Premium Feature — Available with all Premium Editions of LabKey Server. Learn more or contact LabKey.

You can export MS2 data from LabKey Server to several other file types for further analysis and collaboration. You can export data from one or more runs to an Excel file, either from the MS2 Dashboard or from the MS2 Viewer.

Exporting from the MS2 Runs Web Part

  • Navigate to the MS2 Runs web part. If you don't see it, you can add one to any page in an MS2 folder.
  • Select the run or runs to export.
  • Click MS2 Export.
  • Select a saved 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 Export.

Note: 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 View an MS2 Run. If you click Export without picking a view, LabKey Server 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.

Exporting from the MS2 Viewer

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.
  • To select all visible rows, click the box at the top of the checkbox column, then select Export Selected.
  • Click Export All to export all results that match the filter, including those that are not displayed.

Export Formats

You can export to the following formats:

  • Excel (.xlsx
  • TSV
  • Spectra as DTA
  • Spectra as PKL
  • AMT (Accurate Mass & Time) file
  • Bibliospec

Exporting to an Excel file

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. As a result, the exported files could be very large, so use caution when applying your filters. Note that Excel may have limits on the number of rows or columns it is able to import.

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 Spectra as DTA/PKL

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

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 and

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.


See Export Spectra Libraries for details on exporting to a Bibliospec spectrum library.

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