Exporting from the MS2 Dashboard

• Display the Explore the MS2 Dashboard. Alternatively, add the MS2 Runs (Enhanced) web part to a folder's Portal page.
• Select the run or runs to export.
• Click the Export Runs button at the bottom of the list.
• Select a view to apply to the exported data. The subset of data matching the protein and peptide filters and the sorting and grouping parameters from your selected view will be exported to Excel.
• Select the desired export format.
• Click the Go button.

• Before you export, make sure the view you have applied includes the data you want to export. For more information on setting and saving views, see Viewing an MS2 Run. If you click Go without picking a view, CPAS will attempt to export all data from the run or runs. The export will fail if your runs contain more data than Excel can accommodate.
• If you are currently editing a cell in another spreadsheet, Excel will not open a new spreadsheet. If you export results and Excel does not display them, check for cells that are being edited in your active spreadsheet (press Enter or ESC).

You can choose the set of results to export in one of the following ways:

• Select the individual results you wish to export using the row selectors, and click the Export Selected button.
• Click the Select All button, then the Export Selected button, to export all of the displayed data.
• Click Export All to export all results that match the filter, including those that are not displayed, if the number of results exceeds the number that can be displayed on the page (1000 rows with no grouping, or 250 rows if grouping is in effect).

Export Formats

You can export to the following formats:

• Excel
• TSV
• DTA
• PKL
• AMT

You can export any peptide or protein information displayed on the page to an Excel file to perform further analysis. The MS2 module will export all rows that match the filter, not just the first 1,000 or 250 rows displayed in the Peptides/Proteins section. (Excel exports are limited to 65,535 rows, the maximum that Excel will accept.) As a result, the exported files could be very large, so use caution when applying your filters.

Exporting to a TSV file

You can export data to a TSV (tab-separated values) file to load peptide or protein data into a statistical program for further analysis.

You can only export peptide data to TSV files at this time so you must select Grouping: None in the View section of the page to make the TSV export option available.

Exporting to a DTA/PKL file

You can export data to DTA/PKL files to load MS/MS spectra into other analysis systems such as the online version of Mascot (available at http://www.matrixscience.com).

You can export to DTA/PKL files from any ungrouped list of peptides, but the data must be in runs uploaded through the analysis pipeline. The MS2 module will retrieve the necessary data for these files from the archived tar.gz file on the file server.

For more information, see http://www.matrixscience.com/help/data_file_help.html#DTA and http://www.matrixscience.com/help/data_file_help.html#QTOF.

Exporting to an AMT File

You can export data to the AMT, or Accurate Mass & Time, format. This is a TSV format that exports a fixed set of columns -- Run, Fraction, CalcMHPlus, Scan, RetTime, PepProphet, and Peptide -- plus information about the hydrophobicity algorithm used and names & modifications for each run in the export.