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

An MS2 Runs Browser web part allows a user to see all MS2 runs on the entire server. Project- and folder-level permissions still apply, so the user only sees the runs he or she has permission to view. This web part also provides an easy way to filter, view and export a subset of all of the peptide and protein data available for those runs.

Set Up the Web Part

  • In a folder of type MS2:
  • Enter > Page Admin Mode.
  • Choose MS2 Runs Browser from the <Select Web Part> pulldown in the lower left.
  • Click Add.
  • The new web part is titled MS2 Runs Overview and displays all Folders containing MS2 runs on the server. The count of the number of runs in each folder is also displayed.
  • You can see an example in the proteomics demo folder.

Search Runs

  • Use checkboxes on the Folders containing MS2 runs list to select where to search for runs.
  • Then select the Search Engine Type and the FASTA File from the dropdown menus to the right of the folder list.
  • When you are done selecting filters, click Show Matching MS2 Runs.

Review Matching Runs

  • After you have executed a search, you will see a list of matching runs in the Matching MS2 Runs section of the Runs Overview web part. An example is shown in the screenshot above.

Select Results Filters

  • First use the checkbox to select one or more Matching MS2 Runs to filter. If you click the run name, you will open the results outside of this browser view.
  • Use the checkboxes available in the Result Filters section of the web part to narrow your results.
  • Optionally filter by Probability >= or select specific Charge levels to include.
  • Use the Switch to Proteins/Peptides button to switch between peptides and proteins.
  • Click the Preview Results button when you would like to see the results of your filters. An example is shown in the screenshot below.

Export Runs

  • To export, use the Export Results button at the bottom of the Result Filters section, or the Export button above the Results list.
  • Only your filtered list of results will be exported. Results are exported to an Excel spreadsheet.

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