LabKey Server supports running ProteinProphet against MS2 data for analysis. LabKey Server typically runs ProteinProphet automatically as part of protein searches. Alternatively, you can run ProteinProphet outside of LabKey Server and then upload results manually to LabKey Server.


  • Run ProteinProphet automatically within LabKey Server as part of protein searches.
  • Run ProteinProphet outside of LabKey Server and manually uploading results.
    • General Upload Steps
    • Specific Example Upload Steps
  • View ProteinProphet Results Uploaded Manually

Automatically Run ProteinProphet and Load Results via LabKey Server

If you initiate a search for proteins from within your site, LabKey Server will automatically run ProteinProphet for you and load the results.

Run ProteinProphet Outside LabKey Server and Upload Results Manually

You can use LabKey Server functionality on MS2 runs that have been processed previously outside of LabKey Server. You will need to upload processed runs manually to LabKey Server after running ProteinProphet and/or ProteinProphet separately.

General Upload Steps: Set up Files and the Local Directory Structure for Upload

  1. Place the ProteinProphet(protXML), PeptideProphet(pepXML), mzXML and FASTA files into a directory within your Pipeline Root.
  2. Make sure the FASTA file's path is correct in the protXML file. The FASTA file location must be available on the path specified in the file, if it is not available, the import will fail.
  3. Set up the Pipeline. Make sure that the data pipeline for your folder is configured to point to the directory on your file system that contains your ProteinProphet result files. On the Pipeline tab, click the "Process and Upload Data" button and browse to the directory containing your ProteinProphet results.
  4. Import Results. Click on the corresponding "Import ProteinProphet" button. LabKey Server will load the MS2 run from the .pep.xml file, if needed, and associate the ProteinProphet data with it. LabKey Server recognizes protXML and pepXML files as ProteinProphet data.
Note: When you import the ProteinProphet file, it will automatically
  1. Load the PeptideProphet results from the pepXML file
Note: If you use SEQUEST as the search engine, it will produce a *.tgz file. The spectra will be loaded from the *.tgz file if it in the same directory of the pepXML.

Specific Example Upload Steps

This section provides an example of how to upload previously processed results from ProteinProphet. If the pipeline root is set to: i:\S2t, do the following:

  1. Place the pepXML, protXML, mzXML and FASTA file(s) in the directory: i:\S2t
  2. Verify that the path to the FASTA file within the protXML file correctly points to the FASTA file in step #1
  3. In the "MS2 Dashboard > Process and Upload" window, click on the "Import Protein Prophet" button located next to pepXML.

View ProteinProphet Results Uploaded Manually

To view uploaded ProteinProphet results within LabKey Server, navigate to the MS2 run of interest within LabKey Server. If the data imported correctly, there will be a new grouping option, "Protein Prophet". Select one of them to see the protein groups, as well as the indistinguishable proteins in the groups. The expanded view will show you all of the peptides assigned to that group, or you can click to expand individual groups in the collapsed view.

There are additional peptide-level and protein-level columns available in the ProteinProphet views. Click on either the Pick Peptide Columns or Pick Protein Columns buttons to view the full list and choose which ones you want to include.





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