This tutorial walks you through the process of analyzing tandem mass spectrometry (MS2) data with LabKey proteomics tools. The example represents an experiment identifying proteins associated with peroxisomes in yeast.

To get started using LabKey proteomics tools with MS2 data, you create a project or folder of type MS2, then upload results and supporting files from X!Tandem, Comet, Mascot, or SEQUEST searches. Typically, the search engine native file output format is converted to pepXML format, which may be analyzed by additional tools, or loaded directly into the LabKey Server database.

Tutorial Steps:

• Step 1: Set Up for Proteomics Analysis
• Step 2: Search mzXML Files
• Step 3: View PeptideProphet Results
• Step 4: View ProteinProphet Results
• Step 5: Compare Runs
• Step 6: Search for a Specific Protein

First Step