Study Window parameters - Proteome Discoverer Software - Study Window parameters - Proteome Discoverer Software

Study Window parameters - Proteome Discoverer Software - Study Window parameters - Proteome Discoverer Software - Proteome Discoverer Software

Proteome Discoverer 3.1 User Guide

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User Guide

Software version

3.1

The following table describes the parameters available on the pages of a study.

Study page parameters
Parameter	Description
Command buttons
	Opens the Add Files dialog box so that you can select the files to submit to the processing workflow. You can add RAW, MSF, MGF, MZXML, MZDATA, MZML, and result files. This button is available only when the Input Files page is selected.
	Opens the Add Fraction dialog box so that you can select a series of input spectrum files in any format that are fractions. The formats can be RAW, MGF, MZXML, MZDATA, or MZML. This button is available only when input files are selected on the Input Files page.
	Removes the selected input files from the Input Files page. This button is available only when the Input Files page is selected.
	Opens the folder or folders containing the result file and the MSF file corresponding to a selected analysis result on the Analysis Result page. This button opens the folder or folders in Windows Explorer.
	Opens a new Analysis window.
	Opens Windows Explorer so that you can select a .pdAnalysis file to use as a template.
Study Definition page	Displays basic study information, the quantification method, and study factors.
Study Summary	Displays information about the study.
Study Name	Displays the name of the study that you entered in the Study Name box of the Create New Study/Analysis dialog box.
Study Directory	Displays the directory where the study is located. You entered this location in the Study Root Directory box of the Create New Study/Analysis dialog box.
Last Changed	Displays the date and time that you saved the most recent change.
Creation Date	Displays the time and date that you clicked OK in the New Study and Analysis dialog box to create the study.
Study Description	Displays your description of the study.
Quantification Methods	Displays the quantification methods available for the selected input files in the study.
Study Factors	Displays information about the factors that distinguish two or more samples. Examples of factors are drug treatment; time of drug application; differences in tissue, organism, patient, and so forth; differences in sample preparation, chromatography settings, acquisition parameters; or differences in the isobaric or metabolic labels used.
Paste (Study Factors area)	Pastes the copied study factor box into the Study Factors area and assigns each copy the study factor name and an incrementing number: study_factor1, study_factor2, … study_factor_n. This command is only available after you select the Copy command.
Copy (Study Factors area)	Copies the selected study factor box.
Add (Study Factors area)	Specifies the type of study factor to add to the study. The most common are: Categorical Factor—Adds a new study factor box for a factor that belongs to a non-numerical class. Numeric Factor—Adds a new study factor box for a factor that is numerical in nature.
Input Files page	Lists the input files submitted to the Proteome Discoverer application for the analysis.
ID	Displays the identification number that the Proteome Discoverer application assigns to the raw data file when you add the file to the study. File names begin with an F, and sample names begin with an S.
Name	Displays the name of the raw data file.
File Type	Displays the type of the input file, for example, a raw data file.
Quan Method	Displays the type of quantification performed on the samples. A quantification method specifies the available quantification channels. The Proteome Discoverer application currently supports precursor ion quantification methods using stable isotopes and MS/MS reporter ion quantification methods using isobaric tags. You can specify a quantification method for each of the input files.
Sample Information	Displays information about the samples in the input files, such as the sample type, the acquisition method, and the tissue type.
Samples page	Displays information about the samples contained in the input files.
Sample	Specifies the number of the sample.
Sample Identifier	Specifies the name of the sample.
Sample Type	Displays the sample type associated with a sample for quantification purposes. The sample type can be one of the following: Sample—A specimen from a larger biological entity. Control—A sample typically used as a reference sample in a quantification experiment.
Study_variables	Display the factors that distinguish two or more samples, for example, drug treatment; time of drug application; differences in tissue, organism, or patient; differences in sample preparation, chromatography settings, or acquisition settings; or differences in isobaric or metabolic labels.
Samples page shortcut menu	Displays the following commands when you right-click the Samples page: Copy with Headers—Copies the selected rows and the header captions to the Clipboard. Copy—Copies the selected rows to the Clipboard. Clear Selection—Clears all selected items. Row Selection Mode—Copies cell ranges on the Samples page to the Clipboard. Sample Type To—Sets a sample to one of the following: Sample: A specimen from a larger biological entity. Control: A sample typically used as a reference sample in a quantification experiment. Set Study_factor to—Sets multiple samples to be the same study factor.
Analysis Results page	Displays the results of the search.
	Opens the result file containing the search results for the selected file.
	Repeats the analysis if you change the input files or the workflow used to process the RAW data files. You can change the workflows before rerunning the processing or consensus workflows. All Analysis Steps—Re-performs all the analysis steps. Use Results to Create New (Multi) Consensus—Uses a new consensus workflow to reprocess MSF results associated with one or more result files. Use as Analysis Template—Creates a new analysis using the same sequence steps as that in the analysis result selected in the grid. However, it removes the input files and clears the result file name, if they were automatically generated from the input files.
Search	Specifies the string to search for in the search results listed on the Analysis Results page. Specify the string in the Search box. By default, the application searches only in the File Name and Description columns. If you select the column name from the Search For menu to the right of the Search box, the application searches for the string only in that column.
Search for	Specifies the name of the column to search for the string specified in the Search box.
Execution State	Displays the status of the search producing the results. These status states are the same as those displayed by the job queue. For information on these states, refer to Job queue.
Creation Date	Displays the time and date that the Proteome Discoverer application began the analysis.
File Name	Displays the name of the input file being processed or completed. The application uses the name of the first sample as a default if you do not specify an analysis name.
File Type	Displays the file name extension of the analysis results file, either .msf or .pdResult.
Description	Displays your brief description of the analysis. This description has no relation to any other descriptions already introduced on any other level of the study.
Analysis Results page shortcut menu	Displays the following commands when you right-click the Analysis Results page: Open Result—Performs the same function as on the Analysis Results page; that is, it opens a .pdResult file. Open Containing Folder—Opens the folder containing the files associated with a result. Show Details—Opens an Analysis Sequence Details window, which displays the Workflow Editor and the Analysis window containing the processing and consensus workflows used to generate the selected results file. Reprocess—Performs the same function as on the Analysis Results page; that is, it reprocess MSF results associated with one or more .pdResult files after you change the input files or the workflow used to process the raw data files.
Workflow page	For information on the parameters of the Workflow page, see Workflow Editor Parameters.
Grouping & Quantification page	Displays information about how the application groups quantification ratios and samples.
Study Variables	Specifies the categorical study factors to group samples and quantification ratios by. This area contains check boxes for all the study factors that you selected in the Study Factors Area of the Study Definition page. Files—Groups samples and quantification ratios by files. Quan Channels—Groups samples and quantification ratios by quantification channels. Study_factors—Groups samples and quantification ratios by user-defined study factors. Sample Types—Groups factors that include Sample and Control. Variables displayed in italics contain only a single value.
Manual Ratio Generation	Contains menus where you choose the numerator and denominator for each quantification ratio. Numerator: Specifies the numerator of the quantification ratio. Denominator: Specifies the denominator of the quantification ratio.
Bulk Ratio Generation	Displays the study factor values to use as the denominators for semiautomatically generated quantification ratios.
Generated Sample Groups	Displays samples grouped by the values set for the selected study factors. The application ignores any other differences among the samples that might be present.
Generated Ratios	Displays the quantification ratios generated.