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.