You can search for specific proteins in runs that have been loaded into the system.

Specify Your Search

  • Click on the MS2 Dashboard tab at the top of the page.
  • Locate the Protein Search section.
This feature lets you search all your runs in the current folder (and optionally in all the subfolders as well).
  • Enter the name of the protein you want to find in the Protein Name text box. For this tutorial, enter FOX2_YEAST, one of the peroxisomal proteins identified.
  • You can set a minimum ProteinProphet probability or error rate if you like, but for now just leave them blank.
  • Click on Search.

Understand the Results

The results page shows you two lists. Click the "+" next to expand the first list, Matching Proteins.

Matching Proteins, shows all the proteins that LabKey Server knows about that have that name. It will only show proteins that appear in FASTA files that were used for runs in the current folder. However, this top list will show proteins even if they weren't actually found in any of your runs. This helps you validate that you didn't mistype when entering the name.

The second list, Protein Group Results, shows all the ProteinProphet protein groups that contain any of the proteins in the top list. You can see the probability, the run it came from, and so on.

You can use the Customize Grid option under the Grid Views option to add or remove columns from the search results.

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