LabKey Server allows you to quickly search for specific peptide identifications within the search results that have been loaded into a folder.

Performing a Peptide Search

There are a number of different places where you can initiate a search. Your folder dashboard may already have a Peptide Search web part, or if it does not you can add one yourself.

You can also use a Mass Spec Search web part that has a tab for peptide search (alongside another for protein searches).

In some configurations, there may be a Manage Peptide Inventory web part configured to allow searching and pooling of peptides.

Type in the peptide sequence to find. You may include modification characters if you wish. If you select the Exact matches only checkbox, your results will only include peptides that match the exact peptide sequence, including modification characters.

Understanding the Search Results

The results page shows all of the peptide identifications that match the search criteria. You can apply filters, click to see the details for the peptide ID, customize the view to add or remove columns, or export them for analysis in other tools. Matches from the peptide data in the MS2 module and/or Panorama will be shown based on your folder type.

MS2 Runs With Peptide Counts

The MS2Extensions module contains an additional MS2 Runs With Peptide Counts web part offering enhanced protein search capabilities, including filtering by multiple proteins simultaneously and the ability to focus on high-scoring identifications by using peptide filters.

The ms2extensions module is open source, but not shipped with the standard distribution. Contact us if you are interested in obtaining it.

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