File menu - Proteome Discoverer Software - File menu - Proteome Discoverer Software

File menu - Proteome Discoverer Software - File menu - Proteome Discoverer Software - Proteome Discoverer Software

Proteome Discoverer 3.1 User Guide

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Ardia Platform > Software > Proteome Discoverer Software

Document Type

User Guide

Software version

3.1

The File menu contains the commands described in the following table.

Command	Function	Shortcut
File > New Study/Analysis	Opens the New Study and Analysis dialog box so that you can create a study. For more information, see Create a study.
File > Open Study	Opens the Open Study dialog box so that you can open an existing study (filename.pdStudy file).
File > Open Result	Opens the Select Result File dialog box so that you can select a result file to open.
File > Close	Closes any open window in the application, such as a report window, the Start Page, or a study.
File > Save	Saves the all the changes that you made to a report or a study.
File > Save All	Saves all the studies open in the application.	CTRL+SHIFT+S
File > Export	Opens a menu with commands that export spectra; export annotated spectra; export search result rows to a ProtXML file, a PepXML file, and a tab-delimited TXT file; export the proteins in the search results to a FASTA file; and export mass lists to text files.
File > Export > Study	Opens the Export Study dialog box to export the sample information to a study definition file. For more information, see Export study information to a study definition file.
File > Export > Spectra	Opens the Export Spectra dialog box so that you can export specified spectra. For information, see Export Spectra.
File > Export > Annotated Spectra	Opens the Export Annotated Spectra dialog box (Export Annotated Spectra dialog box) so that you can export spectra annotated with observed masses and fragment assignments in a ZIP file. For information, see Export annotated spectra.
File > Export > To Text (Tab Delimited)	Opens the Export To Text (Tab Delimited) dialog box so that you can export search results to a tab-delimited TXT file. For information, see Export search results to a Tab-Delimited TXT file.
File > Export > To Microsoft Excel	Opens the Export to Excel dialog box so that you can export search results to Excel workbooks. For more information, see Export search results to Excel workbooks.
File > Export > To PepXML	Opens the Export To PepXML dialog box so that you can export to an XML file peptides that are included in the results of searches performed by the Sequest HT and Mascot search engines. For information, see Export search results in PepXML format.
File > Export > To ProtXML	Opens the Export to ProtXML dialog box so that you can export selected search result rows to an XML file. For information, see Export search results in ProtXML format.
File > Export > To mzIdentML	Opens the Export to MzIdentML dialog box so that you can export selected proteins to an MZID file. For information about exporting proteins to an MZID file, see Export search results in mzIdentML format.
File > Export > To mzTab	Opens the Export to mzTab dialog box so that you can export protein identification and quantification results to an mzTab-format file. For information, see Export search results in mzTab format.
File > Export > To FASTA	Opens the Export to FASTA dialog box so that you can export the protein sequences, accession numbers, and descriptions in the search results to a FASTA file. For information, see Export protein references to a FASTA file.
File > Export > LTQ Orbitrap Mass List	Opens the Export LTQ Orbitrap Mass List dialog box so that you can export mass lists compatible with the LTQ Orbitrap family of instruments. For information, see Export mass lists.
File > Export > Q Exactive Mass List	Opens the Export Q Exactive Mass List dialog box so that you can export mass lists compatible with the Q Exactive family of instruments. For information, see Export mass lists.
File > Export > Orbitrap Fusion Mass List	Opens the Export Orbitrap Fusion Mass List dialog box so that you can export mass lists compatible with the Orbitrap Fusion family of instruments. For information, see Export mass lists.
File > Recent Studies	Displays the names of the 20 most recently opened studies.
File > Recent Studies > Clear Recent Study List	Removes the names of the .pdStudy files that appear on the Start Page when you choose File > Recent Results.
File > Recent Results	Displays the names of the 20 most recently opened result files.
File > Recent Results > Clear Recent File List	Removes the names of the result files that appear on the Start Page when you choose File > Recent Results.
File > Exit	Closes all opened views and reports without saving any changes before closing the application.