed in the Functions list Mathematical formulas are computed on a row by row basis That is if you type A B as a formula in a User Column the results are computed as follows The value in the first row of column A is added to the value in the first row of column B and the result appears in the first row of the User Column The value in the second row of column A is added to the value in the second row of column B and the result appears in the second row of the User Column This process is continued until all rows of the table have been completed Select a function from the Functions list and click Add Function The Configure Function Dialog Box opens Select the columns to be used with the function When you configure your function and click OK XReport enters the configured function in the Formula box 7 When you have entered your formula click OK to close the Edit Formula For dialog box and return to the Table Properties wizard Continue through the remaining pages of the wizard to finish configuring your table Thermo Scientific XReport User Guide 23 2 Creating a
48. this sample type 6 Repeat steps 4 and 5 to print reports for needed sample types 7 To display the Open Report Template dialog box double click the Report Template Name box Select the previously prepared report template document and click Open The full path and the file name of the report template xrt document appear in the Report Template Name box 8 To print reports for each report template document repeat steps 4 through 7 for the next row 9 To make all of the sample reports you have selected for printing available click the Include Sample Reports check box at the bottom of the Reports dialog box Click the Include Summary Report check box to make summary reports available 10 To select the samples for the report do the following a Click Select Samples to open the Select Report Samples dialog box The samples available from the sld file opened in step 2 appear in the Sample Choices box see Figure 16 Figure 16 Select Report Samples dialog box Select Report Samples Sample Choices Selected Samples Standard Standard Standard Standard Standard Standard Add gt gt Standard Standard Standard L3 Remove Standard Standard Standard Add All gt gt Standard Standard Standard lt lt Remove All Qc Qc ar Cancel Help 38 XReport User Guide Thermo Scientific 3 Generating a Report Creating a Report from the Xcalibur Data System b Select the samples Fora
49. wavelength range nm Type the upper and lower limits for the plot Separate entries by a dash with no spaces To use the entire mass or wavelength range type an asterisk Detector View the type of detector that was used to generate the raw file Valid types are MS and PDA The type of detector determines the available plot types Time View or change the time of the mass scan in the host chromatogram Type a new value or range as required 146 XReport User Guide Thermo Scientific D XReport Reference XReport Dialog Boxes Table 41 Plot Type page parameters Sheet 2 of 2 Parameter Description Scan Filter Specify the scan filter to apply to your data Select a filter from the list or type a new filter using the scan filter format Demo File Specify the path and filename of the demo file raw file that is used to generate a preview of the selected plot Style Page Set parameters on the Style page that determine the appearance of the spectrum Table 42 Style page parameters Parameter Description Plotting Automatic Choose the graphic style based upon the data acquisition method that was used for the active spectrum Point To Point Display point to point peak profiles Stick Display the spectral mass peaks as vertical lines Shade Display the spectrum as a shaded representation of intensity in each amu band for the active spectrum Table Properties Wizard Use the Table Properties wizard t
50. 2 Left to Sample 1 right Chrom 3 Chrom 4 Chrom 1 Chrom 2 Sample 2 Chrom 3 Chrom 4 If you choose instead the Top To Bottom option the report appears as in Figure 80 Figure 80 2 column object behavior in a nonrepeating section with a chromatogram Top to bottom option Resolve A Chrom gt Chrom 1 Chrom 3 Top to Sample 1 bottom Chrom 2 Chrom 4 Chrom 1 Chrom 3 Sample 2 Chrom 2 Chrom 4 If you place an object in the right column and leave the left column empty XReport combines the data as if the object is placed in the left column as illustrated above XReport User Guide 105 4 Configuring Objects and Sections Configuring Columns 106 XReport User Guide If you place an object in each column the Xcalibur data system ignores the Top to bottom and Left to right options The report appears as in Figure 81 Figure 81 2 column object behavior in a nonrepeating section with chromatogram and spectrum objects Chrom Spec Text Resolve Chrom Spec 1 Chrom Spec 2 Chrom Spec 3 Chrom Spec 4 Chrom Spec 1 Chrom Spec 2 Chrom Spec 3 Chrom Spec 4 Text Sample 1 Sample 2 Thermo Scientific m Sample XReport Template Files The Xcalibur data syste
51. Details Select the Peak Labeling Select the Qual Peak Select the Quan Peak Use Container Supplied Qual Peak Use Container Supplied Quan Peak Thermo Scientific D XReport Reference XReport Dialog Boxes Advanced Qual Peak Annotation Options Set advanced Qual peak annotation parameter on the Advanced Qual Peak Annotation Options page When you set advanced labeling options only the Qual peak is labeled Note If you are in a Quan or nonrepeating section choose a Qual results based chromatogram Table 17 Advanced Qual Peak Annotation Options page parameters Parameter Description Use Advanced Qual Peak Annotation Turn on the advanced Qual peak options Custom Peak Labels Custom Text Label Label the Qual peak with a custom label Retention Time Label the Qual peak with the retention time RT Labeling Units Decimals Thermo Scientific Define the units for the retention time Specify the number of decimal places to be displayed in the retention time label XReport User Guide 131 D XReport Reference XReport Dialog Boxes Advanced Quan Peak Annotation Options Set advanced Quan peak annotation parameters on the Advanced Quan Peak Annotation Options page When you set advanced labeling options only the Quan peak is labeled Note If you are in a Qual or nonrepeating section choose a Quan results based chromatogram Table 18 Advanced Quan Peak Annotation Options page paramete
52. Detection Enabled No Enabled No Genesis Genesis Constrain Peak Constrain Peak Width Enabled No Width Enabled No Component Name progesterone Actual RT min 3 16867 Calculated Amount 4 94898 Response 2995893 97127 Base Line BB Signal To Noise 344 16 Diff 1 02 Area Ratio 4 373 Area cts sec Specified Amount 5 00000 Thermo Scientific C Sample Report Peak Integration Report Page 4 NL 9 60E4 m z 266 6 267 6 284 7 285 7 F c Full ms2 303 30 100 00 310 00 MS Genesis steroids02 2995893 97127 XReport User Guide 119 XReport Reference This appendix provides reference material about XReport including the Xreport window and dialog boxes Contents Reports View Reports View XReport Dialog Boxes Report Sections Report Objects Report Templates Use XReport or the Reports view of the Processing Setup window to specify how the Xcalibur data system produces reports for samples and sequences The data system provides several standard report formats You can export results in a number of file formats including xls and html For more information about the Reports view of the Processing Setup window go to the Xcalibur Data Acquisition and Processing User Guide Thermo Scientific XReport User Guide 121 D XReport Reference Reports View XReport Toolbar Buttons Table 7 Toolbar buttons Sheet 1 of 2 Button Description n New Create a new report template for the
53. Guide 5 1 Introduction to XReport Report Templates Overview Text Objects 6 XReport User Guide Text objects contain static text labels and associated customized data fields To customize the specific fields to display right click the object and choose Properties from the shortcut menu The Configuration dialog box opens When the software combines a template with data to generate a report it replaces the text object fields with textual information static text See Text Objects on page 189 for more information The following Xcalibur text objects are available in XReport Annotation Component Ident Detect Cal Settings Component ISTD Settings Summary Component Settings Summary Component Sys Suit Flags Settings Instrument Method Processing Method General Processing Method Qual Quan ISTD Peak Summary Quan Peak Summary Report Info Sample Header Thermo Scientific Table Objects Graphic Objects Thermo Scientific 1 Introduction to XReport Report Templates Overview When the Xcalibur data system combines a template with data it replaces table objects with tabulated information creates a populated data table Configure or change the properties of a table object to customize its output XReport provides the following table objects Avalon Qual Events Table Avalon Quan Events Table Calibration File Table Component Cal Level Table Component QC Level Table Component Spectrum Table Dilution Factor
54. Mass Intensity Toggle between ordering the data in the Spectrum List table by mass or wavelength if the PDA Detector is selected or intensity or Wavelength Intensity Normalization Intensity Range Specify the relative abundance range of mass peaks that are included in the table The valid 152 XReport User Guide range is 200 000 to 200 000 To change the range of relative abundances type the minimum and maximum relative abundance to display in the Intensity Range box separated by a dash For example to display all peaks in a mass spectrum with relative abundances ranging from 50 to 100 type 50 000 100 000 XReport excludes spectrum peaks with relative abundances that range from 0 000 to 49 999 from the table Thermo Scientific D XReport Reference XReport Dialog Boxes Enhancement Page Configure spectrum enhancement parameters for the Spectrum List table on the Enhancement page Note Clear the Use Processing Method Properties For Plot Type And Enhancement Info check box on the Options Page to modify parameters on the Enhancement page Table 49 Enhancement page parameters Parameter Description Smoothing Enable Turn on spectrum smoothing Type Specify the type of smoothing algorithm to apply to the spectrum Choose from Boxcar or Gaussian Points Specify the number of points for spectrum smoothing This must be an odd number from 3 minimum smoothing to 15 maximum smoothing R
55. Mass Range 1 e Wavelength Range 1 Mass Range 2 e Wavelength Range 2 Range Detection Options Peak Detection Algorithm Genesis Peak Integration Genesis Smoothing Points S N Threshold Valley Detection Expected Peak Width Genesis Constrain Peak Width Genesis Peak Height Genesis Tailing Factor Avalon Peak Integration Avalon Smoothing Points Limit Peaks Select Top Peaks Select By Number To Select Relative Peak Height Threshold Percent of Highest Peak Advanced Detection Options Genesis Peak Detection Genesis Identify By Minimum Masses Required Minimum Percent of Masses Found Minimum Peak Height Genesis Peak Edge Detection Peak S N Cutoff Report Noise As ICIS Advanced Parameters Noise Method Minimum Peak Width Multiplet Resolution Area Tail Extension Area Scan Window Spectrum Enhancement Spectrum Enhancement Usage Refine Window Size Noise Threshold Combine Background Subtraction Left Region Left Region Width Region End Peak Top Region Width Options Maximum Number of Hits Reverse Search Search with MW Append to User Library Availability User Library Match Factor Reverse Match Factor Probability Search Libraries Library Search Constraints Molecular Weight Range Other Databases Name Fragment Element Constraints Enabled Elemen
56. Qual or Quan repeating either raw data or processed data for any and nonrepeating acquisition device supported by the data sections system MS Analog A D Card PDA UV Component Cal Curve rst pmd Shows the calibration curve used to Quan repeating repeats quantify a specified component The on component peak curve is specified in the processing Monrspeiti e nscsthe method as response versus amount of specified component standard Spectrum Iaw rst Displays a graphical spectrum that can Qual or Quan repeating show either raw data or processed data for any acquisition device supported by the data system MS PDA Formatting Object Descriptions The table below describes the formatting objects Table 6 Formatting objects and nonrepeating sections Graphic object Data source file Description Section placement Columns none Specify the layout and repeating Any properties of graphic and text objects Page Break none Insert a manual page break in the report Qual or Quan repeating 114 XReport User Guide and nonrepeating sections Thermo Scientific Sample Report This appendix contains a sample Xcalibur report that is generated when you use PeakIntegration xrt located in the Xcalibur templates folder to generate a Quan sample report that contains certain peak integration data The sample report uses the steroids02 rst data file from the Xcalibur examples data folder Contents e Peak Integration R
57. Sequence v Export Sequence v Run This Sample s File T Print Instrument Setup Library Manager Processing Setup Qual Browser Quan Browser Queue Manager 7 Subtract Background Secure Groups Create Delete r Permission Level C Disallowed Signature List C Supervisor Password C Password Required C Allowed r Disallowed State Hidden C Grayed r Other requirements Comment Po Secure Folders Global Security Features IV Predefined Comments E dit Add Delete r Signature List Groups Available groups Current User Must Sign All Features C All applications This application cw Cancel History Log Print ESI Import Thermo Scientific 1 ld Select Print Reports In the Permission Level area select Signature List Signatures req d users Move Group Up Down Set To Same To set permissions for producing signed reports from Quan Browser Choose Start gt All Programs gt Thermo Foundation x x gt Authorization Manager The Authorization Manager window opens see Figure 18 In the tree directory expand the Quan Browser entry and expand the Print entry XReport User Guide 2 3 Generating a Report Creating a Report from the Xcalibur Data System 5 In the Signature List Groups area select a group from the Available groups list and click gt gt to move it t
58. Setup Exiting XReport To save the report template or report and XReport Complete or cancel any active dialog boxes and choose File Exit 14 XReport User Guide Thermo Scientific Creating a Template This chapter explains how to create a custom report template When you create a custom report template you can save the template and use it to generate an Xcalibur report For more information about generating a report see Chapter 3 When you start XReport XReport creates a new template that includes header and footer sections see Figure 4 Either work with this new template or choose File gt Open to open an existing template and select an XReport template xrt file Figure 4 XReport window showing a new template Eile Edit View Layout Report Help ojeju s Bj vata sectons Contents Adding Ordering and Configuring Sections Adding and Configuring Report Objects e Previewing and Saving the Template Thermo Scientific XReport User Guide 15 2 Creating a Template Adding Ordering and Configuring Sections Adding Ordering and Configuring Sections To begin creating a template select sections to include in the report template Choose to include Quan based or Qual based repeating sections or nonrepeating sections in your report template For a description of the different section types and how repeating sections work see Configuring a Repeating Section
59. Single 1 5 Lines or Double Set the amount of space between each line in the text object Font Page Format the currently selected text object on the Font page The parameters in the Font page depend on whether you are configuring an annotation or other text object The Annotation Font page has the standard Microsoft Windows font chooser Here you can choose font font size color emphasis and so on Table 58 Font page parameters Parameter Description Title Font Set and view the font settings for all of the title headings data labels and data in the text Heading Font object Data Label Font Data Font To configure your font click al The Font Dialog Box opens 158 XReport User Guide Thermo Scientific D XReport Reference XReport Dialog Boxes Bitmap Properties Dialog Box Specify the filename of the currently selected bitmap in the Bitmap Properties dialog box Table 59 Bitmap Properties dialog box parameters Parameter Description Bitmap File Specify the filename for the currently selected bitmap Type the full path or click the Browse button to browse for the file Reset to Original Size Reset the size of the image in the template to the original size in the file Thermo Scientific XReport User Guide 159 D XReport Reference XReport Dialog Boxes Column Properties Dialog Box Set parameters in the Column Properties dialog box to specify the number of columns for the column object and whether to repeat by
60. Suitability Data Flags Blank Line and User Text Data Items Quan Peak Summary The Quan Peak Summary object displays component peak summary parameters Required data file pmd rst Section placement Quan nonrepeating repeats on component peak For this object s possible fields see Table 75 Table 73 Quan Peak Summary object fields Component Name Actual RT Specified Amount Calculated Amount 9oDiff Response Response Ratio Area Area Ratio Height Height Ratio Width on Ratio Status Peak Purity Baseline Flags Signal to Noise Saturated Expected RT Sample Type Component Type Peak Status System Suitability Data Flags Calibration Flags Blank Line and User Text Data Items Thermo Scientific XReport User Guide 195 D XReport Reference Report Objects Report Info Sample Header The Report Info object displays general information about the report itself Required data file None Section placement Report header and footer For this object s possible fields see Table 74 Table 74 Report Info object fields Page a of b Date and Time Template File Layered App Name Layered App Version Blank Line and User Text Data Items The Sample Header object displays general information about a sample Required data file raw sld Section placement Report header or foot
61. Template Adding and Configuring Report Objects Changing Font Settings Use XReport to change font settings globally or locally for text and table objects When you change the font settings globally each object added from that point forward appears in the new fonts objects that are already in the template are not updated When you change font settings locally only the selected objects reflect the new font settings itN kod I 24 XReport User Guide To change the font settings for a single object Do one of the following Select the object and click 4 in the toolbar The Font dialog box opens Right click the object and choose Properties from the shortcut menu Then click the Font tab The Font page of the Properties dialog box opens Update the settings and click OK To change the font settings for more than one text or table object at a time Select the first object Hold down the SHIFT key while you select the other objects Click in the toolbar The Font dialog box opens Update the settings and click OK To globally change the font settings used for all new objects to add to the template Click any section and confirm that no objects are selected Click in the toolbar The Font dialog box opens Update the settings and click OK Thermo Scientific 2 Creating a Template Previewing and Saving the Template Changing Page Layout it To change the page layout 1 Choose F
62. Tinin Calculated Amount 4956 Response 1892943 Base Line BI SizralTo Noise 70756 YDitt 088 Area Ratio Areafcte sec Y 1892943 Specified Amount 5000 num 7 26 2004 11 51 10 PM 2 When the report is correct click Close to close the preview window 3 To save the template choose File gt Save To save changes to a locked template choose File gt Save As and rename the file XReport uses the steroid example data that is provided with the Xcalibur data system as the default data set It consists of the following files steroid pmd steroids02 raw steroids02 rst steroid sld When your template is designed for a very different type of data set than the default data you might not see the results you expect when you preview the template In that case choose appropriate data sources for the template and create the report as described in Creating a Report Within XReport on page 29 26 XReport User Guide Thermo Scientific Thermo Scientific 2 Creating a Template Previewing and Saving the Template Use XReport to lock a template so that it can never be modified and saved with the same filename To modify a locked template save it with a different filename Choose File gt Open to open a locked template the same way you open any other template To lock the template 1 Choose File gt Save As The Save As dialog box opens see Figure 10 Figure 10 Save As dialog box showing XReport Templates
63. Y Axis Label Units From detector C Absolute C Custom Relative 60 40 20 Relative Abundance Offset E E 5 Time min ted e 2 To offset the axis label from the chromatogram select the Offset check box 3 To split the chromatograms into two or more separate graphs with equal time ranges select the Split time range check box 4 Type the number of split time range graphs displayed for each chromatogram in the Divisions box This box is active only when you select the Split Time Range check box Thermo Scientific XReport User Guide 91 4 Configuring Objects and Sections Configuring a Chromatogram Object 5 In the Y Axis area select either the From Detector option in the Label area to use the detector specific label for the y axis stored in the raw file or the Custom option to use your own label 6 To specify the setting for the y axis units select either Absolute or Relative in the Units area 7 If you have chosen to use a Custom label for the y axis type a y axis name in the Name box 8 To offset the axis label from the chromatogram select the Offset check box 9 To go to the next page of the wizard click Next Configure Normalization for the Chromatogram Page Use the Normalization page to select the normalization y axis scaling method used for the chromatogram To specify normalization options 1 Define the normalizing method in the Normalize method area see Figure 65 by
64. a and view save and print your report Help E e E Thermo Scientific Open Xcalibur Help XReport User Guide 123 D XReport Reference Reports View XReport Menus The XReport window has the following menus XReport File Menu XReport Edit Menu XReport View Menu XReport Layout Menu XReport Report Menu XReport Help Menu XReport File Menu Table8 File menu commands Command Description New Create a new template Open Open a previously saved template Save Save the current template Note This option is not available if you are using a locked template In this case choose File Save As and give the template a different name Save As Save the current template with a different file name Page Setup Define page layout and margin settings Recently Used Files View the most recently opened template files To open the template select a filename in the list Close Close the current template Exit Close XReport XReport Edit Menu Table 9 Edit menu commands Sheet 1 of 2 Command Description Cut Remove the currently selected objects and place them on the clipboard Copy Copy the currently selected objects to the clipboard Paste Insert the contents of the clipboard in the currently selected section Clear Delete the currently selected objects Select All Select all of the objects in the currently selected section Edit Object Change the current object For example to enable resizing of
65. a source file Description Section placement Report Info none Displays general information about the Header or footer report itself Sample Header raw sld Displays general information about a Nonrepeating Table Object Descriptions sample for example Sample Name Operator Sample Type Run Time Acquisition Date The table below describes the table objects Table4 Table objects Sheet 1 of 3 header or footer Table object Data source file Description Section placement Avalon Qual Events Table pmd Displays details of the Avalon peak Nonrepeating detection algorithm events configured in the Qual section of a processing method Avalon Quan Events Table pmd Displays details of the Avalon peak Quan repeating detection algorithm events configured for a component in the Quan section of a processing method Calibration File Table xcal sld raw Displays component names response factors and 96RSD of standards Nonrepeating Component Cal Level Table pmd Shows the calibration levels amounts Quan repeating or and acceptance test values defined fora Nonrepeating specific component Component QC Level Table pmd Shows the QC levels amounts and Quan repeating percent test values defined for a specific component Component Spectrum Table pmd Displays m z and intensity data for up to Quan repeating fifty spectrum peaks The data system uses this data to identify components when t
66. a spectrum to the right column Combine resolve the template using data of 1 sample with 4 components All objects in the column are repeated for a single sample and the report appears as in Figure 78 Figure 78 2 column object behavior in a nonrepeating section with chromatogram and spectrum objects Resolve Chrom Spec gt Chrom 1 Spec 1 Text Text Chrom 2 Spec 2 Text Sample 1 Chrom 3 Spec 3 Text Chrom 4 Spec 4 Text Thermo Scientific 4 Configuring Objects and Sections Configuring Columns Set Summary Repeat Options Thermo Scientific Use the Summary repeat option to present information relating to all of the samples in an Xcalibur sequence and the results created when processing them Note The Sample repeat and Summary repeat options are applicable only in nonrepeating report sections These options are not available in other types of report sections For example when you place a 2 column object in a nonrepeating section add a chromatogram in either column and combine resolve the template using data of 2 samples with 4 components each the report appears as in Figure 79 Figure 79 2 column object behavior in a nonrepeating section with a chromatogram Left to right option Resolve Chrom gt Chrom 1 Chrom
67. age Use the Use Container Supplied Qual Peak page to ignore the implicit Quan peak and explicitly configure the chromatogram type t To explicitly configure a Qual based chromatogram type 1 To ignore the implicit Quan peak supplied by the container and explicitly configure the chromatogram type select the Explicitly Specify the Chromatogram s Behaviour check box in the Explicit chromatogram type area see Figure 49 Figure 49 Use Container Supplied Qual Peak page Use Container Supplied Qual Peak When a chromatogram control is in a section that automatically supports a Qual peak e g Qual Repeating Section then the default behaviour is to implicitly display the section specific peak when generating a report Explicit chromatogram type The implicit Qual peak supplied by the container can be ignored and the chromatogram type explicitly configured MV Explicitly specify the chromatogram s behaviour Cancel Help 2 Click Next to go to the next page of the wizard 74 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Chromatogram Object Select Chromatogram Type Page Use the Select Chromatogram Type page to set the chromatogram type for the chromatogram report object being configured in the report template To select a chromatogram type 1 Define the chromatogram type in the Chromatogram Type area see Figure 50 by selecting one of the following options Raw fi
68. age 133 Configure Normalization For The Chromatogram page 133 Select Chromatogram Style page 134 Select Chromatogram Type page 135 Select Component page 136 Select Demo File page 136 Select Enhance Details page 137 Select How The Chromatogram Axes Will Be Configured page 137 Select Mass Spectrum Quan Traces to Display page 138 Select Plot Details page 138 Select the Peak Labeling page 140 Select the Qual Peak page 141 Select the Quan Peak page 141 Use Container Supplied Qual Peak page 141 Use Container Supplied Quan Peak page 142 chromatograms configuring 71 column objects configuring 103 introduction 171 repeating behavior 104 resizing in a table 19 summary repeating 104 105 using 21 Column Properties dialog box adding columns 21 parameters 160 combined resolved documents 8 XReport User Guide 203 Index D Component Cal Curve object 171 Component Cal Level table 174 Component Calibration Curve Configuration wizard 10 Component Calibration Curve object configuring 93 Component IdentDetect Cal Settings object 189 Component Ion Ratio table 177 Component ISTD Settings Summary 190 Component QC Level table 175 Component Settings Summary 191 Component Spectrum table 175 Component Sys Suit Flags Settings 192 Configure Component Calibration Curve dialog box 162 Configure Function dialog box 151 Configure Repeating Section dialog box Exclude page 128 Ordering page 129 Page Breaks page 129 reference 128 configuring annotatio
69. alog box opens see Figure 47 Figure 47 Chromatogram Properties dialog box Chromatogram Properties Chromatogram Configuration QUAL RESULT RT 423 571 SM 16 i RT 4 90 NL ip 100 2 1465 Peak Window Use Method Ue as Relative Abundance N o o o oF ihe o 5 Time min Configure Cancel Apply Help 2 Click Configure The Chromatogram Properties wizard opens The Chromatogram wizard guides you through the process of changing the properties of a chromatogram report object contained in the report template The XReport Chromatogram wizard displays different pages and contains different options depending on the type of section containing the chromatogram and the selections for the Chromatogram Type and Peak Type properties Table 1 lists the wizard pages and their order Each wizard page is described in a topic below See the appropriate topic to learn how to complete each wizard page Thermo Scientific XReport User Guide 71 4 Configuring Objects and Sections Configuring a Chromatogram Object Table 1 Possible Chromatogram wizard pages given the section type in order of appearance Nonrepeating section Repeating section Page in the XReport Chromatogram wizard Raw Quan Qual Quan Qual Use Container Supplied Quan Peak Use Container Supplied Qual Peak e Select Chromatogram Type e Select Demo File e e e e Select the Quan Peak e a Select Co
70. ards Target Compounds Show Only Found Discard any components that have not been found Components 128 XReport User Guide Thermo Scientific D XReport Reference XReport Dialog Boxes Ordering Page Set parameters on the Ordering page to indicate the order for peaks or components in the repeating section Table 15 Ordering page parameters Parameter Description Repeating Section Ordering Order By Choose a value that determines the order for the peaks or components in the section RT Component Name Peak Height Intensity Peak Area Intensity Peak Response Intensity Component Concentration Ordering Direction Ascending or Descending Choose an order for the peaks or components in the section by the property in the Order By list from lowest to highest ascending or hightest to lowest descending Repeating Records Maximum Limit number of reported Limit the total number of peaks or components that are included in the repeating peaks or components to section Page Breaks Page Set parameters on the Page Breaks page to indicate where to apply page breaks in your report Table 16 Page Breaks page parameters Parameter Description Each peak contained on its own page s Insert a page break before and after each peak in the repeating section No page breaks between the individual peaks Remove page breaks between each peak in the repeating section Page break before the repeating sec
71. are always displayed unrotated Boxed Place a rectangular outline around each peak mass label Flags are not boxed Label Threshold Specify a peak height level in percent of the base peak Above that level XReport labels a 144 XReport User Guide peak Thermo Scientific Normalization Page D XReport Reference XReport Dialog Boxes Select normalization options for spectrum plots on the Normalization page Table 38 Normalization page parameters Parameter Description Normalize Method Auto Zero Optimize the y axis automatically Intensity Range Set the y axis range Use the box to type the minimum and maximum intensity The valid range is from 200 00 to 200 00 Normalize To Largest Peak In Subsection Largest Peak In Range Normalize each split mass range to the largest peak in the division Normalize the spectrum to the largest peak in the displayed mass range Largest Peak In Scan Normalize the spectrum to the largest peak in the entire spectrum Normalize Multiple Scans Individually Normalize each mass plot individually All The Same Normalize all mass plots equally Options Page Set spectrum parameters on the Options page Table 39 Options page parameters Parameter Use Processing Method Properties For Plot Type and Enhance Info Description Use properties from the selected processing method to set plot type and enhance information for the spectrum Use ISTD Pea
72. ations 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 This document is not part of any sales contract between Thermo Fisher Scientific Inc and a purchaser This document shall in no way govern or modify any Terms and Conditions of Sale which Terms and Conditions of Sale shall govern all conflicting information between the two documents Release history Revision A June 2013 Software version Xcalibur 3 0 and later For Research Use Only Not for use in diagnostic procedures Contents PICTACGs dad AUR n d ae RU a iw acl DR RON RUP GO DU RR amine vii Related Documentation o4 qucacuceto x adh dou See e 9 iade c e ae boe e vii Safety and Special Notices sink cis c eade Anio e eee D TOR UR viii Contacting US uiuo a eae re edo ee len i og nce a c re S gr ix Chapter 1 Introduction to XReport a oce er rrr a mk ma x hear ean cin 1 The XR port Window audae docks ucro eod arteari aden doeet dear asa d 2 Report Templates OVeryieWris a eaae d ek a doi dd o e dedos ba ad dus 3 Report Template x53 cetero edd ebd edad E NE ERA AME cers 3 voro METUIT a E a a E Se E A 4 Report Objects eir serris renunti y acd obs iod whey aciei ow ew acd icai dead 5 D ta MT RU 8 Report uua e ER PRG RR E EGG a Ge Raga CR ER Pur Ra a 8 Conf
73. baseline noise Background Subtraction This area shows details of background subtraction if it was applied to the spectrum The background contribution is determined by averaging the scans from one or two baseline regions Time Range 1 Add a first baseline region that is used for assessing the background When you click this option the Xcalibur data system activates a box Type the time range to use in the box Time Range 2 Add a second baseline region that is used for assessing the background Labels Page Choose the type and style of peak labels on the Labels page Table 37 Labels page parameters Parameter Label With Description Mass or Wavelength Flags Label the peaks with m z values if MS is selected as the detector on the Plot Type Page or wavelength values if PDA is selected as the detector on the Plot Type Page Label spectrum peaks with flags Flags provide supplemental information about peak data For example if a peak is saturated the Xcalibur data system displays an S above the peak Relative To Move the m z labels for the peaks away from the peaks by the specified amount Decimals Specify the number of decimal places to be used in mass labels Label Styles Offset Move a label from its normal position to avoid conflicts with other labels Size Specify the offset size to use in number of characters Rotated Use vertical rather than horizontal mass labels Flags
74. being configured in your report template on the Select Chromatogram Type page Table 23 Select Chromatogram Type page parameters Parameter Description Chromatogram Type Raw File Based Chromatogram Indicate the chromatogram is based on a raw file Quan Results Based Chromatogram Indicate the chromatogram is based on Quan results Qual Results Based Chromatogram Indicate the chromatogram is based on Qual results Show All Qual Peaks In Result File Display all Qual peaks in the finished report Thermo Scientific XReport User Guide 135 D XReport Reference XReport Dialog Boxes Select Component Set parameters on the Select Component page to select a component to display when configuring a chromatogram Table 24 Select Component page parameters Parameter Description Processing View the name of the currently selected processing method pmd file Component List View a list of components found in the processing method file Select Demo File Set parameters on the Select Demo File page to associate a demo file raw or rst with a chromatogram report object Use the demo file to see how the chromatogram report object appears with its current settings when applied to real data The appearance of the Select Demo File page depends on the chromatogram type and the peak type settings chosen in the Chromatogram Type page Table 25 Select Demo File page parameters Parameter Description Use Demo File Use Demo
75. bject see Figure 51 select the Use demo file check box 2 To search for the required demo file raw file click the browse button in the Demo File area The Select Raw Data File dialog box opens 3 Select a demo file and click Open 4 Click Next to go to the next page of the wizard Select the Quan Peak Page Use the Quan Peak page to explicitly specify the Quan peak component for a Quan results based chromatogram report object To specify a Quan peak 1 To specify the Quan peak type the text name of the component in the Quan Peak area see Figure 54 Figure 54 Select the Quan Peak page Select The Quan Peak When a chromatogram that will display Quan results is added to a report template in a non repeating section the Quan component to be applied to this control must be explicitly set Note If the specified Quan component cannot be located this chromatogram cannot be added to the resolved document Quan Peak EE It is possible to display the details of the Internal Standard associated with a particular Quan peak If the selected Quan peak is the Internal Standard this option will not be available and the checkbox will be cleared r HT 2 To search for the required processing method file pmd do the following a Click the browse button The Select Component dialog box opens Thermo Scientific XReport User Guide 79 4 Configuring Objects and Sections Configuring a Chromatogram Object
76. bur data data source files XReport User Guide 3 1 Introduction to XReport Report Templates Overview Sections XReport provides several example report templates for you to use These are located in the Xcalibur Templates folder For details about the preconfigured report templates see Appendix A Sample XReport Template Files Divide the report template in sections to hold report objects Add sections to a report template using the Sections pane in the XReport window The basic types of section used in XReport are as follows Header or Footer Sections e Repeating Sections Nonrepeating Sections A report object that is placed in a repeating section can behave differently from the same report object placed in a nonrepeating section when the software combines a report template with data For information on how a report object functions when it is placed inside or outside a repeating section see Appendix B Types of Report Objects Header or Footer Sections 4 XReport User Guide A header or footer section is a section of the report that is automatically repeated at the top and bottom of each page in the resolved report Header and footer sections can contain objects such as a company logo report information page numbers and date stamps Thermo Scientific 1 Introduction to XReport Report Templates Overview Repeating Sections A repeating section is a section of a report template that is automatically repeat
77. can Filter Selection Dialog Box Library Search Graphics Table Properties Dialog Box Library Search Results Table Properties Dialog Box Sample Table Properties Dialog Box Text Object Properties Dialog Box Bitmap Properties Dialog Box Column Properties Dialog Box Configure Component Calibration Curve Dialog Box Data Sources Dialog Box Electronic Signature Properties Dialog Box Font Dialog Box Preferences Dialog Box Preview Window Save As Dialog Box Template Configuration Dialog Box XReport User Guide 127 D XReport Reference XReport Dialog Boxes Configure Repeating Section Dialog Box Use the Configure Repeating Section dialog box to customize the following settings for your repeating section Including or exclude internal standards or target compounds from a Quan repeating section Specifying the order in which peaks and components are repeated Defining any limit on the number of peaks reported Specifying page breaks in the final report The Configure Repeating Section dialog box has these pages Exclude Page Ordering Page Page Breaks Page Exclude Page Use the Exclude page to indicate components to exclude from a Quan repeating section and whether or not to discard any components that have not been found Table 14 Exclude page parameters Parameter Description Repeating Section Excludes Exclude Component Type Exclude specific compounds from the Quan configurations None nternal Stand
78. ces Dialog Box Set grid and configuration options for your report in the Preferences dialog box Table 64 Preferences dialog box parameters Parameter Description Grid Spacing Width Set the width between gridlines 1 gridline unit 0 1 inches Height Set the height between gridlines 1 gridline unit 0 1 inches Actions Snap To Grid Snap objects to the grid For Snap To Grid to work the grid must be displayed choose View Report Template Grid Show Page End Display a dashed blue line that indicates the location for page breaks Show Template Show the Template Configuration Dialog Box when you open XReport or choose File gt Configuration New Use the Template Configuration dialog box to select a type of report to create for Thermo Scientific example Xcalibur 2 0 This option is available only when two or more types of report templates are installed on the system for example both Xcalibur and LCQuan XReport User Guide 163 D XReport Reference XReport Dialog Boxes Preview Window Preview and adjust the appearance of your report using the parameters in the Preview window To open this window choose Report gt Simulate Report XReport displays a preview of your template filled with sample data In previewing the appearance of your report adjust your template before you combine it with actual data Choose Report gt Resolve Report to see a preview of your report combined with your actual data
79. ces to Display page parameters Parameter Quan Traces Description Quan Traces Specify the Quan traces to display Common Normalization Normalize all of the traces the same way For All Traces Select Plot Details This check box is available only when you select All Quan Traces from the Quan Traces list Set parameters on the Select Plot Details page to configure how the plot is drawn when you configure a raw file based chromatogram To configure a plot 1 If you are in a Qual or Quan repeating section the Use Container Supplied Qual or Quan Peak page opens Select the Explicitly Specify The Chromatogram s Behavior check box and click Next 2 On the Select Chromatogram Type page select a raw file based chromatogram and follow the pages of the wizard until the Select Plot Details page opens Table 29 Select Plot Details page parameters Sheet 1 of 2 Parameter Description Plot Type Detector View the type of detector used to generate the raw file Delay min Specify the delay for the start of the chromatogram trace Filter 138 XReport User Guide View the processing that is applied to a subset of the scans in the raw file The list displays scan filter options that are stored in the selected demo raw file If no demo file is selected type a valid filter string This option is only available when an MS detector is selected Thermo Scientific D XReport Reference XReport Dialog Bo
80. columns in the table object 124 XReport User Guide Thermo Scientific D XReport Reference Reports View Table 9 Edit menu commands Sheet 2 of 2 Command Properties Description Configure the current object For example for a bitmap object you can select the source file Delete Section Delete the currently selected section This option is not available when objects are selected XReport View Menu Table 10 View menu commands Command Description Report Template Grid View or hide the grid in the current section To change your grid settings choose Layout gt Preferences Report Template View or hide the Report Template Outline pane This pane displays an overview of all Outline sections and objects in your report template and opens at the right side of the XReport window Toolbars View or hide the toolbars Status Bar View or hide the status bar at the bottom of the XReport window XReport Layout Menu Table 11 Layout menu commands Sheet 1 of 2 Command Description Align gt Align the left edges of the currently selected objects to the left edge of the first selected Left object To select more than one object click and drag a selection box around the objects or hold down the SHIFT key and click each object Align gt Align the right edges of the currently selected objects to the right edge of the first selected Right object To select more than one object click and drag a selection box around
81. ction see Figure 21 Figure 21 Ordering page in the Repeating Section Properties dialog box Repeating Section Properties Exclude Ordering Page Breaks The default ordering of processed results can be changed so that the order of peaks and or components can be tailored to each user s specific needs m Repeating Section Ordering Order By RT Ordering Direction Ascending C Descending Repeating Records Maximum Limit number of reported peaks or components to 4 a To specify the order for the repeating section in the Repeating Section Ordering area select one of the following options from the Order By list RT Retention Time the default Component Name Quan only Peak Height Intensity Peak Area Intensity Peak Response Intensity Quan only Component Concentration Quan only Thermo Scientific XReport User Guide 47 4 Configuring Objects and Sections Configuring a Repeating Section b To define the direction for the ordering in the Ordering Direction area select one of the following options Ascending Sort data in ascending order Descending Sort data in descending order c Toseta maximum number of peaks or components to order up to 999 in the Limit Repeating Records maximum area select the Limit number of reported peaks or components check box and select a value from the active box 5 Click the Page Breaks tab to display the Page Breaks page Use t
82. customize table columns Specify an order for the table Thermo Scientific XReport User Guide 9 1 Introduction to XReport Configuring XReport Objects Overview Using the Chromatogram Wizard Overview Use the Chromatogram wizard to do the following Select chromatogram type and peak type e Use a demonstration demo file Select plot details Select smoothing parameters Use MS Quan traces Configure the Chromatogram display style labeling axes and normalization methods Configuring a Component Calibration Curve Overview Use the Component Calibration Curve wizard to specify the name of the component plotted for a nonrepeating Component Cal Curve report object in a report Using the Data Source Browser Overview Use the Data Source Browser to select data files that can be used to generate reports from within XReport Sample XReport Templates Overview An XReport template is an XReport document xrt file with XReport objects embedded within it You do not have to create personal XReport templates XReport provides customized report templates for you to use with your data For full details of these report templates see Appendix A Sample XReport Template Files 10 XReport User Guide Thermo Scientific 1 Introduction to XReport Using XReport Using XReport To use XReport read these topics Starting XReport Selecting a Report Template Creating and Generating Reports with XReport Exiting XReport Star
83. dance Units C Absolute Relative Offset Cancel Apply Help 2 To offset the axis label from the spectrum select the Offset check box 3 To split the spectra into two or more separate graphs with equal ranges select the Split mass range check box Type the number of split range graphs displayed for each spectrum in the Divisions box 100 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Spectrum 4 Select one of the following options in the Y Axis area under Label From detector Use the detector specific label for the y axis stored in the raw file Custom Use your own label 5 To specify the setting for the y axis units select the Absolute or the Relative option 6 Type a y axis name in the Name box 7 To move the axis label away from the spectrum select the Offset check box Select Normalization Options Use the Normalization Page to select normalization options for spectrum plots To select normalization options 1 To define the normalization method select one of the following options in the Normalize method area see Figure 74 Auto zero Automatically optimize the y axis Intensity Range 96 Set the y axis range Use the box to type the minimum and maximum intensity The valid range is 200 00 to 200 0096 Figure 74 Normalization page Spectrum Properties Options Plottype Enhance Style Labels Axis Normalization Peak Normal
84. e Enhancement page To add smoothing to the data select the Enable check box in the Smoothing area see Figure 43 Figure 43 Enhancement page in the Spectrum List Table Properties dialog box Spectrum List Table Properties Options Plot type Enhancement Display Smoothing Refine Enable Enable Background subtraction Time Range 1 0 Time Range 2 0 To select a type of smoothing select Boxcar or Gaussian from the Type list Select the number of smoothing points odd numbers from 3 to 15 to be used in the Points list To refine the data select the Enable check box in the Refine area To define an area for drawing a peak type the number of seconds on either side of the specified point A reasonable initial value for the window is the peak width in seconds Type the cutoff point for peaks in the Noise Threshold box To show all peaks in the spectrum type 0 Return to this box to eliminate more noise Slowly increase the value until the noise peaks are eliminated Use this setting to eliminate peaks generated from baseline noise To turn on a first baseline region that is used for assessing background subtraction select one or both of the Time Range check boxes Type the time range to use in the box The Background Subtraction area shows details of background subtraction if applied to the spectrum The background contribution is determined by averaging the scans from one or two base
85. e Text Object Properties dialog box for these tasks Configuring Text Fields Adding Custom Text Fields Configuring Text Attributes Setting Text Fonts Thermo Scientific XReport User Guide 49 4 Configuring Objects and Sections Configuring a Text Object Configuring Text Fields 50 XReport User Guide To configure the text object To include a custom title for the object select the Include the title on the resolved report check box on the Data page of the Text Object Properties Dialog Box Click Include and type a name in the active Title box Select the items to include from the Available Items list Select an item and click Add Double click an item To move all available fields click Add All The fields you have chosen appear in the selected list Select the fields in the Selected list that you do not want to include and click Remove To change the order of the selected items in the Selected list box select an item and click Move Up or Move Down To edit a data label select it in the Selected list and edit its text in the Data label box Headings cannot be edited However use User Text items to add custom Headings to a text object See Adding Custom Text Fields Click OK to save your changes and close the dialog box Thermo Scientific 4 Configuring Objects and Sections Configuring a Text Object Adding Custom Text Fields Add a custom text field to the text object to use as
86. e column up in the list This action moves the column to the left in the finished table Move Down Move a column down in the Selected list Select a column in the Selected list and click Move Down to move the column down in the list This action moves the column to the right in the finished table Set Table Sort Filter Page Set parameters on the Set Table Sort Filter page to define the order for table data when you generate a report using the chosen table object in the report template Note This page is not available for the Library Search Graphics Results table Table 45 Set Table Sort Filter page parameters Parameter Column List Description View the list of columns that are currently selected for the table Current Sorting Configuration First Order Select the first column that the Xcalibur data system uses to sort the table Select to sort in Ascending Descending ascending or descending order Second Order Select the second column that the data system uses to sort the table For instance use this Ascending Descending option in columns that have identical entries in the First Order column Select to sort in ascending or descending order Third Order Select the third column that the data system uses to sort the table For instance use this Ascending Descending option in columns that have identical entries in the First Order and Second Order columns Select to sort in ascending or descendi
87. e mail reports or display them on the Internet Create Xcalibur reports containing the following Textual information for example sample information Tabulated information for example a calibration file table Graphical information for example a spectrum or a chromatogram Contents The XReport Window Report Templates Overview Configuring XReport Objects Overview Using XReport Thermo Scientific XReport User Guide 1 1 Introduction to XReport The XReport Window The XReport Window The XReport window is split in four different panes Sections pane Objects pane Template pane Report Template Outline pane See Figure 1 for the location of the panes Figure 1 XhReport window Pee pe SS z m n EH EB foo z 4 Peak Integration Report Sections pane te Data File DataFile Original Data Path OrigDataPath Current Data Path Sample Type SampType Sample ID SampID Sample Name Operator Operator Acquisition Date AcqDate Run Time min 1 Non Repeating Section Comments Comments Vial Scans 1 Low Mass m z LowMass l Mass m z HighMass Sample Weight ISTD Amount ISTDAmt Calibration Level CalLevel Dilution Factor GIN Quan Repeating Section Instrument Method InstMthd Original Processing Method ProcMthd Footer Section Current Processing Method CurrentProcMthd UserLabell UserVall
88. e menus toolbars or mouse to align resize and reposition objects 4 Save the report template For more detailed information on how to create and configure a report template see Chapter 2 Creating a Template and Chapter 4 Configuring Objects and Sections Thermo Scientific XReport User Guide 13 1 Introduction to XReport Using XReport Generating a Report Using a Report Template After creating a report template generate a report or resolved document by combining a report template with one or more data source files for example Xcalibur pmd raw rst sld and xcal files For detailed information on how to generate a report from within the Xcalibur data system see Chapter 3 There are three ways to generate a report From a report template open in XReport Search for the required data source files and combine the data with the template to generate a report Preview print and save the report in txt doc xls rtf pdf or htm format From a data processing application for example Xcalibur Associate the data you produce in the application with a report template for example do this in Quan Browser and combine the data with the template to generate a single report From a data processing application for example Xcalibur Insert the name of the template to a processing method such as Processing Setup and generate reports automatically when you batch process data such as in Sequence
89. e next page of the wizard Thermo Scientific XReport User Guide 85 4 Configuring Objects and Sections Configuring a Chromatogram Object Select Enhance Details Page Use the Select Enhance Details page to enhance a chromatogram plot by applying smoothing see Figure 59 Figure 59 Select Enhance Details page Select Enhance Details lt is possible to enhance a chromatogram plot by smoothing Select whether to apply smoothing to the plot and if smoothing is being used to configure the smoothing criteria RT 0 00 7 02 t NL Enable smoothing 100 214E5 TICF MS 80 drugs 01 60 40 v o m zzi a X v 2 A w a 20 3 19 0 0 5 Time min cme eo To enhance a chromatogram 1 To apply smoothing to the chromatogram select the Enable Smoothing check box 2 To select a type of smoothing select Boxcar or Gaussian from the Type list in the Smoothing Details area 3 Select the number of smoothing points odd numbers from 3 to 15 to use in the Points list 4 Click Next to go to the next page of the wizard 86 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Chromatogram Object Select Chromatogram Style Page Use the Select Chromatogram Style page to determine the appearance of the chromatogram To define styles for a chromatogram 1 To define the plotting style select one of the following options in the Plotting area see Fi
90. e peak reached the Constrain Peak Height Tailing Factor limit before the Height Percent Tilt An error occurred before the edge of the peak could be determined Unknown An unknown error occurred Thermo Scientific Thermo Scientific D XReport Reference Report Objects Data Flags XReport can display Data Flag letters in the Quan Summary Table Quan ISTD Peak Summary Quan Peak Table and Quan Summary Table objects to indicate when a peak has exceeded threshold area or height values specified in Quan Browser These are the data flags that can appear Table 78 Data flags Flag Description A Indicates that the peak area is outside the specified tolerance H Indicates that the height is outside the specified tolerance Calibration Flags XReport can display Calibration Flag letters in the Quan Peak Summary Quan Summary Table and Quan Peak Table objects to indicate when certain peak characteristics exceed values specified in Quan Browser These are the calibration flags that can appear Table 79 Calibration flags Flag Description E Detection limit Indicates that the detection threshold for the concentration of the quantified peak is outside the specified tolerance L Carry Over limit Indicates that the carryover threshold for the concentration of the quantified peak is outside the specified tolerance Q R squared Indicates that the coefficient of determination is outside the specified tolerance
91. eading Font selection is also used for User Text See Adding Custom Text Fields on page 51 Configuring an Annotation Object You can include an annotation object in any section type To configure the Annotation object 1 Right click the annotation object in the template and choose Properties from the shortcut menu The Annotation Properties dialog box opens see Figure 29 Figure 29 Data page in the Annotation Properties dialog box Annotation Properties Data Attributes Font Enter vour text here 2 On the Data page click the box on the Annotation Properties dialog box to get a cursor Delete the words Enter your text here and type annotation text 3 On the Attributes page select the number of columns to display annotation text in the Number of columns area see Figure 30 Figure 30 Attributes page in the Annotation Properties dialog box Annotation Properties m Number of columns Ka C 2 C 3 m Horizontal alignment C Left Center Right Vertical spacing Single 1 5lines Double Cancel ip Help Thermo Scientific XReport User Guide 55 4 Configuring Objects and Sections Configuring an Annotation Object 4 In the Horizontal alignment area select an alignment option for the annotation text Left Center or Right 5 In the Vertical spacing area select a spacing option for the annotation text line Single 1 5 lines or Double 6 On the Font pa
92. ect o0 o 0 Auto Align 122 XReport User Guide Snap all objects selected or not in the current section to the nearest upper and right gridlines Thermo Scientific Table 7 Toolbar buttons Sheet 2 of 2 Button Center Horizontally D XReport Reference Reports View Description Center the current object on the page so that it is an equal distance from the left and right sides of the page Center Vertically Center the current object on the page so that it is an equal distance from the top and bottom sides of the page Make Same Height Enlarge all selected objects except for the first selected to match the height of the first selected object 3 x s e Le Make Same Width Enlarge all selected objects except for the first selected to match the width of the first selected object Make Same Heightand Enlarge all selected objects except for the first selected to match the height Width and the width of the first selected object Shrink Wrap Shrink the template workspace to remove all unused workspace at the bottom HE of the section Expand Enlarge the template workspace to the full height of the section size 100 Increase or decrease the magnification of the template display Zoom Font Change the font that is used in the currently selected object or change the global font settings if no object is selected Resolve Report Combine your report template with your dat
93. ections Configuring a Chromatogram Object Figure 55 Select the Qual Peak page Select The Qual Peak When a chromatogram that will display Qual results is added to a report template in a non repeating section the retention time of Qual peak to display must be explicitly set Qual Peak To Display Retention time min m The retention time entered for a Qual peak can be any time after the left hand edge and before the right hand edge of the peak Note If a Qual peak cannot be located at the retention time specified this chromatogram cannot be added to the resolved document lt Back Next Cancel Help lt Back 2 Click Next to go to the next page of the wizard Select Mass Spectrum Quan Traces to Display Page Use the Select Mass Spectrum Quan Traces to Display page to configure the Quan Traces property for MS data This page is only applicable to MS data and is inactive for other detector types When a chromatogram report object displays a Quan component there are potentially six traces associated with the component as follows Quan Mass QM Trace the actual component peak Up to five Confirmation Ions Note The Ion Ratio Confirmation settings on this page apply only to GC MS data Select any of these possible six traces to be displayed in the Chromatogram or display all available traces of the component To specify a Quan trace 1 Select the Quan trace in the Quan Traces area to be used fr
94. ed for every component or peak in a resolved document Change the properties of a repeating section to customize its behavior Two types of repeating section can be used in an XReport template Qual repeating section Use a Qual repeating section to display details relating to a single Qual peak within some data The section is repeated for all Qual peaks found Quan repeating section Use a Quan or component repeating section to display details relating to a single Quan peak in some data or a component configured in a processing method The section is repeated for all Quan peaks or components Nonrepeating Sections A nonrepeating section usually displays static details associated with data or methods that apply once and globally within the system for example processing method settings instrument method settings filename confirmation ion information and so on Report Objects Report objects are customized tables graphics or text that indicate what kind of data appears in the report When the Xcalibur data system combines a report template with data it replaces the report objects in the report template with data to generate a report See Report Objects on page 170 for more information Report objects include the following Text Objects Table Objects Graphic Objects Formatting Objects For a descriptive listing of XReport objects see Appendix B Types of Report Objects Thermo Scientific XReport User
95. efine Enable Turn on refine spectrum enhancement Window Define an area for drawing a peak by specifying the number of seconds on either side of the specified point A reasonable initial value is the peak width in seconds Noise Threshold Specify the cutoff point for peaks Type 0 to show all peaks in the spectrum and slowly increase the value until the noise peaks are eliminated Use this setting to eliminate peaks generated from baseline noise Background Subtraction This area shows details of background subtraction if it was applied to the spectrum The background contribution is determined by averaging the scans from one or two baseline regions Time Range 1 Activate a first baseline region that is used for assessing the background Clicking this option activates a box Type the time range to use in the box Time Range 2 Activate a second baseline region that is used for assessing the background Thermo Scientific XReport User Guide 153 D XReport Reference XReport Dialog Boxes Options Page Configure general parameters relating to the Spectrum List table on the Options page Table 50 Options page parameters Parameter Use Processing Method Properties For Plot Type And Enhancement Info Description Use the information in the processing method when determining the plot type and other enhancement details Use ISTD Peak When Include internal standard peaks in the spectrum list This parameter is only a
96. el select the Custom Text Label check box Type a custom label for the Quan peak in the active box 5 To label the Quan peak with the retention time select the Retention Time check box When you turn on this check box the Labels page shows the change when you return to it 6 In the RT Labeling area select the type of unit for the retention time from the Units list 7 Select the number of decimal places to be displayed in the retention time label from the Decimals list 8 Click OK to save the changes and close the dialog box Advanced Options Qual Click Advanced in the Select the Peak Labeling page The Advanced Qual Peak Annotation Options dialog box opens When you set Advanced Labeling options the Xcalibur data system labels only the Qual peak Tosetadvanced Qual peak annotation options 1 To activate the advanced Qual peak options select the Use advanced Qual peak annotation check box see Figure 63 Figure 63 Advanced Qual Peak Annotation Options dialog box Advanced Qual Peak Annotation Options When advanced peak annotation is used a general purpose label may be applied to annotate Qual peaks If retention time has been selected to be displayed its units may be configured here Cancel If a change is made to the retention time checkbox it will be reflected on the peak labeling dialog when you return Help Use advanced Qual peak annotation jz aaa v Retention Time 2 To specify a custom labe
97. elect Component Processing C Xcalibur examples methods drugx pmd Cae Select a component from the list available drugx Help from the processing method 3 Select the required component from the list available for the chosen processing method and click OK The Component Name page opens displaying the specified name of the component in the box 4 Click OK 94 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Spectrum Configuring a Spectrum To configure a Spectrum report object right click it and choose Properties from the shortcut menu The Spectrum Properties Dialog Box opens to the Options page see Figure 68 Figure 68 Options page Spectrum Properties Axis Normalization Options Plottype Enhance Style Labels Use processing method properties for plot type and enhance info J Use ISTD peak when repeating on component OK Cancel Apply i Use the XReport Spectrum Control Properties pages to do the following Configure Options Configure Plot Types Enhance Spectra Configure Spectrum Style Configure Peak Labels Configure Axes Select Normalization Options Specify a Peak To configure the Spectrum report object make selections on each page based on these corresponding procedures Thermo Scientific XReport User Guide 95 4 Configuring Objects and Sections Configuring a Spectrum Configure Options To configure Spectrum op
98. elines for a Chromatogram peak Quan or Qual see Figure 57 When you clear this option XReport does not display the baselines peak tracing or full peak annotation 82 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Chromatogram Object Figure 57 Configure How the Peak Window Will Look page Configure How The Peak Window Will Look v L Custom width min 2 To manually override the default value of the peak window width the default is peak width plus 1 min select the Set Custom Window Width check box Use the Custom width edit box to type a value for the window width min The default value for this field is 0 75 min 3 Click Next to go to the next page of the wizard Thermo Scientific XReport User Guide 83 4 Configuring Objects and Sections Configuring a Chromatogram Object Select Plot Details Page Use the Select Plot Details page to configure how the plot is drawn when raw data is being displayed in a chromatogram report object To configure a plot on a raw file based chromatogram 1 Select the type of detector used to generate the raw file from the Detector list in the Plot Type area see Figure 58 The type of detector determines the available traces Figure 58 Select Plot Details page Select Plot Details When raw data is being displayed in a chromatogram control it is possible to configure the plot that will be drawn Plot Type Detector X Delay m
99. eport Page 1 Peak Integration Report Page 2 Peak Integration Report Page 3 Peak Integration Report Page 4 Thermo Scientific XReport User Guide 115 C Sample Report Peak Integration Report Page 1 Peak Integration Report Page 1 Data File steroids02 Sample Type Std Bracket Start Operator jackc Comments Low Mass m z 100 00 ISTD Amount 0 000 116 Peak Integration Report Original Data Path C pitcon trial2 Current Data Path Sample ID Sample02 Sample Name Acquisition Date 02 28 96 11 20 31 AMRun Time min Vial l Scans High Mass m z 375 00 Sample Weight Calibration Level 3 Dilution Factor Instrument Method C pitcon trial2 steroidMSMSis Original Processing Method C pitcon trial2 steroidmsmsIS Current Processing Method C Xcalibur examples methods steroid XReport User Guide C Xcalibur examples data 3 79 336 0 00 1 00 Thermo Scientific Peak Integration Report Page 2 Peak Integration Report C Sample Report Peak Integration Report Page 2 hydrocortisone methyltestosterone Expected RT i vB SEM re TOP Expected RT d Ta Ma Pe ETETA Retention 268287 6 ime min E 90 9e396r cP Time min 2 0 i m2308 301 Eei PSL s min mE us s 80 Genesis steroids02 Retention 80 Genesis steroids02 Time Window Time Window 25 sec um 30 00000 sec 30 00000 8 View Widt a View Width 3 min 1 00000 E min 1 00000 d m Retention 4 Retenti
100. er object of the same type to the report XReport inserts it with the default settings Contents Thermo Scientific Configuring a Repeating Section Configuring a Text Object Configuring an Annotation Object Configuring a Table Object Configuring a Bitmap Object Configuring a Chromatogram Object Configuring a Component Calibration Curve Configuring a Spectrum Configuring Columns XReport User Guide 45 4 Configuring Objects and Sections Configuring a Repeating Section Configuring a Repeating Section There are two different types of repeating sections in XReport Qual repeating Displays details related to a single Qual peak in some data The section section is repeated for all Qual peaks found Quan repeating Displays details related to a single Quan peak in some data or a section component configured in a processing method The section is repeated for all Quan peaks or components In the Repeating Section Properties dialog box specify these parameters 46 XReport User Guide Whether to exclude internal standards or target compounds from a Quan repeating section The repeat order for peaks and components Any limit on the number of peaks to be reported How the individual peaks or components are split across pages in the final report To configure a Qual or Quan repeating section Scroll to where you can see the QL or QN icon at the top left side of the Template pane and right click the icon Choose Propertie
101. er or Nonrepeating section For this object s possible fields see Table 75 Table 75 Sample Header object fields Data File Original Data Path Current Data Path Sample Type Sample ID Sample Name Operator Acquisition Date Run Time Comments Vial Scans Low Mass High Mass Sample Volume Injection Volume Sample Weight ISTD Amount Calibration Level Dilution Factor Instrument Method Processing Method Current Processing Method Calibration File Revision Barcode Barcode Status User Labels 1 to 5 Blank Line and User Text Data Items 196 XReport User Guide Thermo Scientific D XReport Reference Report Objects System Suitability Flags The Quan Summary Table Quan ISTD Peak Summary Sample Table and Quan Peak Table objects have an available System Suitability field which displays the results of any system suitability tests carried out on the specified peak Each test is represented by a flag letter XReport displays the flags in categories according to whether the peak passed failed or was not tested These are the System Suitability flags Table 76 System Suitability flags Flag Description S Symmetry A peak passes this test if its calculated symmetry is greater than the symmetry threshold specified in the System Suitability page of Quan View in Processing Setup R Resolution A peak passes this test if its calculated resolution is
102. ers Sheet 2 of 2 Parameter Description Repeat Type Summary repeat D XReport Reference XReport Dialog Boxes View information relating to all of the samples in an Xcalibur sequence and the results created when processing them This setting is ignored when the column object is not located in a nonrepeating section Example 3 If you place a 2 column object in a nonrepeating section add a chromatogram in either column and resolve the template given data of 2 samples with 4 components each the report appears as follows Chrom Resolve Left to right Chrom 1 Chrom 2 Chrom 3 Chrom 4 Chrom 1 Chrom 2 Chrom 3 Chrom 4 Sample 1 Sample 2 If you choose instead the Top To Bottom option the report appears as follows Chrom Resolve Top to bottom Chrom 1 Chrom 3 Chrom 2 Chrom 4 Chrom 1 Chrom 3 Chrom 2 Chrom 4 Sample 1 Sample 2 If you place an object in the right column and leave the left column empty the data is resolved as if the object is placed in the left column as illustrated above If you place an object in each column the Xcalibur data system ignores the Top To Bottom and Left To Right options The report appears as follows Resolve
103. escriptions 25 1 coe pp C eek Pas RR CoRR RAS 109 Table Object Descriptions oe docdveniitd v ode pit xac Dea earl Ae Saas 111 Graphic Object Descriptions oz Lure tae bee hee eet wR Ere 114 Formatting Object Descriptions eese cee eee hen 114 Sample Report eed ret md Ei Ne acne de C b ERR 115 Peak Integration Report Page Tu adu dere obe rk olg e ael e cde erd NEU pa 116 Peak Integration Report Page 2 5v ose Ee PARIET tEP RPAUR FS 117 Peak Integration Report Page 3 51 Re p ER 118 Peak Int gration Report Page d i252 ud bapu aoo sods RO PE P RES 119 XReport User Guide v Contents vi XReport User Guide Appendix D XReport Reference 20 cee eee eee eee eee 121 Reports VIEW ice doe OR Ae abe inked kG bee GU Det he yg UN Caper alah 121 Report Toolbar Buttons 4 25 ren Vez pet Vett pd a A 122 SS Report Menus sesu ace x aset audi Ses dari Dad alo uec ae dard 124 XRBeportDialog Bores sypreis depen EA re EL KRESS WEL RS 127 Configure Repeating Section Dialog Box 0000 eee eee 128 Chromatogram Properties Dialog Box and Wizard 130 Spectrum Properties Dialog Boxsa 3241 use eben nwo aie 142 Table Properties Wizard 22209 osdodues Sow docere Xa Dem DRM er Ra Ru 147 Edit Formula For Dialog Box v iie RR Hi ERE Ae Ate 150 Configure Function Dialog Box wi i540 carta hella e Rp eR ER 151 Spectrum List Table Properties Dialog Box 2 0 00 cee eee eee 152 Ave
104. esponds to the dimension you want to resize x Same Width E Same Height Same Width and Height To resize the columns in a table object Double click the table Handles small blue boxes appear on the interior column borders Drag the handles to resize the columns To align one or more objects Select the first object to align The position of the first object selected determines how subsequent objects are aligned Hold down the SHIFT key and select each object to align Click the button in the toolbar that corresponds to the edge to align Left Right Top Bottom BE sa m H Or click Auto Align to snap all objects to the nearest grid line Doe one t Choose View gt Report Template Grid to view the grid lines To adjust the grid settings choose Layout gt Preferences The Preferences dialog box opens Figure 6 XReport User Guide 19 2 Creating a Template Adding and Configuring Report Objects Centering Objects To center one or more objects 1 Select the first object to center Then hold down the SHIFT key and select each object to center with respect to the first object 2 To center the objects on the page do the following Click the Center Horizontally icon HH Click the Center Vertically icon E Using the Report Template Grid The Template pane has a grid built in it Choose View Report Template Grid to view the grid lines To adjust the grid settings
105. et parameters that determine the appearance of the spectrum use the Style Page see Figure 71 Figure 71 Style page Spectrum Properties Axis Normalization Peak Options Plottype Enhance Style Labels T i O o C Shade 8 6 8 Relative Abundance o Cancel Apply Help XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Spectrum To set plotting options To define the plotting style select one of the following options in the Plotting area Configure Peak Labels Automatic Choose the graphic style based on the data acquisition method used for the active spectrum Point to Point Display a point to point peak profile Stick Display spectral mass peaks as vertical lines Shade Display the spectrum as a shaded representation of intensity in each amu band for the active spectrum To choose the type and style of peak labels use the Labels Page To configure peak labels 1 To label spectrum peaks with m z value select the Mass check box see Figure 72 in the Label With area Figure 72 Labels page Spectrum Properties Axis Normalization Options Plot type Enhance m Label with MV Mass Relativeto 0 0 Flags Decimals Label styles Offset Size 5 Rotated Boxed Label threshold o Relative Abundance Cancel Apply Help 2 To label spectrum peaks with flags select the Flags check box
106. ettings The Component Sys Suit Flags Settings object displays calibration quantitation and detection flags along with system suitability parameters which allow automatic chromatographic checks that assign a pass fail qualification to a target peak Required data file pmd Section placement Quan nonrepeating repeats on component peak For this object s possible fields and headings see Table 69 Table 69 Component Sys Suit Flags Settings object fields headings System Suitability Component Name Resolution Parameters e Resolution Threshold Detect Column Overload Detect Tailing Detect Baseline Clipping Quantitation Flags Tail Peak Height Num of Peak Widths Detection Limit for Noise Detection un o Tail Failure Threshold Quantitation Limit Detect Minimum Li ity Limit Signal to Noise Ratio inearity Limi Symmetry Parameters Over Peak Height enable Noe dU Carry Over Limit e Symmetry Peak Height Over Failure Threshold Calibration and Detection Flags Symmetry Threshold Quantitation Flags Area Threshold Peak Classification Calibration Flag Height Threshold Parameters Rigu Gia Detect Peak Width e Width Peak Height e Min Peak Width Max Peak Width Instrument Method 192 XReport User Guide Blank Line gt and lt User Text gt Data Items The Instrument Method object displays general instrument method parameters Required data file raw Section placement Nonrepeating sectio
107. f the wizard Advanced Options Quan Click Advanced in the Select The Peak Labeling page The Advanced Quan Peak Annotation Options dialog box opens When you set Advanced Labeling options the data system labels only the Quan peak To set advanced Quan peak annotation options 1 To activate advanced Quan peak options select the Use advanced Quan peak annotation check box see Figure 62 Figure 62 Advanced Quan Peak Annotation Options dialog box Advanced Quan Peak Annotation Options When advanced peak annotation is used then only the Quan peak which is the purpose of a report chromatogram is labeled therefore thresholding is N A If retention time has been selected to be displayed its units may be configured here Cancel If a change is made to the retention time checkbox here it will be reflected on the peak labeling dialog when you return Help The component name and key are available for use as peak labels amp general purpose label that is manually entered here can also be used to annotate Quan peaks Use advanced Quan peak annotation r r r v Retention Time Thermo Scientific XReport User Guide 89 4 Configuring Objects and Sections Configuring a Chromatogram Object 2 To label the Quan peak with the component name select the Component Name check box in the Custom Peak Labels area 3 To label the Quan peak with the component key select the Component Key check box 4 To specify a custom lab
108. fic D XReport Reference Report Objects Avalon Qual Events Table The Avalon Qual Events table displays details of the Avalon peak detection algorithm events configured in the Qual section of a processing method This table provides information for each peak with each sample There is a separate row for each sample peak combination The rows are grouped so that all peaks in a sample are shown together Required data file pmd Section placement Nonrepeating section This table has the following possible fields Time ms Kind Event OPCode Event Value e Value 2 User Columns 1 to 5 Avalon Quan Events Table Thermo Scientific The Avalon Quan Events table displays details of the Avalon peak detection algorithm events configured for a component in the Quan section of a processing method This table provides information for each peak with each sample There is a separate row for each sample peak combination The rows are grouped so that all peaks in a sample are shown together Required data file pmd Section placement Nonrepeating section This table has the following possible fields Time Kind Event OPCode Event Value Value2 User Columns 1 to 5 XReport User Guide 173 D XReport Reference Report Objects Calibration File Table The Calibration File table displays calibration levels raw file names and acquisition dates of standards This table provides information for each peak with each sam
109. fixed by AA if detected automatically or MA if detected manually Height Label the peaks with the apex height prefixed by AH if detected automatically or MH if detected manually Label Styles Offset Move a label away from its normal position to avoid conflict with another label Size Specify the offset size measured in number of characters Rotated Use vertical rather than horizontal mass labels Flags are always displayed unrotated Boxed Place a rectangular outline around each peak mass label Flags are not boxed Label Threshold Limit the labeling of peaks to those exceeding the specified percentage of the base peak Advanced Set advanced labeling options Only the Quan or Qual peak is labeled if you click this 140 XReport User Guide option Thermo Scientific D XReport Reference XReport Dialog Boxes Select the Qual Peak Set the parameter on the Select the Qual Peak page to explicitly specify the Qual peak for a Qual results based chromatogram report object Table 31 Select the Qual Peak page parameters Parameter Description Qual Peak To Display Retention Time min The retention time of the Qual peak The retention time can be any time between the start and end peak boundaries You must select a valid retention time to combine template and data correctly If the file used to resolve the report does not contain the specified retention time the Xcalibur data system removes the chromatogram from the report Selec
110. g Section 3 Click OK XReport User Guide 65 4 Configuring Objects and Sections Configuring a Table Object 66 XReport User Guide Plot Type Page Before viewing and selecting the parameters on the Plot Type page clear the Use processing method properties check box on the Options page and click the Plot Type tab itN 1 To set parameters on the Plot Type page Type the mass range to display in the Mass range box Separate the values by a dash lowmass highmass Type to display the entire range see Figure 42 Figure 42 Plot Type page in the Spectrum List Table Properties dialog box Spectrum List Table Properties Options Plot type Enhancement Display Mass range i Detector Ms v Time Scan filter Demo file C Xcalibur examples data steroids02 raw ES DK Cancel Appl Help OK Select the type of detector that you are using from the Detector list MS or PDA Type the time range to display in minutes in the Time box Type the values separated by a dash firsttime secondtime Type to display the entire range Enter the scan filter to use with the data in the Scan Filter list Type or search in the Demo File box for the name of the file you to use as a demonstration file for the settings in the template Click OK Thermo Scientific Thermo Scientific 4 Configuring Objects and Sections Configuring a Table Object Enhancement Page To set parameters on th
111. g graphic and formatting objects are available in XReport Chromatogram Bitmap Spectrum Columns Component Cal Curve Page Break Thermo Scientific Chromatogram Spectrum Component Cal Curve Bitmap Columns Thermo Scientific D XReport Reference Report Objects The Chromatogram object displays a graphical trace that can show either raw data or processed data for any acquisition device that is supported by the Xcalibur data system MS Analog A D card PDA UV Required data file raw rst Section placement Qual Quan and nonrepeating sections The Spectrum object displays a graphical spectrum that can show either raw data or processed data for any acquisition device supported by the Xcalibur data system MS PDA Required data file raw rst Section placement Qual Quan and nonrepeating sections The Component Calibration Curve object displays the calibration curve that is used to quantify a specified component The curve is specified in the processing method as the response versus the amount of standard Required data file pmd rst Section placement Quan or nonrepeating sections For the nonrepeating section specify which component to display in the Configure Component Calibration Curve Dialog Box The Bitmap object displays a graphical image for example a company logo Required data file bmp dib gif jpg or ico Section placement possible in all sections Use the Columns object to man
112. ge When you insert the lt Blank Line gt data item in the Selected list XReport inserts a blank line at that spot You can use this to control the spacing between items in a text object Unlike ordinary data items a lt Blank Line gt can appear in the Selected list more than once The lt User Text gt item allows you to insert additional custom text into the text object The lt User Text gt item can be added to the Selected list more than once and each instance can be configured to display different custom text Custom text is displayed using the font settings for Headings Baseline Flags The Quan Peak Summary Quan ISTD Peak Summary Quan Peak Table Qual Peak Table Qual Summary Table and Quan Summary Table objects have an available Baseline flags field that displays how the data system detected the left and right peak edges of the current peak The flags are displayed in pairs with the first letter of the pair indicating the detection method for the left edge of the peak and the second letter indicating the detection method for the right edge of the peak These are the baseline flags Table 77 Baseline flags Flag Description B Baseline The edge of the peak is at baseline level V Valley The edge of the peak is in a peak valley M Manual The edge of the peak has been adjusted manually S Stripe The edge of the peak reached the Constrain Peak Height Percent specified in the method T Tail The edge of th
113. ge configure the font by setting the font parameters see Figure 31 Figure 31 Font page in the Annotation Properties dialog box Annotation Properties Data Attributes Font Font Font Style Size Times New Roman Bold fia a Times New Roman M Trebuchet MS Tw Cen MT Bold a5 Effects v Underline Strikeout Color a Black OK Cancel ok 7 Click OK to save your changes 56 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Table Object Configuring a Table Object t To configure a table object 1 Right click the table object 2 Choose Properties from the shortcut menu The Table Properties wizard opens see Figure 32 named for the type of table you selected For a description of each table including the sections where a table can appear see Appendix B Types of Report Objects Figure 32 Select Table Fields page Avalon Qual Events Table Select Table Fields Available columns Selected Value Add gt Kind Value2 Event OPCode User Column 1 Add All gt gt Order User Column 2 Selected User Column 4 SIU ee User Column 5 lt lt Remove All Move Down The type of Avalon Event The time in milliseconds associated with the valon event Column header Time mS Decimal setting 2 Cancel Help Using the Table Properties wizard configure a table object included in the report
114. group of contiguous samples click the first of the sequence scroll until you see the last sample in the sequence and while holding down the SHIFT key click the last sample in the sequence The data system highlights the selected sequence Fora group of non contiguous samples hold down CTRL while you click each sample to select or clear it The data system highlights the selected samples c To copy the selected samples to the Selected Samples area click Add d To return to the Reports dialog box click OK 11 To print reports click Print Reports Prior to printing reports the data system does the following Displays the Printer Activity icon at the bottom of the Quan Browser window Combines the data in the sample file with the selected Report Template document Adds the report printing tasks to the processing queue and displays the Printing message box After printing the reports the data system returns you to the Quan Browser window The application saves reports created from the processing method in the same directory as the source data files and names files The reports use this format data file name template name xxx where data file name is the name of the data file from which the report was generated template name is the name of the template used to generate the report and xxx is the suffix for example doc or pdf indicating the file type When more than one report is generated from the same data file and te
115. gure 60 Point To Point Display point to point peak profiles Stick Display the chromatogram as vertical lines Figure 60 Select Chromatogram Style page Select Chromatogram Style Select the style to use when plotting the chromatogram trace The arrangement is only really applicable when there will be more than one trace on the chromatogram RT 0 00 3 79 Plotting Arrangement 0 58 NL k 100 3 99E6 e Point To Point e S TICF MS C Stick 80 steroids02 60 40 fT lt 4 o 0 E Time min coc Hee 2 To define the plotting arrangement select one of the following options in the Arrangement area v o iS m c E a X v 2 m w c Stack 2D Stack plots vertically same x axis with no overlap own y axis Overlay 3D Overlay plots vertically same x axis Use the 3D arrangement when you selected Multiple Quan Traces on the Select Mass Spectrum Quan Traces page of the wizard 3 When you select an Overlay 3D arrangement set the following in the active 3D area a To set the Elevation angle from 0 to 60 degrees for the 3D plot style adjust the Elevation slider bar Either drag the Elevation slider bar or click the Elevation slider left or right arrows until you reach the desired angle b To set the skew angle for the 3D plot style adjust the Skew slider bar Either drag the Skew slider or click the Skew slider left or right arrow until you reach the desired angle from 0 t
116. gure Function Dialog Box Thermo Scientific Configure the settings for a function in a formula for use in a custom column of your table in the Configure Function dialog box The Configure Function dialog box varies depending on which function you are configuring FALSE and TRUE No configuration options ABS AVERAGE INT MAX MIN PRODUCT ROUND SIGN SUM Select one or more columns to perform the function on These expressions all have the same options but ROUND has the additional option to select the number of decimal places AND NOT and OR enter one NOT or two AND and OR expressions to be evaluated These expressions all have the same options COUNT Enter a list MOD Select either a column or a value for each of the first and second parameters XReport User Guide 151 D XReport Reference XReport Dialog Boxes Spectrum List Table Properties Dialog Box Display Page Use the Spectrum List Table Properties dialog box to configure settings that apply to the Spectrum List table The Spectrum List Table Properties dialog box has the following pages Display Page Enhancement Page Options Page Plot Type Page Configure display parameters for the Spectrum List table on the Display page Table 48 Display page parameters Parameter Description Display All Peaks Display all peaks in the Spectrum List table Top Limit the number of peaks in the table to a specified number Order By
117. he Spectrum Peak Identification Method is specified in the processing method This object is used only for GC chromatography Thermo Scientific XReport User Guide 111 B Types of Report Objects Table Object Descriptions Table 4 Table objects Sheet 2 of 3 Table object Data source file Description Section placement Dilution Factor Table ISt Displays the names of calibration levels and dilution factors for components that are not internal standards Nonrepeating Electronic Signature none Displays up to five electronic signatures in table format This object is not editable in XReport Any Ion Ratio Confirmation Results Table IRC Settings Table ISt pmd Displays the following data about each qualifier ion based on search criteria specified in the processing method Mass e Coclution test pass fail on Ratio Test Target 96 on Ratio Test Window 96 Displays up to five qualifier ions within tolerance limits to confirm the detection ofa target analyte The ions are specified in the processing method Quan repeating Quan repeating IRC Summary Table ISt Displays all of the information for the confirmation ion for each component Most useful when the Name column is the first column Nonrepeating Lib Search Graph Table Ist TaW Displays the graphical results from a library search on a Qual peak for example Hit Spectrum Delta and Co
118. hese procedures Adding Deleting Repositioning and Resizing Objects Aligning Objects Centering Objects Using the Report Template Grid Using Columns Using Page Breaks Configuring Objects Adding User Text to a Text Object Adding a Formula to a Table Changing Font Settings Changing Page Layout Adding Deleting Repositioning and Resizing Objects 18 XReport User Guide You can add delete reposition and resize objects in a report template t bd To add an object to the report Drag an object from the Objects pane lower left to the currently selected section in blue in the Template pane center Add only one object to the template at a time To delete an object from the report Select the object in the Template pane center Blue handlebars on each side and at each corner become visible Press DELETE To reposition an object Drag the object to the preferred location Thermo Scientific itN v Aligning Objects Thermo Scientific 2 Creating a Template Adding and Configuring Report Objects To resize an object Drag the object by one of the corner handles small blue squares until the object is the preferred size To make two or more objects the same size Select the first object to size The size of the first object selected determines the size of subsequent objects Hold down the SHIFT key and select other objects to resize Click the icon in the toolbar that corr
119. his page to define the layout for the individual peaks that appear in the Qual or Quan repeating section in the final report see Figure 22 Figure 22 Page Breaks page in the Repeating Section Properties dialog box Repeating Section Properties Exclude Ordering Page Breaks How do you want the individual peaks that will appear in the repeating section to be layed out in the final report Each peak fully contained on its own page s C No page breaks between the individual peaks Page break before the repeating section Page break after the repeating section Cancel Apply Help Select the option either to print each peak on its own pages or to avoid page breaks between the individual peaks 6 When you have made selections in the Repeating Sections Properties dialog box click OK 7 Choose File Save to save any changes 48 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Text Object Configuring a Text Object To configure a text object right click the object and choose Properties A dialog box opens see Figure 23 named for the type of object you chose For a description of each text object including which section each object is in see Appendix B Types of Report Objects Figure 23 Data page in the Sample Header dialog box Sample Header lt Blank line gt bet Dase Use the dialog box to configure a text object within the report Use th
120. iguring XReport Objects Overview ccd dece dece sacopS e etna e 9 Configuring a Repeating Section Overview 0 6 0c cece ee eee eee 9 Configuring a Table Ovetviewsii 4o corr bas en e ses ieee 9 Using the Chromatogram Wizard Overview 00 cece eee eee 10 Configuring a Component Calibration Curve Overview 10 Using the Data Source Browser Overview cuoco dr duxere e 10 Sample XReport Templates Overview isses saa cies che Rer Ra Res 10 Using XRepott cesser e Rc Rege ENE heh RR RIS UR e dues 11 Starting XREport 0 sso visit erre ses ste eee ee Dae E alee ew ae n 11 Selecting a Report Templates oii os sosbeeiree o hr hee dee dss ces 12 Creating and Generating Reports with XReport 0 0 00000 13 EXE S RSBORE La c haw sarsar E d SAKA Ghee eee RACER aired 14 Chapter2 Creating a Template LuuususleeseseeeeenennnnnnnB 15 Adding Ordering and Configuring Sections 0 0 0 0 0000 ce eee ee 16 Adding Deleting or Reordering Sections 0 0 s0e08epeue ewes 16 Resizing Sections irise code cereals ades det dde Puce dev awh 16 Configuring a Qual or Quan Repeating Section 000 17 Thermo Scientific XReport User Guide iii Contents iv XReport User Guide Chapter 3 Chapter 4 Adding and Configuring Report Objects lesse 18 Adding Deleting Repositioning and Resizing Objects 18 Aligning Objects yei sun ee nr are a Ea ee ar ea a Ro eos
121. ile gt Page Setup The Page Setup dialog box opens see Figure 8 2 Change any of the following header and footer section heights portrait or landscape page orientation or margins 3 Click OK to change the page layout Figure 8 Page Setup dialog box Page Setup Paper Size z Source Automatically Select m Orientation m Margins inches Portrait Left jos Right 0 5 Landscape Top 0 25 Bottom 0 25 m Heights inches _ Header fos Footer jos Cancel Printer Help Previewing and Saving the Template Before you use a template to print reports preview the template with the example data provided with the Xcalibur data system or with a representative data file Thermo Scientific XReport User Guide 25 2 Creating a Template Previewing and Saving the Template To preview the appearance of the template 1 Choose File gt Simulate Report The Preview window opens see Figure 9 The Preview window shows the report with the default data Figure 9 Preview window se XReport Application Peaklntegration xrt for Xcalibur2 0 Simulate 2 Print Save First Page Prev Page Paw of2 Next Page Peak Integration Component Mame hr recort amp one E metfyiestosterone RT Di8 148 SM 7G RT 145 245 8M 7G qm AT 088 Retention AT 156 8 h pe 35 Sa a sm zm Reislue Aburdance na os 10 Time mir Component Name hydrocortieone Actual R
122. ime box For example to select a time range from 0 10 to 9 10 minutes type 0 10 9 10 Thermo Scientific D XReport Reference XReport Dialog Boxes Table 51 Plot Type page parameters Sheet 2 of 2 Parameter Description Scan Filter View or change the scan filter used for the active spectrum Select a filter from the list or use the scan filter format to type a scan filter in the Filter box This box is available only for MS detectors Demo File View the filename of the demo file that is used in the template Average Scan Filter Selection Dialog Box Configure the average scan filter that is used for the Spectrum List table in the Average Scan Filter Selection dialog box Display the Plot Type page and type an asterisk in the Time box Table 52 Average Scan Filter Selection dialog box parameters Parameter Description Scan Filter View a list of all scan filters in the time range If there is more than one scan type in the selected time range choose one scan type to average Library Search Graphics Table Properties Dialog Box Configure additional parameters that apply to the Library Search Graphics Table in the Library Search Graphics Table Properties dialog box Table 53 Library Search Graphics Table Properties dialog box parameters Parameter Description Max Of Hits To Specify the maximum number of matches from the library search to display in the Library Display Search Graphics table Display Column Labe
123. implicit Quan peak or ignore the implicit Quan peak and explicitly configure the chromatogram type Table 34 Use Container Supplied Quan Peak page parameters Parameter Description Implicit Quan Peak Options Use Quan Peak s Associated View the details of the internal standard associated with the implicit Quan peak Internal Standard Explicit Chromatogram Type Explicitly Specify Ignore the implicit Quan peak supplied by the container and explicitly configure the The Chromatogram s chromatogram type Behaviour Spectrum Properties Dialog Box Use the Spectrum Properties dialog box to configure the settings for your spectrum report object Spectrum Properties dialog box pages e Axis Page Enhance Page Labels Page Normalization Page Options Page e Peak Page Plot Type Page Style Page 142 XReport User Guide Thermo Scientific Axis Page D XReport Reference XReport Dialog Boxes Set spectrum axis labels and display options on the Axis page Table 35 Axis page parameters Parameter Description X axis Name View or change the name for the x axis Offset Move the axis label away from the spectrum Split Mass Range Split the spectrum into two or more separate graphs with equal ranges Divisions View the number of split range graphs for each spectrum Y axis Label From Detector Use the detector specific label for the y axis stored in the raw file Custom Use your
124. in o Filter Trace Tic m Autofilter coct_ e 2 Type in the offset of the start of a chromatogram trace in the Delay box This box is available only when you select a non MS detector type such as UV or PDA 3 From the Filter list select the processing applied to a subset of the scans in a raw file This option is available only when you select MS detectors The list displays scan filter options stored in the selected demo raw file If no demo file is selected type a valid filter string 4 From the Trace lists select the following a From the first list select a basic chromatogram type for example TIC b From the second list select a logical operator or Selecting an operator makes the third list active c From the third list select a second chromatogram type to add to or subtract from the first trace for example Mass Range The list features valid plot types 84 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Chromatogram Object The list of valid traces depends on the detector used to generate the data as follows Detection Valid traces MS Mass Range TIC and Base Peak Analog Analog 1 4 A D card A D Card Ch 1 4 PDA Wavelength Range Total Scan and Spectrum Maximum UV Channel A D 5 Depending on the type of chromatogram you select do the following a If you choose MS detector types specify the mass or ma
125. in a processing method 1 Open the Processing Setup window and set up a processing method For more information refer to the Xcalibur Data Acquisition and Processing User Guide 2 Choose View gt Reports The Reports view opens 3 To add one or more reports to either the sample or summary report tables do the following The sample table lists the reports to be produced for processed samples in a sequence The Summary table lists the reports to be produced for sequences or brackets a Click the Enable column to display a check box and select the check box to enable the report To create a sample table select the Std QC Unk and Other check boxes Select the output for the report in the Save As column Choose from None this prints the report but does not save it or txt doc html pdf rtf or xls select one of these options to save the report in the selected format The Xcalibur data system saves reports created from the processing method in the same directory as the source data files and names files The reports use this format data file name template name xxx where data file name is the name of the data file from which the report was generated template name is the name of the template used to generate the report xxx is the suffix for example doc or pdf indicating the file type When more than one report is generated from the same data file and template XReport adds a date stamp before the suffix
126. in the Sample Table Properties dialog box 1 To include standards QCs blanks or unknowns in the Sample table select the corresponding check boxes 2 Click OK 64 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Table Object Spectrum List Table Properties Thermo Scientific To set Spectrum List Table properties right click the table and choose Properties from the shortcut menu The Table Properties wizard opens After completing the wizard the Spectrum List Table Properties dialog box opens see Figure 41 Figure 41 Options page in the Spectrum List Table Properties dialog box Spectrum List Table Properties Options Pla type Enhancement Display Cancel Apply Help This dialog box has four pages Options Page Plot Type Page Enhancement Page Display Page Options Page To set parameters on the Options page 1 Select or clear the Use processing method properties check box see Figure 41 When you select this check box the application hides the parameters on the Plot Type and Enhancement pages 2 To use the ISTD peak when repeating on a component select the corresponding check box You must select the Use processing method properties for plot type check box to activate the ISTD peak option This option only applies when this object is used in a Quan repeating section It is not available when the Spectrum List Table is used in a Qual Repeatin
127. ing method pmd file to apply to the current report Raw Data File Select the raw raw file to apply to the current report Result File Select the result rst file to apply to the current report Sequence List File Select the sequence list sld file to apply to the current report Electronic Signature Properties Dialog Box Configure the order of information displayed in the Electronic Signature Table object in the Electronic Signature Properties dialog box Table 63 Electronic Signature Properties dialog box parameters Parameter Description Signature Information Order Created By First Display the Created By signature block first This block displays the electronic signature information for the person who created the report Signed By First Display the Signed By signature block first This block displays the electronic signature information for the people who signed the report 162 XReport User Guide Thermo Scientific Font Dialog Box D XReport Reference XReport Dialog Boxes Use the Font dialog box to select the global fonts for all objects in your report or customized fonts for the selected objects in the report This dialog box has three pages that are the same as in the individual Font Properties pages that you access when you configure an individual object Annotation see Font Page on page 158 Text see Font Page on page 158 Tables see Table Properties Wizard on page 147 Preferen
128. ipulate the layout and repeating properties of graphic and text objects Format the columns in the Column Properties Dialog Box Required data file none Section placement possible in all sections XReport User Guide 171 D XReport Reference Report Objects Page Break Table Objects 172 XReport User Guide Use the Page Break object to insert a manual page break in your report Required data file None Section placement Possible in Qual repeating Quan repeating and nonrepeating sections Table objects contain tabular information The columns of table objects can be added deleted and ordered You can also create custom columns The columns in the table fill with data when a report template is resolved with Xcalibur data These table objects are available in XReport Avalon Qual Events Table Avalon Quan Events Table Calibration File Table Component Cal Level Table Component QC Level Table Component Spectrum Table Dilution Factor Table Electronic Signature Table Ion Ratio Confirmation Results Table IRC Settings Table IRC Summary Table Library Search Graphics Table Library Search Results Table Processing Method Programs Table Processing Method Sample Reports Settings Table Processing Method Summary Reports Settings Table Qual Peak Table Quan Peak Table Qual Summary Table Quan Summary Table Sample Table Sequence Table Spectrum Candidate Results Table Spectrum List Table Thermo Scienti
129. ize method C Auto zero Intensity Range 0 0 100 0 a 80 r Normalize to C Largest peak in subsection Largest peak in range C Largest peak in scan 60 40 Relative Abundance 20 0 Normalize multiple scans Individually C Allthe same Thermo Scientific XReport User Guide 101 4 Configuring Objects and Sections Configuring a Spectrum 2 To define the peak that the spectrum is normalized to select one of the following options in the Normalize To area Largest peak in subsection Normalize each split mass range to the largest peak in the division Largest peak in mass range Normalize the spectrum to the largest peak in the displayed mass range Largest peak in scan Normalize the spectrum to the largest peak in the entire spectrum 3 To define how multiple scans are normalized select one of the following options in the Normalize multiple scans area Individually Normalize each mass plot individually All the same Normalize all mass plots equally Specify a Peak To explicitly specify the peak to display in the Spectrum report object use the Peak Page To specify a peak 1 To specify a specific type of peak to appear in the spectrum select the Enable explicit peak type check box see Figure 75 Figure 75 Peak page Spectrum Properties Options Plot type Enhance Style Labels Axis Normalization Peak It is possible to explicitly specify the peak that should ap
130. k Area Peak Height BL S N Area Peak Width Saturated User Column 1 to 5 Thermo Scientific Quan Peak Table Thermo Scientific D XReport Reference Report Objects The Quan Peak table displays information specific to component peaks detected by quantitative analysis for a single sample Note To display component peak information for all samples in a sequence use the Quan Summary Table object Required data file pmd rst Section placement Nonrepeating section The Quan Peak table has the following possible fields Component Name RT Calculated Amount Response BL Diff Area Area Area Ratio Calibration Flags Component Found Component Type Data Flags Expected RT Height Height Ratio Ion Ratio Status ISTD Area ISTD Height ISTD Name ISTD Response Keys Peak Purity Peak Status Response Ratio S N Sample Type Saturated Specified Amount System Suitability Units Width User Columns 1 to 5 XReport User Guide 183 D XReport Reference Report Objects Qual Summary Table 184 XReport User Guide The Qual Summary table displays information specific to chromatogram peaks detected by qualitative analysis for all samples in a sequence Note To display peak information for a single sample only use the Qual Peak Table object Required data file sld rst Section placement Nonrepeating section The Qual Summary table has the following possible fields RT
131. k When Repeating On Component Thermo Scientific Use the selected ISTD internal standard peak when repeating on a component Select the Use Processing Method Properties For Plot Type and Enhance Info option to modify this parameter XReport User Guide 145 D XReport Reference XReport Dialog Boxes Peak Page Set parameters on the Peak page to explicitly specify the peak to display in the spectrum report object Table 40 Peak page parameters Parameter Description You can explicitly specify the peak that you want to appear in a spectrum control Enable Explicit Peak Type Activate controls so you can specify the type of peak to appear in the spectrum Peak Type Quan Peak Specify a Quan peak Qual Peak Specify a Qual peak Peak Identification Component Name Define the name of the Quan peak or the retention time of the Qual peak If you are entering a Qual peak you can type any time between the start time and end time of the peak Plot Type Page Configure how the spectrum is drawn on the Plot Type page Note The parameters in the Plot Type page are enabled only when you clear the Use Processing Method Properties For Plot Type And Enhancement Info check box on the Options Page Table 41 Plot Type page parameters Sheet 1 of 2 Parameter Description Mass Range or Specify the mass or mass range for MS detector types For PDA detector types use this box Wavelength Range to specify the wavelength or
132. l select the Custom Text Label check box in the active Custom Peak Labels area Type a custom label for the Qual peak in the box 90 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Chromatogram Object 3 To label the Qual peak with the retention time select the Retention Time check box When you turn on this check box the Labels page shows the change when you return to it 4 In the RT Labeling area select the type of unit for the retention time from the Units list 5 Select the number of decimal places to be displayed in the retention time label from the Decimals list 6 Click OK to save the changes and close the Advanced Qual Peak Annotation Options dialog box Select How the Chromatogram Axes Will Be Configured Page Use the Axes page to set chromatogram axes label and display options To specify the appearance for chromatogram axes 1 To set the name of the x axis in the X Axis area type it in the Name box see Figure 64 Figure 64 Select How the Chromatogram Axes Will Be Configured page Select How The Chromatogram Axes Will Be Configured It is possible to configure how the axes are labeled and whether they are offset It is also possible to split the X axis into several divisions and the units on the Y axis can be made absolute or relative A Axis New Offset RT 4 23 5 71 SM 16 z NL RT 4 90 Time min E 100 2 14E5 TICF MS Split time range 2 80 drugs_01
133. le based chromatogram Quan results based chromatogram Qual results based chromatogram Figure 50 Select Chromatogram Type page Select Chromatogram Type chromatogram control can be used to display raw data explicitly or processed raw data in the form of a results file When results are being displayed these results can be specifically Quan or Qual results r Chromatogram Type Select the type of chromatogram control you want to add to the report template C Raw file based chromatogram C Quan results based chromatogram Qual results based chromatogram Show all Qual peaks in result file lt Back Cancel Help 2 Ifyou select a Qual results based chromatogram in step 1 select the Show all Qual peaks in result file check box to display all Qual peaks in a resolved Xcalibur report This is a Peak Type setting 3 Click Next to go to the next page of the wizard Thermo Scientific XReport User Guide 75 4 Configuring Objects and Sections Configuring a Chromatogram Object Select Demo File Page Use the Select Demo File page to associate a demonstration file raw or rst file with a chromatogram report object A demo file shows how the chromatogram report object appears in the report template and in wizard page previews with its current settings when applied to real Xcalibur data The appearance of the Select Demo File page depends on the chromatogram type and the peak type settings chosen in the Chromatogra
134. licit Quan peak and explicitly configure the chromatogram type To explicitly configure a Quan based chromatogram type 1 To display the details of the internal standard associated with the implicit Quan peak select the Use Quan peak s associated Internal Standard check box in the Implicit Quan peak options area see Figure 48 Figure 48 Use Container Supplied Quan Peak page Use Container Supplied Quan Peak When a chromatogram control is in a section that automatically supports a Quan peak e g Quan Repeating Section then the default behaviour is to implicitly display the section specific peak when generating a report Implicit Quan peak options lt is possible to display the details of the Internal Standard associated with the implicit Quan peak Use Quan peak s associated Internal Standard Explicit chromatogram type The implicit Quan peak supplied by the container can be ignored and the chromatogram type explicitly configured Explicitly specify the chromatogram s behaviour Cancel Help 2 To ignore the implicit Quan peak supplied by the container and explicitly configure the chromatogram type select the Explicitly specify the chromatogram s behaviour check box in the Explicit chromatogram type area 3 Click Next to go to the next page of the wizard Thermo Scientific XReport User Guide 73 4 Configuring Objects and Sections Configuring a Chromatogram Object Use Container Supplied Qual Peak P
135. line regions Click OK XReport User Guide 67 4 Configuring Objects and Sections Configuring a Table Object 68 XReport User Guide Display Page To set parameters on the Display page To display all peaks in the spectrum select the All Peaks check box or to limit the display to the strongest peaks type a value in the Top box see Figure 44 Figure 44 Display page in the Spectrum List Table Properties dialog box Spectrum List Table Properties Options Plot type Enhancement Display m Normalization Allpeaks Top o Intensity range 0 01 00 0 Order by Mass C Intensity To order the data by mass or by intensity select the appropriate option in the Order by area Type a value representing the relative abundance range of mass peaks to include in the table in the Normalization area Click OK Thermo Scientific 4 Configuring Objects and Sections Configuring a Table Object Electronic Signature Table Properties Use the Electronic Signature table object to specify whether the Created By signature block appears before or after the Signed By signature block To configure the Electronic Signature table object 1 Right click the Electronic Signature table object and choose Properties from the shortcut menu The Electronic Signature Properties dialog box opens see Figure 45 Figure 45 Electronic Signature Properties dialog box Electronic Signature Properties Data
136. ll m Other requirements All Features Print Comment C All applications saTeSaw Print Reports This application Queue Manager Subtract Background s Xcalibur Configuration v Cancel History Log Print Export Import Help C Supervisor Password 7 Click OK to save the settings and close the Authorization Manager dialog box 42 XReport User Guide Thermo Scientific 3 Generating a Report Creating a Report from the Xcalibur Data System Generating Signed Reports Thermo Scientific Once you have a template containing an Electronic Signatures object generate the report as described in Generating Reports when Batch Processing a Sequence on page 35 or in Generating a Report From Quan Browser on page 37 The Xcalibur data system prompts you to type signature information when the report is generated Each user whose signature is required must type their log on name and password to sign the report Figure 19 displays an example of a signature dialog box Figure 19 Example of a signature dialog box Xcal users 1 of 1 Sequence Operations Batch Reprocess x Name Enter password Cancel Help XReport User Guide 43 Configuring Objects and Sections You can configure the following objects and sections in XReport When you configure an object you can change or edit only the individual properties of that specific object When you add anoth
137. ls Display labels at the top of the columns in the table Show Peak Spectrum Display the peak spectrum in the table This check box is available only when you have selected to include the Hit Spectrum column in the Table Properties dialog box Thermo Scientific XReport User Guide 155 D XReport Reference XReport Dialog Boxes Library Search Results Table Properties Dialog Box Configure an additional parameter that applies to the Library Search Results Table in the Library Search Results Table Properties dialog box Table 54 Library Search Results Table Properties dialog box parameters Parameter Description General Max Of Hits To Specify the maximum number of matches from the library search to display in the Library Display Search Results table Sample Table Properties Dialog Box Configure additional settings that apply to a Sample table in the Sample Table Properties dialog box Table 55 Sample Table Properties dialog box parameters Parameter Description Include Standards Include data from standards in the Sample table Include QCs Include data from QCs in the Sample table Include Blanks Include data from blank samples in the Sample table Include Unknowns Include data from unknown samples in the Sample table Text Object Properties Dialog Box Use the Text Object Properties dialog box to configure the settings of the currently selected text object This dialog box has the following pages Data Page Attrib
138. lumns Using Page Breaks To add a page break to the template drag the Page Break object from the Objects pane to the Template pane After adding a page break to the template drag the page break to reposition it If you do not manually insert page breaks objects automatically shift to a new page when there is not enough room on the current page To preview where these automatic breaks occur choose Layout gt Preferences The Preferences dialog box opens Figure 6 Select the Show Page End check box Thermo Scientific XReport User Guide 21 2 Creating a Template Adding and Configuring Report Objects Configuring Objects To configure an object 1 Right click the object 2 Choose Properties from the shortcut menu The Properties dialog box opens For information about configuring each of the specific objects see Chapter 4 For a description of each object including which sections each object can be used in see Appendix B Types of Report Objects Adding User Text to a Text Object To add additional customized text headings to text objects use the lt Blank Line gt and lt User Text gt Data Items These items are available for all text objects except the Annotation object and the Instrument Method object To add custom text to a text object 1 Right click the text object and choose Properties from the shortcut menu The Data Page opens 2 Select User Text in the Available Items list 3 To add a text ite
139. m Type page of the wizard Raw File Based Chromatogram Quan Result Based Chromatogram e Qual Result Based Chromatogram Explicit Peak e Qual Result Based Chromatogram All Available Peaks Raw File Based Chromatogram When configuring a chromatogram report object based on a raw file use this procedure to select a file To select a demo file for a raw file based Chromatogram 1 To associate a demo file with the chromatogram report object select the Use demo file check box see Figure 51 Figure 51 Select a raw file based chromatogram Select Demo File 4 demo file can be associated with a chromatogram control This demo file allows the control to show how the current settings for the chromatogram will look when applied to real data v Use demo file Demo File c VcaliburvexamplessdataNdrugs T1 raw gl HET 2 To search for the required demo file raw file click the browse button in the Demo File area The Select Raw Data File dialog box opens 3 Select a demo file and click Open 4 Click Next to go to the next page of the wizard 76 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Chromatogram Object Quan Result Based Chromatogram When configuring a chromatogram report object based on Quan results use this procedure to select a file To select a demo file for a Quan based chromatogram 1 To associate a demo file with the chromatogram report object
140. m provides several sample XReport templates for you to use when creating your own reports This appendix provides details of these report templates stored at the following location Xcalibur templates Table 2 Sample XReport template files Sheet 1 of 2 Report template file name Data source files Description Use CalibrationFile xrt raw xcal Generates sample reports with calibration data CompCalReport xrt rst raw pmd sld Generates summary reports showing processing method details calibration curve and sample table Quan results Can be used from Batch Processing and Quan Browser in the CompCalReport_ICIS xrt Xcalibur data system CompCalReport_Avalon xrt CompCalReport_Genesis xrt CustLibrSearRept xrt Ist raw Generates Qual sample reports that display Qual peaks and library search LibrarySearchReport xrt details Use from Batch Processing in the Xcalibur data system IonRatioConfirmation xrt rst raw pmd Generates a Quan sample report containing non graphical ion ratio confirmation results IonRatioConfirmationGraphicalxrt rst raw pmd Generates Quan sample reports containing graphical ion ratio IonRatioConfirmationGraphical confirmation results These report Simple xrt templates take advantage of the f explicit confirmation ion settings IonRatioConfirmationGraphical P 5 Stacked xrt available when using the XReport Chromatogram wizard PeakIntegration xrt rst raw pmd
141. m to the Selected list click Add 4 To position the User Text item where you want your text displayed click Move Up or Move Down 5 Select the User Text item 6 Type the text to display in the box below the Selected list and press Apply The Xcalibur data system displays the text you entered in the Selected list To edit a User Text item 1 Select the item to edit in the Selected list 2 Edit your text in the User box 3 Press Apply 22 XReport User Guide Thermo Scientific 2 Creating a Template Adding and Configuring Report Objects Adding a Formula to a Table You can create custom formulas in XReport to perform mathematical operations on table data and display the result in a table column To add a formula to a table 1 In your XReport template right click a table object and choose Properties The Select Table Fields Page opens 2 Select one of the User Columns fields in the Available Columns list User Column 1 User Column 2 User Column 3 User Column 4 or User Column 5 For the five User Column fields available you can create up to five separate formulas for a single table Qo Click Next to go to the Configure User Column Parameters Page A Type a title for this column in the User Column Title box 5 Click Edit Formula The Edit Formula For Dialog Box opens 6 Enter a formula in the Formula box Formulas can be entered in one of several ways Type formulas directly in
142. mber of search results to display in the table in the Max of hits to display box 2 To display column labels select the Display Column Labels check box 3 To show the peak spectrum select the Show Peak Spectrum check box 4 Click OK 5 Choose File Save to save any changes made XReport User Guide 63 4 Configuring Objects and Sections Configuring a Table Object Library Search Results Table Properties To set Library Search Results Table properties right click the table and choose Properties from the shortcut menu The Table Properties wizard opens When you complete the wizard the Library Search Results Table Properties dialog box opens see Figure 39 Figure 39 library Search Results Table Properties dialog box General Max of hits to display itN To set the parameters in the Library Search Results Table Properties dialog box 1 Type the total number of search results to display in the table in the Max of hits to display box 2 Click OK Sample Table Properties To set Sample Table properties right click the table and choose Properties from the shortcut menu The Table Properties wizard opens After completing the wizard the Sample Table Properties dialog box opens see Figure 40 Figure 40 Sample Table Properties dialog box Sample Table Quan Results Properties General Iv Include Standards Iv Include OCs v Include Blanks Iv Include Unknowns itN To set parameters
143. meter Autosampler Yes Run Rows 1 4 Priority Sequence Iv Start When Ready Change Instruments Processing Actions Instrument Method Start Up Browse Quan Qual Shut Down Browse Programs Programs Pre Acquisition Browse r u Post Acquisition Browse Run Synchronously v Pre Acquisition v Post Acquisition V Reports After Sequence Set System On C Standby C Off Cancel Help Thermo Scientific 3 Generating a Report Creating a Report from the Xcalibur Data System 6 Select the Reports check box in the Processing Actions area 7 Set all of the other parameters 8 Click OK The data system submits the selected sample or samples to the acquisition queue Generating Reports when Batch Processing a Sequence Thermo Scientific To generate reports when batch processing a sequence Set report parameters in the processing method as described in Setting Report Options in a Processing Method on page 33 In the Xcalibur Sequence Setup window open the sequence that you want to batch reprocess Enter the processing method that includes all of the report options in the Proc Meth column Select the rows that you want to process Choose Actions Batch Reprocess The Batch Reprocess Setup dialog box opens see Figure 14 The Process Rows box lists the selected sequence rows XReport User Guide 35 3 Generating a Report Creating a Report fr
144. mn heading text in the Column Header box To arrange the order of the selected columns in the Selected Columns list click Move Up or Move Down Click Next to go to the next page of the wizard Thermo Scientific 4 Configuring Objects and Sections Configuring a Table Object Configuring Custom User Columns The Configure User Column Parameters page of the Table wizard appears only if you chose to include custom User Columns in the table Use this page to define parameters for each User Column in the table see Figure 33 You can use the User Columns to define mathematical formulas for calculating table data Formulas obey the following syntax rules The formula must begin with an equals sign Each table column is represented by an alphabetic letter identifier A B C and so on that appears beneath the column title in the Table object The mathematical expressions are kept simple for instance type A B A B A B or A B This is true as well for any of the functions listed in the Functions list of the Edit Formula dialog box Formulas are computed on a row by row basis That is if you type A B as a formula in a User Column the results are computed as follows a The Xcalibur data system adds the value in the first row of column A to the value in the first row of column B and displays the result in the first row of the User Column b The data system adds the value in the second row of column A to the value in
145. mplate XReport adds a date stamp before the suffix Thermo Scientific XReport User Guide 39 3 Generating a Report Creating a Report from the Xcalibur Data System Creating a Signed Report When generating reports from Quan Browser or by batch processing in Sequence Setup you can create signed reports containing electronic signatures t bd 1 3 To create a signed report Create a report template containing the Electronic Signature table object or choose one of the preconfigured templates supplied with XReport All of the preconfigured templates contain the Electronic Signature table object in the footer Confirm that the Xcalibur Authorization Manager settings are set to require electronic signatures at the report generating step See Configuring Authorization Manager Settings for Signed Reports for that process Generate the report Configuring Authorization Manager Settings for Signed Reports 40 XReport User Guide To produce signed reports with electronic signatures configure the Xcalibur Authorization Manager Settings to require signatures The Xcalibur data system administrators must perform this configuration before setting permissions in either Quan Browser or Sequence Setup itN kod I To set permissions for producing signed reports from Sequence Setup Choose Start gt All Programs gt Thermo Foundation x x gt Authorization Manager The Authorization Manager window opens see Figure 17
146. mponent E Select the Qual Peak e e Select Mass Spectrum Quan Traces to Display e s Configure How the Peak Window Will Look e e e Select Plot Details Select Enhance Details e Select Chromatogram Style e Select the Peak Labeling e E e e Select How the Chromatogram Axis Will Be Configured E e Configure Normalization for the Chromatogram e This page is not displayed if you selected Explicitly Specify the Chromatogram s Behavior on the Use Container Supplied Quan or Qual peak page This page is only displayed if you selected Explicitly Specify the Chromatogram s Behavior on the Use Container Supplied Quan or Qual peak page Note When you click the All Qual Peaks option for a Qual Result Based Chromatogram the wizard page order is the same as for the Qual Result Based Chromatogram Type without the Select Qual Peak page When the chromatogram report object to be configured is contained in a Quan or Qual repeating section the default Chromatogram Type is Quan or Qual Result Based with no explicit Peak Type set The next page of the wizard Use Container Supplied Quan or Qual asks you to confirm this 72 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Chromatogram Object Use Container Supplied Quan Peak Page Use the Use Container Supplied Quan Peak page to display the details of the internal standard associated with the implicit Quan peak or ignore the imp
147. mpound Structure Qual repeating Lib Search Results Table Ist TaW Displays the results of a Library Search on a Qual peak for example Name Probability RSI SI CAS Area Qual repeating Proc Method Programs Table pmd Displays a list of programs to be run by the Xcalibur data system after the sample has been analyzed and the data has been processed The data system runs the programs in the order listed Nonrepeating Proc Method Sample Reports Table Displays Sample Report information for each sample in a sequence including Template name and the Report file name Specify Sample Type in the processing method Nonrepeating 112 XReport User Guide Thermo Scientific Table 4 Table objects Sheet 3 of 3 B Types of Report Objects Table Object Descriptions Table object Data source file Description Section placement Proc Method Summary Reports pmd Displays Summary Reports to be issued Nonrepeating Table after processing the samples in a bracketed or non bracketed sequence Qual Peak Table Ist Displays information specific to Nonrepeating chromatogram peaks detected by qualitative analysis for a single sample Qual Summary Table sld rst Displays information specific to Nonrepeating chromatogram peaks detected by qualitative analysis for all samples in a sequence Quan Peak Table st pmd Displays information specific to Nonrepeating component peaks detected by q
148. n This object displays instrument method information for all the instruments associated with a raw file This object uses the default data attribute and font settings from Qual Browser and has no configurable properties Thermo Scientific Processing Method General Table 70 Processing Method General object fields headings D XReport Reference Report Objects The Processing Method General object displays general processing method parameters Required data file pmd Section placement Nonrepeating section For this object s possible fields and headings see Table 70 Identification Baseline Options Other Created By When Created Last Modification Modified By Summary Void Time Baseline and Noise Window Baseline Noise Tolerance Min Number of Scans in Baseline Processing Method Qual Thermo Scientific Chromatography By Calibration By Blank Line and User Text Data Items The Processing Method Qual object displays Qual processing method parameters Required data file pmd Section placement Nonrepeating section For this object s possible fields and headings see Table 71 XReport User Guide 193 D XReport Reference Report Objects Table 71 Processing Method Qual object fields headings Identification Detector Type Detector Delay Filter e Ist Trace Type Operator 2nd Trace Type
149. n objects 55 bitmap objects 70 chromatograms 71 Component Calibration Curve objects 93 repeating sections 17 spectra 95 table objects 57 text attributes 53 XReport Objects 9 creating reports from Xcalibur 32 reports within XReport 29 templates 13 custom columns configuring 59 text fields adding 51 text fields editing 52 Data Source Browser 10 data source files 8 Data Sources dialog box selecting data sources 30 Data Sources dialog box reference 162 default data set 26 deleting objects 18 sections 16 Dilution Factor table 176 204 XReport User Guide E Edit Formula For dialog box configuring custom columns 60 parameters 150 electronic signatures creating a report with 40 table object 176 exiting XReport 14 F Font dialog box 54 62 fonts settings 24 54 table 62 footer sections 4 formatting objects 8 G generating reports using a report template 14 when running a sample or sequence 34 graphic objects 7 grid report template 20 H header sections 4 instrument method 192 Ion Ratio Confirmation Result table 177 IRC Settings table 177 IRC Summary table 178 L Layout menu 125 Library Search Graphic Table Properties dialog box parameters 155 setting properties 64 Library Search Graphics table 178 Library Search Results table 179 Library Search Results Table Properties dialog box parameters 156 setting properties 64 locking a template 27 nonrepeating sections 5 166 Thermo Scie
150. n repeated for all Quan peaks or components A Quan repeating section can have the following objects Formatting Objects Page Break Columns Graphic Objects Electronic Signature Table Bitmap e Chromatogram Component Cal Curve Spectrum Table Objects Avalon Quan Events Table Component Cal Level Table RC Settings Table Thermo Scientific XReport User Guide 169 D XReport Reference Report Objects Report Objects Component QC Level Table Component Spectrum Table IRC Settings Table Spectrum List Table Sample Table Text Objects Annotation Component IdentDetectCal Settings Component ISTD Settings Summary Component Settings Summary Component Sys Suit Flags Settings Quan ISTD Peak Summary Quan Peak Summary Report objects are predefined chunks of data that you can drag to the XReport template from the Objects pane When you combine a report template with Xcalibur data data source files XReport replaces the report objects in the template with data to generate an Xcalibur report Report objects include the following Graphic and Formatting Objects Table Objects Text Objects Graphic and Formatting Objects 170 XReport User Guide Graphic objects display graphics Graphic objects can be configured and customized The graphic object is replaced with a graphic when a report template is resolved with Xcalibur data Formatting objects help to configure the layout of the report The followin
151. nd bottom of each page in your report for example the report date page number and a company logo A Report Header or Footer section can have these objects Formatting Objects Columns Graphic Objects Bitmap Electronic Signature Table Table Objects Text Objects Annotation Report Info Sample Header Repeating Sections A repeating section is a section of a report template that is automatically repeated for every component or peak in a resolved document You can change the properties of a repeating section to customize its behavior XReport can have two types of repeating sections Qual Repeating Section Quan Repeating Section Qual Repeating Section A Qual Repeating section displays details relating to a single Qual peak within some data This section is then repeated for all Qual peaks found A Qual Repeating section can have these objects Formatting Objects Page Break Columns 168 XReport User Guide Thermo Scientific D XReport Reference Report Sections Graphic Objects Electronic Signature Table Bitmap e Chromatogram e Spectrum Table Objects Library Search Graphics Table Library Search Results Table Spectrum List Table Text Objects Annotation Quan Repeating Section A Quan repeating section is also called a Component section Its purpose is to display details relating to a single Quan peak in some data or a component configured in a processing method This section is the
152. ng Section t To configure a Qual or Quan repeating section 1 Scroll to where you can see the QL or QN icon at the top left side of a section in the Template pane 2 Right click the icon and choose Properties from the shortcut menu The Repeating Section Properties dialog box opens see Figure 5 Figure 5 Repeating Section Properties dialog box Repeating Section Properties Exclude Ordering Page Breaks The Repeating Section type is m Repeating Section Excludes When processing Quan Exclude Component Type configurations or results it is possible to exclude specific None v elements from the process It is also possible to discard any Show only found components components that haven t been found 3 Set the parameters and dick OK Thermo Scientific XReport User Guide 17 2 Creating a Template Adding and Configuring Report Objects Adding and Configuring Report Objects After adding and configuring sections select the report objects you want to include in a specified section of the report template Select from these options text objects table objects graphic objects and text depending on the selections you made in Configuring a Qual or Quan Repeating Section XReport displays the objects that are available for the currently selected section in the Objects pane lower left The contents of this pane change when you select different sections To add and configure report objects follow t
153. ng order Buttons Add Add the selected column to the next available sort order Remove Remove the last selected sort order Thermo Scientific XReport User Guide 149 D XReport Reference XReport Dialog Boxes Set Table Font Page Configure the formatting of the currently selected table object on the Font page Table 46 Set Table Font page parameters Parameter Description Title Font Set and view the font settings for all of the title headings and cells in the table object To Heading Font configure your font click the button The Font Dialog Box opens Cell Font Edit Formula For Dialog Box Edit a formula for use in a custom column of your table in the Edit Formula For dialog box For more information on formula syntax see Adding a Formula to a Table on page 23 Table 47 Edit Formula For dialog box parameters Sheet 1 of 2 Parameter Description Formula View the current formula Type in this box directly or add functions from the list Functions A list of available functions A brief description of each of the functions appears at the bottom of the dialog box when each function is selected Function Syntax Description ABS ABS x Return the positive value of a number of a formula regardless of its actual positive or negative value AND AND x y Return the value 1 if the logical expressions x and y are both true or the value 0 if either expression is false AVERAGE AVERAGE x1 Return the average of
154. ntific 0 objects XReport adding 18 aligning 19 annotation 55 centering 20 configuring 22 configuring bitmap 70 deleting 18 formatting 8 graphic 7 repositioning 18 resizing 18 table 7 57 111 text 6 109 text objects 189 types of objects 5 P page breaks 21 172 page layout 25 Page Setup dialog box 25 Preferences dialog box reference 163 Preview window 26 31 164 previewing a template 25 processing methods fields 193 general 193 Programs table 180 Qual 193 Sample Reports Settings table 181 sample table 181 Summary reports settings table 181 summary table 181 Q Qual Peak table 182 Qual repeating section 168 Qual Summary table 184 Quan Browser window Reports dialog box 37 Quan Browser generating a report from 37 Quan ISTD Peak summary 195 Quan Peak summary 195 Quan Peak table 183 Quan repeating section 169 Quan Summary table 185 reordering sections 16 repeating objects in columns 104 Thermo Scientific Index 0 Repeating Section Configuration dialog box 9 Repeating Section Properties dialog box configuring a repeating section 17 Exclude page 46 Ordering page 47 Page Breaks page 48 repeating sections 5 report info 196 report objects 189 report template grid 20 Report Template Outline pane 3 report templates 200 reports adding to processing methods 33 creating from Xcalibur 32 creating within XReport 29 generating 14 generating from Quan Browser 37 generating from Sequence Set
155. o 45 degrees c To add a backdrop to 3D plots select the Draw Backdrop check box 4 Click Next to go to the next page of the wizard Thermo Scientific XReport User Guide 87 4 Configuring Objects and Sections Configuring a Chromatogram Object Select the Peak Labeling Page Basic Options XReport User Guide Use the Select The Peak Labeling page to choose the type and style of peak labels From this page click Advanced to open a dialog box to set advanced labeling options Basic Options Advanced Options Quan Advanced Options Qual To select peak labeling options To label peaks with the time in minutes in the chromatogram plot select the Retention Time check box in the Label With area see Figure 61 The data system displays RT before the label Figure 61 Select the Peak Labeling page Select The Peak Labeling Configure peak labels and the style of these labels Advanced Label With RT 4 23 5 71 SM 16 MV Retention Time Flags RT 4 90 Scan Number Area d BasePeak Height drugs 01 Signalto Noise Label Styles Offset Size X Rotated Boxed a o c m r E a Ed v m a a 5 Label Threshold zz 0 Time min coc eo To label peaks with the number of mass scans at peak maximum select the Scan Number check box The data system displays S before the label To label the base peak in the mass spectrum of the chromatogram peak
156. o customize the following settings for your table Which columns to include in the table Custom table column settings Table sort order The Table Properties wizard has these pages Configure User Column Parameters Page Select Table Fields Page Set Table Sort Filter Page Set Table Font Page Thermo Scientific XReport User Guide 147 D XReport Reference XReport Dialog Boxes Configure User Column Parameters Page Configure any custom User columns that you selected to include in your table on the Configure User Column Parameters page Complete the parameters on this page for each custom column that you selected Table 43 Configure User Column Parameters page parameters Parameter Description User Columns Define the custom columns to include in your table Select the column to customize User Column Title User Column Title Provide a descriptive title for the column User Column Formula User Column Formula View the formula for the current column read only box To edit the formula click Edit Formula Edit Formula Change your formula Select Table Fields Page Choose the columns for the table on the Select Table Fields page The columns available for a table are given in alphabetical order but can be added to a report template in any order The columns that you can select depend on the type of table object that you are configuring Table 44 Select Table Fields page parameters Sheet 1 of 2
157. o the Signatures Reqd list The members of this group are required to type their log on names and passwords to electronically sign the report when it is generated Repeat this step for each group that you want to add to the Signatures Reqd list Note If you do not have any groups available or if the groups do not contain the correct members refer to the Foundation Administrator Guide for information on how to create and modify groups 6 To require a signature from the current user when the report is generated select the Current User Must Sign check box At this point the settings should be similar to the settings in Figure 18 Figure 18 Quan Browser settings for producing signed reports Authorization Manager r Available Groups 1 m Secure Groups r Global Security Features C Domain workstation Private Create Delete IV Predefined Comments Edit m Permission Level 4 r Signature List Groups CRC Validator Disallowed Available groups Signatures req d Home Page cal users Instrument Setup Signature List Library Manager Processing Setup Qual Browser C Password Required 0 Quan Browser m Run Application C Allowed m Dataset Selection s Export Disallowed State 31 5 1 Move Group m Export Data To Excel i i s View All Samples IS I s Options 2 ss Uown m Results Grid Grayed aT File amp Save A
158. ol rege e ica 200 I er Em 203 Thermo Scientific Preface Thermo XReport is the custom reports application for the Thermo Xcalibur mass spectrometry data system Use XReport to create custom reports Contents Related Documentation Safety and Special Notices Contacting Us To provide us with comments about this document please click the link below Thank you in advance for your help SURVEY Related Documentation Thermo Scientific Thermo Fisher Scientific provides these documents for the Xcalibur data system Xcalibur Quantitative Analysis Getting Started Guide Xcalibur Data Acquisition and Processing User Guide Xcalibur Quan Browser User Guide Xcalibur Qual Browser User Guide Xcalibur Library Browser User Guide XReport User Guide Help from within the software XReport User Guide vii Preface Safety and Special Notices Make 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 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 viii XReport User Guide Thermo Scientific Preface Contacting Us
159. om the Quan Traces list see Figure 56 Thermo Scientific XReport User Guide 81 4 Configuring Objects and Sections Configuring a Chromatogram Object Figure 56 Select Mass Spectrum Quan Traces To Display page Select Mass Spectrum Quan Traces To Display The Quan traces properties allow confirmation ion traces in Mass Spectrum data to be plotted This section is only applicable to MS data and will be ignored for any other detector types When a Quan component is being displayed in a chromatogram control there are potentially six traces associated with that component the Quan mass QM trace and up to five confirmation ion traces lt is possible to select any of these six traces to be displayed in the control or alternatively all of the component s available traces can be displayed r Quan Traces Quan Mass QM Trace v Iz HET 2 Select All Quan Traces from the list 3 To normalize all the traces the same way select the Common normalization for all traces check box 4 Click Next to go to the next page of the wizard Configure How the Peak Window Will Look Page Use the Configure How the Peak Window Will Look page to control the display of the baselines Quan and Qual peaks and the peak window width active for Qual peak and Quan peak in some cases when a peak from a result file is set to display in a Chromatogram To configure the Peak window 1 Select the Show Baselines check box to display the bas
160. om the Xcalibur Data System Figure 14 Batch Reprocess Setup dialog box Batch Reprocess Setup Processing Actions Quan Process Rows r7 v Reports IV Print Sample Reports Print Summary Reports MV Programs Create Quan Summary Spreadsheet Advanced ptions r Cancel Help 6 If necessary change the rows to be processed by entering the first and last row to be processed in the Process Rows box The format is either zRow for one sample or First Row Last Row for multiple samples 7 Select Quan or Qual processing actions and select from active options 8 Select from these XReport processing options To create reports while batch processing select the Reports check box To print reports for the samples displayed in the Process Rows box select the Print Sample Reports option You defined the Sample report parameters in the Reports view of the Processing Setup window Select the Print Summary Reports option to print reports for the samples that are displayed in the Process Rows box You defined the summary report parameters in the Reports view of the Processing Setup window Select programs spreadsheet and advanced options 9 Click OK The data system initiates batch processing of the selected samples 36 XReport User Guide Thermo Scientific 3 Generating a Report Creating a Report from the Xcalibur Data System Generating a Report From Quan Browser To generate a report from the Quan B
161. on ao Time Time Reference No 2 Reference Yes i Genesis 20 Genesis 20 Minimum Peak i6 Minimum Peak 40 Height S N 3 00 Height S N 3 00 Genesis a rs Genesis 1s 20 Smoothing Time min Smoothing Time min Points 7 Points 7 S eie Type MS Detector Type MS Valley Valley Detection Detection Enabled No Enabled No Genesis Genesis Constrain Peak Constrain Peak Width Enabled No Width Enabled No Component Name hydrocortisone Actual RT min 0 67783 Calculated Amount 4 95592 Response 1892942 72621 Base Line BB Signal To Noise 707 56 Diff 0 88 Area Ratio 2 763 Area cts sec 1892942 72621 Specified Amount 5 00000 Thermo Scientific XReport User Guide 117 C Sample Report Peak Integration Report Page 3 Peak Integration Report Page 3 deoxycorticosterone Expected Retention Time min 1 4 90 Retention 80 Time Window sec View Width min Retention Time Reference No 30 Genesis 20 Minimum Peak Height S N 3 00 Genesis o Smoothing Points 7 Detector Type MS Valley Detection Enabled Genesis Constrain Peak Width Enabled No x i 30 00000 8 8 1 00000 Relative Abundance No 1 0 Component Name deoxycorticosterone Response 1040530 60245 9 oDiff 2 17 Specified Amount 5 00000 118 XReport User Guide RT 0 90 1 90 SM 7G 121 12 Peak Integration Report RT 1 40 14 Time min Base Line Area Ratio 16 Actual RT min
162. ormalization page 101 Options page 95 Plot Type page 96 Style page 98 starting XReport 11 summary reports 32 T table columns choosing 58 Table Configuration wizard 9 table objects 7 table properties library search graphics 63 library search results 64 sample table 64 spectrum list 65 Table Properties dialog box Configure User Column Parameters page 59 Set Table Sort Filter page 61 206 XReport User Guide Table Properties wizard Configure User Column Parameters page 148 Font page 150 reference 147 Select Table Fields page configuring a table object 57 parameter descriptions 148 Set Table Sort Filter page 149 table properties setting 63 table sort order specifying 61 Template Configuration dialog box 165 templates choosing data sources 29 creating 13 15 definition 3 locking 27 overview 3 prebuilt 10 previewing 25 saving 25 text attributes configuring 53 text fields adding custom 51 configuring 50 Text Object Properties dialog box adding custom text fields 51 Attributes page 158 Data page 49 157 Font page 54 158 reference 156 text objects 6 U user columns configuring 59 user text adding 198 X XReport Spectrum Control Properties 95 XReport window features 2 new template 12 Report Template Outline pane 3 Thermo Scientific
163. pear in a Spectrum control Enable explicit peak type Cancel spply Help 102 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring Columns 2 To specify the peak type to appear in the Spectrum select the Quan Peak option to specify a Quan peak or select the Qual Peak option to specify a Qual peak 3 For a Quan peak type a name for the component in the Peak Identification area For a Qual peak type the retention time any time between the start time and end time of the peak or click the browse button The Select a Peak dialog box opens Select a peak and click OK to close the dialog box Configuring Columns Thermo Scientific To configure a column object right click it and choose Properties from the shortcut menu The Column Properties Dialog Box opens After you have configured a column object drag objects to the columns To configure a column object 1 Select the number of columns to use in the Number of columns area see Figure 76 Figure 76 Column Properties dialog box Column Properties Number of columns 2 C 3 Repeat type Sample repeat C Summary repeat Cancel Help 2 If the column object is in a nonrepeating section configure the Repeat type The Repeat type options are not available in Quan repeating or Qual repeating sections In the Repeat type area select Sample repeat or Summary repeat by clicking the appropriate option For an example of using the two
164. ple Required data file xcal sld raw Section placement Nonrepeating section This table has the following possible fields Level Response Factor Component Name Average Response Factor RSD User Columns 1 to 5 Component Cal Level Table 174 XReport User Guide The Component Cal Level table displays the calibration levels amounts and acceptance test values defined for a specific component Required data file pmd Section placement Nonrepeating section This table has the following possible fields Component Name Cal Level Amount User Columns 1 to 5 Thermo Scientific D XReport Reference Report Objects Component OC Level Table The Component QC Level table displays the QC levels amounts and percent test values defined for a specific component Required data file pmd Section placement Nonrepeating section This table has the following possible fields QC Level Amount Test 96 Component Name User Columns 1 to 5 Component Spectrum Table The Component Spectrum table displays m z and intensity data for up to fifty spectrum peaks The Xcalibur data system uses this data to identify components when the Spectrum Peak Identification Method is specified in the processing method This table provides information for each peak with each sample There is a separate row for each sample peak combination The rows are grouped so that all peaks in a sample are shown together Note This me
165. port Reference Report Sections The title bar of XReport indicates whether the displayed template is locked or unlocked For a locked template Locked appears in the title bar For an unlocked template nothing appears in the title bar There is no audit trail when a new template is created or when an existing template is changed Template Configuration Dialog Box Select the type of report to create in the Template Configuration dialog box This dialog box is only displayed if you have more than one type of report installed for example Xcalibur and LCquan Table 66 Template Configuration dialog box parameters Parameter Report Types Description View a list of available report types Select the program for which you would like to create a report Do Not Show This Dialog Again Hide this dialog box when you open XReport or choose File New again To redisplay this dialog box choose Layout Preferences and select the Show Template Configuration check box Report Sections Thermo Scientific You can divide your report template into sections and add report objects to those sections To add sections into a report template drag them from the Sections pane The types of sections used in XReport are as follows Nonrepeating Section Report Header and Footer Qual Repeating Section Quan Repeating Section A report object that is placed in a repeating section can behave differently from the same report object
166. pplicable Repeating On Component to the Quan nonrepeating and is not available when this object is used in a Qual Plot Type Page nonrepeating Configure plot information for the Spectrum List table on the Plot Type page Note Clear the Use Processing Method Properties For Plot Type And Enhancement Info check box on the Options Page to modify the parameters in the Plot Type page Table 51 Plot Type page parameters Sheet 1 of 2 Parameter Mass Wavelength Detector Description For Detector MS View or change the current mass range of the active spectrum To change the mass range type the first mass and last mass of the scan in the Mass Range box The format is First Mass Last Mass For example to display mass charge 100 through 200 type 100 200 For Detector PDA View or change the current wavelength range in nanometers To change the wavelength range input the short wavelength and long wavelength of the scan in the Wavelength Range box The format is Short Wavelength Long Wavelength For example to display a wavelength range of 195 through 795 nanometers type 195 795 View or change the currently selected detector data type MS PDA Time 154 XReport User Guide View or change the time range in minutes for the active spectrum The valid range is 0 00 to 200 00 minutes To select a time range type the lower and upper time limits in minutes separated by a dash no spaces in the T
167. rage Scan Filter Selection Dialog Box iiis nodo hes vena eee 155 Library Search Graphics Table Properties Dialog Box 155 Library Search Results Table Properties Dialog Box esse 156 Sample Table Properties Dialog Box 2 ek dae e ee ne 156 Text Object Properties Dialog Box 243 25295 Toce EE da ates rtp es 156 Bitmap Properties Dialog Boxeuue sod esa bee de teo de ette aes 159 Column Properties Dialog Box 2 eene aebasetbte tu en aet dicte 160 Configure Component Calibration Curve Dialog Box 162 Data Sources Dialog Box acc ier baie a aoe eda cto eda RP e gate Odd 162 Electronic Signature Properties Dialog Box 2 0 0 00 00 162 Font Iri FM MU 163 Picterences Dialog Box setan otio di ettet pe ken tne 163 Preview WIBdOW o ed e e OR E ER A KE Rp Cu aad 164 Save As Dialog BOX ach deserere Mer ha bata prieka dud n ANE ene Real a 164 Template Configuration Dialog Box ine ede Pte UT RES UR PARURE 165 irpo CMM PME pH M 165 Nonrepeating Section opeet sisp ts Mop sapere GGE Pon opo ON wl poke cease 166 Report Header and Footer users etr aco b i a Er bc Pio 168 Repeating Sechionsis kosetes aes tas awe Dele e e PO eh eet 168 Report Objects cesso bia ck cere a E e a gute dU Ee d a eet ena 170 Graphic and Formatting Objects uunc er own are 170 Table Objects ex hb tar bee bare edicere Mdb tds 172 Text Objects sid oth nod da SAP doo a pde SR PINO VER t EPI 189 Report Templates etant enctaredie tectae aree e wi e
168. rates a Quan sample report containing non graphicalion rst raw pmd Confirmation ratio confirmation results IonRatio Generates Quan sample reports containing graphical ion ratio rst raw pmd Confirmation confirmation results These report templates take advantage of Graphical GraphicalSimple GraphicalStacked the explicit qualifier ion settings available when using the Chromatogram Properties Dialog Box and Wizard Peak Integration Generates a Quan sample report containing peak integration data generated using the Genesis peak integration algorithm Ist raw pmd ProcessingMethod Generates processing method reports Use this report with pmd Avalon Genesis ICIS results from Xcalibur Processing Method Setup QualPeak Report Generates a simple Qual sample report Use this report with rst raw results from Xcalibur batch processing QuanPeakResults Generates Quan sample reports Use this report with results rst raw pmd _ISTD ESTD from Xcalibur batch processing or Quan Browser QuanResults QuanSimple QuantifySampleReport Generates Quan sample reports containing chromatograms sld pmd rst 200 XReport User Guide and a Quan summary table araw Thermo Scientific D XReport Reference Report Templates Table 80 XReport templates Sheet 2 of 2 Report names Description Files needed Sequence Generates a summary report showing the sequence being sld Report processed U
169. repeats see Set Sample Repeat Options and Set Summary Repeat Options 3 If you selected Summary repeat select whether you would like to repeat from Left to right or from Top to bottom by clicking the appropriate option 4 To start each sample on a new row select the New sample new row check box XReport User Guide 103 4 Configuring Objects and Sections Configuring Columns Set Sample Repeat Options 104 XReport User Guide Use the Sample repeat option to present information relating to a raw file of a single sample and the results created when processing it Use this repeat type as a layout tool to indicate where objects are placed on the page of the resolved report Note The Sample repeat and Summary repeat options are applicable only in nonrepeating report sections These options are not available in other types of report sections For example when you place a 2 column object in a nonrepeating section add a Quan based chromatogram to the left column and combine or resolve the template using data of 1 sample with 4 components the report appears as in Figure 77 Figure 77 2 column object behavior in a nonrepeating section with a chromatogram object Resolve p E Chrom 1 Chrom 2 Chrom 3 Chrom 4 Sample 1 In another example place a 2 column object in a nonrepeating section and add a chromatogram and a text object to the left column and
170. report object see Figure 50 on page 75 Figure 53 Selecting an explicit peak in a Qual result based chromatogram Select Demo File 4 demo file can be associated with a chromatogram control This demo file allows the control to show how the current settings for the chromatogram will look when applied to real data MV Use demo file Demo File c Xcalibur examples data drugx_01 rst gl When using result data for the chromatogram demo you must explicitly specify the peak to demo Demo Peak Qual peak RT 4 833 coc e 2 To search for the required demo file raw file click the browse button in the Demo File area The Select Raw Data File dialog box opens 3 Select a demo file and click Open 4 To specify the peak to demo click the browse button in the Demo Peak area The Select a Peak dialog box opens 5 Select a peak from the list located in the result file 6 Click OK to apply the selection and return to the wizard 7 Click Next to go to the next page of the wizard 78 XReport User Guide Thermo Scientific 4 Configuring Objects and Sections Configuring a Chromatogram Object Qual Result Based Chromatogram All Available Peaks When configuring a chromatogram report object that is Qual result based with Show all Qual peaks set peak type setting use this procedure to select a file To select a demo file for all available peaks 1 To associate a demo file with the chromatogram report o
171. rowser window 1 Open the Quan Browser window The Open dialog box opens 2 To select a sequence select an sld file with samples to use in the reports Then click Open 3 Choose View gt Reports Dialog The Reports dialog box opens see Figure 15 Figure 15 Reports dialog box in the Quan Browser window Reports Sample Reports 0 selected samples Enabled Stds QCs Unks Other Save As Report Template Name PDF C NX caliburtemplatessPeaklIntegration srt None Summary Reports Enabled Save As Report Template Name 1 di Yes PDF C X caliburstemplatessQ uantifyS ampleR eport rt None Select Samples Print Reports Cancel Help 4 To make a row of the sample reports area active do the following a Click the Enable box in the first row and click the Enable box again A check box appears in the box b Click the check box When you click the check box again the word Yes appears in the Enable box to indicate that the entire row of options is selected Thermo Scientific XReport User Guide 37 3 Generating a Report Creating a Report from the Xcalibur Data System 5 To select the report type to print for the sample do the following a Click one of the following boxes Stds QCs Unks or Other A check box control appears b Click the check box When you click the check box again the word Yes appears in the Enable box to indicate that reports are to be printed for all selected samples of
172. rs Parameter Description Use Advanced Quan Peak Turn on the advanced Quan peak options Annotation Custom Peak Labels Component Name Label the Quan peak with the component name Component Key Label the Quan peak with the component key Custom Text Label Label the Quan peak with a custom text label Retention Time Label the Quan peak with the retention time RT Labeling Units Specify the units for the retention time Decimals Define the number of decimal places to be displayed in the retention time label Overlaid QI Identifier Show QI Peak Label Label overlaid qualifier ion peaks with a label identifying the qualifier ion This option is only available when you select The All Quan Traces option on the Select Mass Spectrum Quan Traces to Display page The Overlay 3D option on the Select Chromatogram Style page 132 XReport User Guide Thermo Scientific D XReport Reference XReport Dialog Boxes Configure the Look of the Peak Window Set parameters on the Configure How The Peak Window Will Look page to control the display of baselines Quan and Qual peaks and the peak window width Qual peak and in some cases Quan peaks when a peak from a result file is set to display in a chromatogram Table 19 Configure How the Peak Window Will Look page parameters Parameter Description Show Baselines View the baselines for a chromatogram peak Quan or Qual If you do not select this option the
173. s Name View or change the name of the x axis Offset Move the x axis label away from the chromatogram Split Time Range Split the chromatogram into two or more separate graphs with equal time ranges Divisions Define the number of split time range graphs to be displayed for each chromatogram Yaxis Label From Detector Use the detector specific label for the y axis stored in the raw file Custom Use your own label for the y axis Units Absolute Use absolute units for the y axis Relative Use relative units for the y axis Name Define the custom name of the y axis This box is available only when you click the Custom option in the Label area Offset Move the y axis label away from the chromatogram Thermo Scientific XReport User Guide 137 D XReport Reference XReport Dialog Boxes Select Mass Spectrum Quan Traces to Display Set parameters on the Select Mass Spectrum Quan Traces To Display page to configure the Quan Traces property for MS data Options on this page only apply to MS data and are ignored for other detector types When a chromatogram report object displays a Quan component there are potentially six traces associated with the component the Quan Mass QM trace the actual component peak and up to five qualifier ions Select any of these possible six traces to be displayed in the chromatogram or display all of the available traces of the component Table 28 Select Mass Spectrum Quan Tra
174. s che swine kee Sew oe Bohs She ie ds 49 Configuring Text Fields oec eae aol se Shad Vetbedeka eiu co teda 50 Adding Custom Text Fields iud c tret y s Pen e ae Roa de c wie ele wee 51 Configuring Text Attributes s a cos ipee rr ipa eere ded vas oes ee ep IRS 23 Settings Text Ponts 0 ioo cov Manne iex tte oett et aes eat s 54 Configuring an Annotation ObJect ossium vehe be deb tose eels 55 Configuring a Table Object be anaesthesia 57 Choosing Table Columitigan zie erar uS pee EE dE 58 Configuring Custom User Columns 0 0 0 0 0c eee cee eee eee 59 Specifying Table Sort Order iiri uei gcepe E PRe ed weed tere 61 Setting Table Ponts as xe Gaetan bs an PI e ey RENE NUR 62 Setting Additional Table Properties onnu era Pat nee Pee ees 63 Configuring a Bitmap Object os cose da katte docte etes dn are edi dera eeu 70 Thermo Scientific Thermo Scientific Appendix A Appendix B Appendix C Contents Configuring a Chromatogram Objects uuo sss ee ke d xw be dre 71 Use Container Supplied Quan Peak Page i coe ee retine 73 Use Container Supplied Qual Peak Page iis Leer es 73 Select Chromatogram Type Page 22 us dea ved be a ER ea 75 Select Demo File Page ed ve dx PES e boe RES 76 Select the Quan Peak Page 4 otic adios ek eol ei c foa S 79 Select the Qual Peake Pasar sien cule sian ede A t per A de es 80 Select Mass Spectrum Quan Traces to Display Page 0004 81 Configure How the Peak Window Will Look Page
175. s from the shortcut menu The Repeating Section Properties dialog box opens see Figure 20 This dialog box has three pages Exclude available for a Quan repeating section only Ordering and Page Breaks Figure 20 Exclude page in the Repeating Section Properties dialog box Repeating Section Properties Exclude Ordering Page Breaks The Repeating Section type is Repeating Section Excludes When processing Quan Exclude Component Type configurations or results it is possible to exclude specific None elements from the process Sh ly f t It is also possible to discard any xis EMI emoe components that haven t been found Cancel Help Thermo Scientific 4 Configuring Objects and Sections Configuring a Repeating Section 3 When configuring a Quan repeating section use the Exclude page to exclude specific elements from the process and discard any components that have not been found a From the Exclude Component Type list define the exclusions for the Quan repeating section by selecting one of the following options None no exclusions the default Internal Standards Target Compounds b To discard any components that have not been found select the Show Only Found Components check box 4 Click the Ordering tab to display the Ordering page Use this page to change the default ordering of processed results defining the order of peaks and components in either a Qual or Quan repeating se
176. s parameter to specify the wavelength or wavelength range nm Type the lower and upper limits for the plot Separate entries by a dash no spaces To use the entire mass wavelength range type an asterisk 2 Select the type of detector used to generate the raw file from the Detector list Valid types are MS and PDA The type of detector determines the available Plot types 3 Select the time of the mass scan in the host chromatogram in the Time box Type a new value or range as required 4 From the Scan Filter list select a filter or type a new one in the box using the scan filter format 5 Click the browse button in the Demo File box and select the file This box shows the path and filename of the demo file raw used to generate the selected plot Use the Enhance Page to apply smoothing the refine algorithm to the spectrum and set background subtraction time ranges If you selected the Use processing method properties for plot type and enhance info check box on the Options page this page is blank To define spectrum enhancement options 1 To turn on spectrum smoothing select the Enable check box in the Smoothing area see Figure 70 Figure 70 Enhance page Spectrum Properties Axis Normalization Peak Options Plot type Enhance Style Labels Smoothing r Refine Enable Enable Background subtraction Time Range 1 00 TimeRange 2 00 Cancel if Help 2 To select a type of smoo
177. sample or summary Table 60 Column Properties dialog box parameters Sheet 1 of 2 Parameter Description Number of Columns 2 3 4 or 5 Specify the number of columns in the column object Repeat Type Sample repeat View information relating to a particular raw file of a sample and the results created when processing it Use this repeat type as a layout tool to indicate where objects are placed on the page of the resolved report Example 1 When you place a 2 column object in a Quan repeating section add a chromatogram to the right column and resolve the template given data of 1 sample with 4 components each the report appears as follows Resolve Chrom 2 Sample 1 Chrom 3 Chrom 4 Example 2 Place a 2 column object in a Quan repeating section add a chromatogram to the left column a spectrum to the right column and a text object below the column Then combine the data with the template given data of 1 sample with 4 components All objects in the section are repeated by sample and the report appears as follows Resolve _ _ __ _ _ Text Text Chrom 2 Spec 2 Text Sample 1 Chrom 3 Spec 3 Text Chrom 4 Spec 4 Text 160 XReport User Guide Thermo Scientific Table 60 Column Properties dialog box paramet
178. se this report with results from Xcalibur batch processing Spectrum Generates a Quan sample report only applicable to GC MS rst raw Candidates Use this report with results from Xcalibur batch processing or Quan Browser Thermo Scientific XReport User Guide 201 Index Numerics 2 column objects in a nonrepeating section with chromatogram and spectrum 104 in a nonrepeating section with chromatogram and spectrum objects 106 in nonrepeating section with chromatogram 104 Left to right option 105 Top to bottom option 105 A adding custom text fields 51 objects 18 sections 16 Advanced Qual Peak Annotation Options page 131 Advanced Qual Peak Annotation Options setting 90 Advanced Quan Peak Annotation Options page 132 aligning objects 19 annotation object 189 Annotation Properties dialog box Attributes page 55 configuring an object 55 Font page 56 Avalon Qual Events table XReport 173 Avalon Quan Events table XReport 173 Average Scan Filter Selection dialog box 155 Batch Reprocess dialog box 36 batch reprocessing generating reports while 35 bitmap object configuring 70 details 171 Bitmap Properties dialog box 159 blank line adding to a report 198 Thermo Scientific C Calibration File table 174 centering objects 20 choosing data sources 29 table columns 58 chromatogram object 171 Chromatogram Properties dialog box 71 Chromatogram Properties wizard 130 Configure How the Peak Window Will Look p
179. so that all peaks in a sample are shown together Required data file sld Section placement Nonrepeating section The Sample table has the following possible fields Sample ID Data File Name Area Area Ratio ISTD Area Specified Amount Diff RSD Actual RT Calculated Amount Calibration Flags Data Flags Excluded Height ISTD Height Height Ratio QC Failed System Suitability User Columns 1 to 5 Thermo Scientific Sequence Table Thermo Scientific D XReport Reference Report Objects The Sequence table displays the contents of the sequence file This table provides information for each peak with each sample Required data file sld Section placement Nonrepeating section The Sequence table has the following possible fields Sample Type File Name Sample ID Path Inst Method Cal File Dil Factor Inj Vol ISTD Corr Amt Level Proc Method Sample Vol Sample Wt Position User Labels 1 to 5 User Columns 1 to 5 XReport User Guide 187 D XReport Reference Report Objects Spectrum Candidate Results Table Spectrum List Table 188 XReport User Guide The Spectrum Candidate Results table displays the results of spectrum candidate processing for GC MS data on a per component basis Required data file rst Section placement Nonrepeating section The Spectrum Candidate Results table has the following possible fields Component Name Cand Forward Fit Reverse Fit Match
180. ss range for Mass Range or Base Peak Traces in the Mass list as follows If you choose Base Peak Mass Range or Mass Range Mass Range plot combinations in step 4 above the identification page displays a Mass m z field for each trace type b Ifyou choose other detector types use this field to specify the wavelength or wavelength range for the chromatogram If you use a plot combination such as Wavelength Range Wavelength Range an additional Wavelength nm box appears for you to specify the second wavelength range The valid range depends on the configured detector The format is Low Mass Wavelength High Mass Wavelength Separate entries by a dash with no spaces For example for the range m z 123 through 456 type 123 456 6 Specify the lower and upper time limits for the plot in minutes to 1 decimal place in the Time Range box Separate entries by a dash with no spaces Type the default setting to display the complete time range for the plot 7 Select the Fixed Scale check box to set the y axis maximum to a specific value Selecting the Fixed Scale check box activates the Normalize To area on the final page of the wizard and the box where you type the maximum y axis value on the current page 8 Select the Autofilter check box to repopulate a chromatogram view with the following A plot showing the chromatogram without any scan filters Plots for each scan filter applied to the chromatogram 9 Click Next to go to th
181. t in columns select the number of columns in the Number Of Columns area 2 To include data labels in the object in the Horizontal Spacing area select the Include data label check box 3 To add extra space between data labels and data select the Include spacing between a label and its data check box 4 Select a line spacing option in the Vertical Spacing area 5 Click OK to save your changes XReport User Guide 53 54 4 Configuring Objects and Sections Configuring a Text Object Setting Text Fonts To set text fonts right click a text object and choose Properties from the shortcut menu A dialog box opens and you can select a font type for the title heading data label and data Click the Font tab see Figure 27 Figure 27 Setting fonts t v Sample Header Data Attributes Font sample Header Object Heading font Sample Header Data label font Data font Data File To set the font for a specific type of text for each button on the page 1 Click a text type button The Font dialog box opens see Figure 28 XReport User Guide Figure 28 Font dialog box Font Font Style Size Times New Roman Bold E OK Trebuchet MS Verdana ZwlAdobeF Cancel Effects v Underline Strikeout Color Black Thermo Scientific 4 Configuring Objects and Sections Configuring an Annotation Object 2 Make the font selections and click OK Note The H
182. t the Quan Peak Set parameters on the Select the Quan Peak page to explicitly specify the Quan peak component for a Quan results based chromatogram report object Table 32 Select the Quan Peak page parameters Parameter Description Quan Peak Quan Peak Set the name of the Quan peak To select a processing method pmd file and select a component click the Browse button The Select Component dialog box opens Use Quan Peak s Associated Use the associated internal standard of the Quan peak instead of the Quan peak Internal Standard You must select a valid peak for XReport to resolve the report correctly If the file used to resolve the report does not contain the specified peak the chromatogram is removed from the resolved report Use Container Supplied Qual Peak Set the parameter on the Use Container Supplied Qual Peak page to ignore the implicit Qual peak and explicitly configure the chromatogram type Table 33 Use Container Supplied Qual Peak page parameters Parameter Description Explicit Chromatogram Type Explicitly Specify Ignore the implicit Quan peak supplied by the container and The Chromatogram s Behaviour explicitly configure the chromatogram type Thermo Scientific XReport User Guide 141 D XReport Reference XReport Dialog Boxes Use Container Supplied Quan Peak Set parameters on the Use Container Supplied Quan Peak page to either display the details of the internal standard associated with the
183. te with Xcalibur data Save and present reports in any of these formats Microsoft Word document doc file Text txt file Microsoft Excel workbook xls file Rich text rtf file PDF pdf file Web page htm or html file 8 XReport User Guide Thermo Scientific 1 Introduction to XReport Configuring XReport Objects Overview Configuring XReport Objects Overview Use the Template pane of the XReport window to configure objects by right clicking them and choosing Properties from the shortcut menu Set parameters in the configuration dialog box that opens You can configure nearly all items in XReport including the following Repeating sections Tables Chromatograms Spectra Component calibration curves Text objects For specific information on configuring each object see Chapter 4 Configuring Objects and Sections Configuring a Repeating Section Overview Use the Repeating Section Configuration dialog box to specify The type of repeating section Qual or Quan e Whether to exclude Internal Standards or Target Compounds from a Quan repeating section The order in which peaks and components are repeated Any limit on number of peaks to be reported How the individual peaks or components are split across pages in the final report Configuring a Table Overview Use the Table Configuration wizard to do the following Specify the columns to be included in the table Define and
184. template by changing its properties Use the wizard for the following e Choosing Table Columns Configuring Custom User Columns Specifying Table Sort Order Setting Table Fonts Setting Additional Table Properties Thermo Scientific XReport User Guide 57 4 Configuring Objects and Sections Configuring a Table Object Choosing Table Columns 58 XReport User Guide To select the columns to include in the table see Figure 32 use the Select Table Fields page of the Table wizard The columns available for a table appear in alphabetical order but can be added to a report template in any order Your column options to select depend on the type of table object you are configuring To select options for the Select Table Fields page of the Table wizard To include a custom title for the table type the title in the Title box and select the Include the title on the resolved report check box To select the columns to include in the table from the Available Columns list do one of the following Select an item and click Add Double click an item To move all available fields click Add All The fields you have chosen appear in the selected list Note All table objects have user columns available for selection Use the user columns to define formulas for calculating table data and to display the results in the table For more information on user columns see Configuring Custom User Columns Type the colu
185. ter the current object on the page so that it is an equal distance from the top and Horizontal bottom sides of the page Shrink Wrap Shrink the current section to fit all of the objects that it contains Expand Enlarges the current section so you can add additional objects Preferences Change grid settings enable actions and view or hide template configuration dialog box XReport Report Menu Table 12 Report menu commands Command Data Sources Description Specify the data files for the report Simulate Report View your template before adding real data Resolve Report Display the report with data filled in Select data in the Data Sources dialog box Print Report Print the current report XReport Help Menu Table 13 Help menu commands Command Description Xcalibur Help View Xcalibur Help Glossary View the glossary How to Use Help View How to Use Help About XReport Open the About XReport dialog box 126 XReport User Guide The About XReport dialog box displays the version number of XReport along with copyright information Thermo Scientific D XReport Reference XReport Dialog Boxes XReport Dialog Boxes Thermo Scientific Configure Repeating Section Dialog Box Chromatogram Properties Dialog Box and Wizard Spectrum Properties Dialog Box Table Properties Wizard Edit Formula For Dialog Box Configure Function Dialog Box Spectrum List Table Properties Dialog Box Average S
186. the list of values x2 5X72 COUNT COUNT list Return the count of the number of items in a list FALSE FALSE Return 0 zero INT INT x Return the number to the left of the decimal place in the value or formula x MAX MAX xl x2 xn Return the largest value in a list MIN MIN x1 x2 xn Return the smallest value in a list 150 XReport User Guide Thermo Scientific D XReport Reference XReport Dialog Boxes Table 47 Edit Formula For dialog box parameters Sheet 2 of 2 Parameter Description Function Syntax Description MOD MOD x y Return the remainder from dividing the value x by the value y a number of times in integers NOT NOT x Return the value 0 zero false if the logical expression x is true or the value 1 true of the expression x is false OR OR x y Return the value 1 true if either or both logical expressions x and y are true or the value 0 zero false if both expressions are false PRODUCT PRODUCT xl Return the result of multiplying a list of values x2 XN ROUND ROUND x y Return the value of x rounded to the specified number of decimal places y x can be either a number or a result of a formula SIGN SIGN x Return the value 1 if x is a positive value or the value 1 if x is a negative value SUM SUM x1 x2 xn Return the sum of a list of values or formulas TRUE TRUE Return 1 Add Function Configure the currently selected function and add it to the current formula Confi
187. the objects or hold down the SHIFT key and click each object Align gt Align the top edges of the currently selected objects to the top edge of the first selected Top object To select more than one object click and drag a selection box around the objects or hold down the SHIFT key and click each object Align gt Align the bottom edges of the currently selected objects to the bottom edge of the first Bottom selected object Thermo Scientific To select more than one object click and drag a selection box around the objects or hold down the SHIFT key and click each object XReport User Guide 125 D XReport Reference Reports View Table 11 Layout menu commands Sheet 2 of 2 Command Align gt Auto Description Snap all objects selected or not in the current section to the nearest upper and right gridlines Make Same Size gt Width Enlarge all selected objects except for the first selected to match the width of the first selected object Make Same Size gt Height Enlarge all selected objects except for the first selected to match the height of the first selected object Make Same Size gt Both Center In Page gt Vertical Enlarge all selected objects except for the first selected to match the height and the width of the first selected object Center the current object on the page so that it is an equal distance from the left and right sides of the page Center In Page gt Cen
188. thing select Boxcar or Gaussian from the Type list XReport User Guide 97 4 Configuring Objects and Sections Configuring a Spectrum 3 Type the number of points for spectrum smoothing in the Points list Type an odd number from 3 minimum smoothing to 15 maximum smoothing 4 To turn Refine spectrum enhancement on or off select the Enable check box in the Refine area 5 To apply the refining algorithm and specify a length of time for mass chromatograms type a value in the Window box indicating the number of seconds on either side of the specified point A reasonable initial value is the peak width in seconds 6 To eliminate peaks generated from baseline noise type 0 this shows all peaks in the spectrum in the Noise threshold box After you close this box to display the results you can open the box again to increase the value until noise peaks are eliminated 7 To specify a first baseline region used for assessing the background select the Time Range 1 check box in the Background Subtraction area Type the time range in the box The Background Subtraction area shows details of background subtraction when this value has been applied to the spectrum The background contribution is determined by averaging the scans from one or two baseline regions 8 To specify a second baseline region used for assessing the background select the Time Range 2 check box Type the time range in the box Configure Spectrum Style 98 To s
189. thod is only used for GC chromatography Required data file pmd Section placement Nonrepeating section This table has the following possible fields 2 mz Intensity 96 User Columns 1 to 5 Thermo Scientific XReport User Guide 175 D XReport Reference Report Objects Dilution Factor Table The Dilution Factor table displays the names of calibration levels and dilution factors for components other than internal standards Required data file rst Section placement Nonrepeating section This table has the following possible fields Calibration Level Dilution User Columns 1 to 5 Electronic Signature Table 176 XReport User Guide The Electronic Signature table object displays up to six electronic signatures in table format Required data file none Section placement possible in all sections Note The data system generates Electronic Signature information at the time the report is created and the signature information can only be included in reports generated from either the Xcalibur Sequence Setup or Quan Browser Reports generated from within XReport do not display signature information The Electronic Signature table object displays two blocks of signatures The Created By block displays the signature of the person who created the report The Signed By block displays the signatures of the people who entered electronic signature information at the time the report was created This object displa
190. ting XReport To start XReport 1 From your computer taskbar double click b on the desktop or choose Start gt All Programs gt Thermo Xcalibur gt XReport When more than one application is installed that uses XReport for reporting for example both Xcalibur 3 0 and LCquan the Template Configuration dialog box opens see Figure 2 Figure 2 Template Configuration dialog box Report Types Do not show this dialog again Re enable this option using Layout Preferences Show template configuration sa u Thermo Scientific XReport User Guide 11 1 Introduction to XReport Using XReport 2 Select the application for the report template and click OK XReport opens and creates a new template see Figure 3 Figure 3 XReport window showing a new template lt lt Add a section by dragging an icon from the Available sections pane to here gt gt pm s NUM 07 17 13 18 56 46 7 Selecting a Report Template To select a report template 1 In the Reports view choose File gt Open A browse dialog box opens 2 To select the required report template click the template name If the name does not appear browse to the correct folder The template name appears in the File name box 3 To view the report template and close the dialog box click Open 12 XReport User Guide Thermo Scientific 1 Introd
191. tion Insert a page break before the repeating section Page break after the repeating section Insert a page break after the repeating section Thermo Scientific XReport User Guide 129 D XReport Reference XReport Dialog Boxes Chromatogram Properties Dialog Box and Wizard 130 XReport User Guide The Chromatogram Properties dialog box displays a preview of the current chromatogram settings To change these settings click Configure The Chromatogram Properties wizard opens Use this wizard to configure any of these settings for the Chromatogram report object that is contained in your report template Chromatogram and peak type Use of a demo file Plot details Smoothing parameters Use of MS Quan traces Chromatogram display style labeling axes and normalization methods This wizard displays different pages and contains different options depending on the type of section containing the chromatogram report object and the selections for the chromatogram type and peak type properties This wizard can contain the following pages Advanced Qual Peak Annotation Options Advanced Quan Peak Annotation Options Configure the Look of the Peak Window Configure Normalization For The Chromatogram Select A Peak Dialog Box Select Chromatogram Style Select Chromatogram Type Select Component Select Demo File Select Enhance Details Select How the Chromatogram Axes Will Be Configured Select Mass Spectrum Quan Traces to Display Select Plot
192. tions use the Options Page To configure Spectrum options 1 To use processing method properties for Plot type and Enhance information select the Use processing method properties for plot type and enhance info check box see Figure 68 on page 95 When you select this check box the options on the Plot type and Enhance pages are not available 2 To use the Internal Standard peak when repeating on a component select the Use ISTD peak when repeating on component check box This option is only available when you select the Use processing method properties for plot type and enhance info check box Configure Plot Types When raw data is being displayed in a Spectrum report object use the Plot Type Page to configure how the plot is drawn If you selected the Use processing method properties for plot type and enhance info check box on the Options page this page is blank To configure plot types 1 Specify the mass or mass range for MS detector types in the Mass Range box see Figure 69 Figure 69 Plot type page Spectrum Properties Axis Normalization Peak ptions Plot type Enhance Style Labels Mass range E Detector MS v Time fo 00 Scan filter m Demo file Ic V caliburexamplessdata steroids02 raw m Cancel Help 96 XReport User Guide Thermo Scientific Enhance Spectra Thermo Scientific 4 Configuring Objects and Sections Configuring a Spectrum For PDA detector types use thi
193. ts in Compound Element Infiltration Mass Spectral Peak Constraints Enabled Mass Spectral Peak Measurement ICIS Peak Integration ICIS Smoothing Points Baseline Window Area Noise Factor Peak Noise Factor CIS Constrain Peak Width CIS Peak Height CIS Tailing Factor 194 XReport User Guide Genesis Apex Detection Window Size e Filter Width Genesis Valley Detection Rise 96 Valley S N Genesis Background Subtraction Recomputation Interval Number of Scans in Background Background Subtraction Right Region Right Region Width Region Start Threshold e Cutoff Threshold Library Search Options Search Type Identity Similarity Peak Purity Options Scan Threshold Peak Coverage Limit Scan Wavelength Range Other Blank Line and User Text Data Items Thermo Scientific Quan ISTD Peak Summary D XReport Reference Report Objects The Quan ISTD Peak Summary object displays summary parameters for a Quan component s associated ISTD peak Required data file pmd rst Section placement Quan nonrepeating repeats on component peak For this object s possible fields see Table 72 Table 72 Quan ISTD Peak Summary object fields Component Name ISTD Name Actual RT Response Height Width Baseline Flags Area Signal to Noise Saturated Expected RT Peak Status System
194. u have selected the Fixed Scale check box on the Plot Type Page see Plot Type Page on page 66 Finishing the Chromatogram Wizard To change selections in the Chromatogram wizard click Back to go back through the previous pages When the page is done click Finish Configuring a Component Calibration Curve To configure a Component Calibration Curve object right click it and choose Properties from the shortcut menu The Component Calibration Curve Properties dialog box opens see Figure 66 Figure 66 Component Calibration Curve Properties dialog box Component Calibration Curve Properties Component It is possible to force a component calibration curve to be plotted for a specific component If this is required then the name of the component should be entered here Component D4 H Cancel Apply Help If your report has a nonrepeating Component Cal Curve report object use the Component Calibration Curve wizard to specify the name of the component Thermo Scientific XReport User Guide 93 4 Configuring Objects and Sections Configuring a Component Calibration Curve To specify the name of the component 1 To search for the required processing method file pmd click the browse button A dialog box opens By default the wizard searches in the Xcalibur methods folder 2 To open a file select it and click Open The Select Component dialog box opens see Figure 67 Figure 67 Select Component dialog box S
195. uantitative analysis for a single sample Quan Summary Table sld rst pmd Displays information specific to Nonrepeating component peaks detected by quantitative analysis for all samples in a sequence Sample Table Quan Results Sequence Table sld sld Displays system suitability and flag processing results for each component in a sample and repeats this information for every sample in a sequence Displays the contents of the sequence file Quan repeating Nonrepeating Spectrum Candidate Results Table ISt Displays the results of spectrum candidate processing for GC MS data on a per component basis Parameters include the following Forward fitStart RT Reverse fitEnd RT e MatchArea Found RTHeight Nonrepeating Spectrum List Table Thermo Scientific Ist TaW Displays the text equivalent of the Spectrum graphic object The Spectrum List Table contains a header and lists values for the m z intensity and relative intensity Qual or Quan repeating XReport User Guide 113 B Types of Report Objects Graphic Object Descriptions Graphic Object Descriptions The table below describes the graphic objects Table 5 Graphic objects Graphic object Data source file Description Section placement Bitmap bmp dib gif Displays a graphical image for example Any jpg or ico a company logo Chromatogram raw rst Displays a graphical trace that can show
196. uction to XReport Using XReport Creating and Generating Reports with XReport There are two distinct stages in the process of producing a customized Xcalibur report using XReport Creating a Report Template Generating a Report Using a Report Template These stages are discussed in more detail in these chapters Creating a Template on page 15 and Generating a Report on page 29 The Xcalibur data system provides sample XReport templates for you to use These are xrt files with XReport objects embedded within them and are located in the Xcalibur templates folder For details on these report templates see Appendix A Sample XReport Template Files Creating a Report Template Use XReport to create a customized report template xrt file that defines how the final report looks and defines the specific information in the report To create a report template 1 Click the XReport icon ed on the desktop to start XReport A new XReport document appears in the report window see Figure 3 2 Add sections and report objects to the report template by dragging items from the Available Sections and Available Objects panes to the report preview pane 3 Configure the sections and report objects included in the report template to adjust their properties and customize their output Right click objects and sections to configure and choose Properties from the shortcut menu Set parameters in the configuration dialog boxes Use th
197. ument Method pmd aw Displays Calibration Quantitation and Detection flags and system suitability parameters to specify automatic chromatographic checks that assign a pass fail qualification to a target peak Displays general instrument method parameters This text object does not have any editable properties Quan repeating Nonrepeating Processing Method General Processing Method Qual pmd pmd Displays general processing method parameters including date created date modified baseline definition chromatography type LC GC Displays Qual processing method parameters including the following Identification Spectrum Enhancement Detection Options Advanced Detection Options Library Search Constraints Library Search Options Nonrepeating Nonrepeating Quan ISTD Peak Summary Quan Peak Summary 110 XReport User Guide rst pmd st pmd Displays summary parameters for a Quan components associated ISTD peak For example ISTD NameBase Line Actual RTSignal To Noise Response Expected RT Displays Component Peak summary parameters for example Actual RT Diff Calculated AmountArea Ratio Response Area ISTD Base Line Specified Amount Signal To Noise Quan repeating Quan repeating header or footer Thermo Scientific Table 3 Text objects Sheet 3 of 3 B Types of Report Objects Table Object Descriptions Text object Dat
198. up 32 generating when batch reprocessing a sequence 35 generating when running a sample or sequence 34 resolved combined documents 8 Reports view 121 repositioning objects 18 resizing objects 18 resizing sections 16 Run Sequence dialog box 34 S sample header object 196 sample reports 32 sample table fields 186 properties 64 Sample Table Properties dialog box 64 Save As dialog box 27 164 saving XReport templates 26 sections XReport adding 16 deleting 16 footer 4 header 4 nonrepeating 5 166 Qual repeating 168 Quan repeating 169 reordering 16 repeating 5 repeating configuring 17 46 reports 165 resizing 16 types of sections 4 Select A Peak dialog box 134 XReport User Guide 205 Index T Select Component dialog box 94 Select Report Samples dialog box 38 Sequence Setup generating a report from 32 sequence table Xreport object 187 setting table fonts 62 setting table properties 63 signatures electronic 40 sorting tables 61 spectra configuring report object 95 Spectrum Candidate Results table 188 Spectrum Configuration dialog box Axis page 143 Enhance page 143 Labels page 144 Normalization page 145 Options page 145 Peak page 146 Plot Type page 146 Style page 147 Spectrum List Table Properties dialog box Display page 68 152 Enhancement page 153 Options page 65 154 Plot Type page 189 reference 152 spectrum object 171 Spectrum Properties dialog box Enhance page 97 Labels page 99 N
199. ur data system Thermo Scientific FF Types of Report Objects The following tables list the report objects you can place onto a report template text objects table objects graphic objects and formatting objects The tables briefly describe an object and indicate in which sections the object is available Contents e Text Object Descriptions e Table Object Descriptions e Graphic Object Descriptions e Formatting Object Descriptions Text Object Descriptions The table below describes the text objects Table 3 Text objects Sheet 1 of 3 Text object Data source file Description Section placement Annotation none Displays static text Use this object for Any adding headings or comments Component Ident Detect Cal pmd Displays the peak detection calibration Quan repeating Settings and integration parameters for a single component Component ISTD Settings pmd Displays a summary of the configuration Quan repeating Summary details for each components ISTD configuration in the Quantitation section of a processing method Component Settings Summary pmd Displays a short list of peak detection Quan repeating and integration parameters for a specified component Thermo Scientific XReport User Guide 109 B Types of Report Objects Text Object Descriptions Table 3 Text objects Sheet 2 of 3 Text object Data source file Description Section placement Component Sys Suit Flags Settings Instr
200. utes Page Font Page 156 XReport User Guide Thermo Scientific D XReport Reference XReport Dialog Boxes Data Page Indicate what text appears in the text object on the Data page The Data page of the Text Object Properties dialog box changes depending on the text object you select To create an Annotation object you can type the annotation text to add to your report You can either type the text directly in the box or copy and paste it in Paste text in the box by either right clicking in the box and choosing Paste from the shortcut menu or by pressing CTRL V Add line breaks by pressing the ENTER key while the cursor is still in the box Table 56 Data page parameters Sheet 1 of 2 Parameter Description Title The custom title of the selected object Include The Title In The Resolved Include the custom title in the final report Report Available Items This box lists the items that are available to add to the text object To add an item to the Selected list select it to highlight it and click Add The Available Items list varies depending on which text object is selected Component ISTD Settings Summary Component Settings Summary Component Sys Suit Flags Settings nstrument Method Processing Method General Processing Method Qual Quan ISTD Peak Summary Quan Peak Summary Report Info Sample Header Add Add the currently highlighted item in the Available Items list to
201. ver the second order which then takes precedence over the third order Test Current Sorting Configuration Component Name First Order jf de T rde QC Level Amount User Column 3 User Column 5 9 Ascending J C Descending C De wo eho C C lt Back Next gt Cancel Help XReport displays the columns selected for the table in a list on the left side of the dialog box Set the order for the table using any of the selected columns Use up to three columns for ordering the table The first order takes precedence over the second order which takes precedence over the third order To define a method for ordering data in the table 1 To select a variable to provide the first level of sorting for the table double click the item in the column list to move it to the First Order box 2 To define how to sort the First Order column data in the Current Sorting Configuration area select one of the following options Ascending Sort data in ascending order Descending Sort data in descending order 3 To define the second and the third variable used to order table columns repeat the first two steps 4 To move to the Font page click Next Thermo Scientific XReport User Guide 61 4 Configuring Objects and Sections Configuring a Table Object Setting Table Fonts Use the final page of the Table wizard the Set Table Font page to set the font type for elements in the table see Figure 36 Figure 36
202. x Required data file None Section placement Possible in all sections Component IdentDetectCal Settings The Component IdentDetectCal Settings object shows the peak detection calibration and integration parameters for a single component Required data file pmd Section placement Quan repeating section repeats on component peak For this object s possible fields and headings see Table 67 Thermo Scientific XReport User Guide 189 D XReport Reference Report Objects Component ISTD Settings Summary The Component ISTD Settings object displays a summary of the configuration details for each component s ISTD configuration in the Quantitation section of a processing method Required data file pmd Section placement Quan repeating section repeats on component peak For this object s possible fields see Table 67 Table 67 Component ISTD Settings object fields Component Name Time Detector Type Retention Time Filter Window P dace View Width Mass Range 8 Retention Time e Wavelength Range 1 Reference e Wavelength Range 2 Component Type ISTD Name Peak Detection Algorithm 190 XReport User Guide Expected Retention Genesis Peak ICIS Peak Integration Detection Integration Detection Genesis Smoothing ICIS Smoothing Points Points CIS Constrain Peak Valley Detection Width Enabled CIS Identify By Genesis Constrain Peak a e CIC Minimum Peak Width
203. xes Table 29 Select Plot Details page parameters Sheet 2 of 2 Parameter Trace Description The first list indicates the basic chromatogram type for example TIC The second list indicates a logical operator or The third list indicates a second chromatogram type to add to or subtract from the first trace For example Mass Range The list of traces depends on the detector used to generate the data as follows Detector Type Valid Traces MS Mass Range TIC Neutral Fragment and Base Peak Analog Analog 1 4 A D Card A D Card Ch 1 4 PDA e Wavelength Range Total Scan and Spectrum Maximum UV Channel A D Mass m z Define the display for the mass or mass range for Mass Range or Base Peak traces for MS detector types as follows If you choose Base Peak Mass Range or Mass Range Mass Range plot combinations the identification page displays a Mass m z field for each trace type If you use other detector types use this field to specify the wavelength or wavelength range for the chromatogram If you use a plot combination such as Wavelength Range Wavelength Range an additional Wavelength nm box opens The valid range depends on the configured detector The format is low mass iwavelength high mass wavelength Separate entries with a dash no spaces For example for the range m z 123 through 456 type 123 456 Time Range min Specify the upper and lower time limits
204. ys the electronic signature data in the following columns Logon Name Full Name Date and Time Comment Thermo Scientific D XReport Reference Report Objects lon Ratio Confirmation Results Table The Ion Ratio Confirmation Results table displays data about each qualifier ion based on search criteria specified in the processing method Required data file rst Section placement Nonrepeating section This table has the following possible fields Qualifier Ion Mass Qualifier Ion Found e Coelution Passed on Ratio Passed Absolute Window 96 Actual Ion Ratio 96 Target 96 Target Range 96 User Columns 1 to 5 IRC Settings Table The IRC Settings Table displays up to five qualifier ions within tolerance limits to confirm the detection of a target analyte The ions are specified in the processing method Required data file pmd Section placement Nonrepeating section This table has the following possible fields Qualifier Ion mlz Target Ratio 96 Window x96 User Columns 1 to 5 Thermo Scientific XReport User Guide 177 D XReport Reference Report Objects IRC Summary Table The IRC Summary table displays all of the information for the qualifier ion for each component Most useful when the Name column is the first column Required data file rst Section placement Nonrepeating section This table has the following possible fields Component Name RT Mass Response

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