LabKey Server provides a data pipeline for importing and processing mass spectrometry data from raw and mzXML data files. This pipeline manages the chain of processing steps needed to infer protein identifications and expression levels from the output of a mass spec machine. It integrates with leading search engines, including X!Tandem™, Mascot™, and Sequest™, and components of the Trans Proteomic Pipeline™, such as PeptideProphet™, ProteinProphet™ , and XPRESS™.

The data processing pipeline can be configured to apply a series of tools in sequence: for example, after importing MS2 data from raw and mzXML data files, it can search the files for peptides using the X!Tandem search engine against a specified FASTA database. Once the data has been searched and scored, the pipeline optionally runs PeptideProphet, ProteinProphet, or XPRESS quantitation analyses on the search results.

Analyzed results can be dynamically displayed, enabling you to filter, sort, customize, compare, and export experiment runs. You can share data securely with collaborators inside or outside your organization, with fine-grained control over permissions.

Topics

• Discovery Proteomics Tutorial - Import and analyze mzXML files using X!Tandem, SEQUEST, Mascot, or Comet.
• Work with MS2 Data - Detailed documentation for configuring the pipeline and data views.
• Loading Public Protein Annotation Files - Load data from public databases of protein annotations.
• Using Custom Protein Annotations - Load custom annotation data.
• Using ProteinProphet - Run ProteinProphet against MS2 data.
• Using Quantitation Tools - Load quantitation data from XPRESS, Q3, and Libra.
• MaxQuant Module - Import, analyze, and present MaxQuant analysis data.
• Protein Expression Matrix Assay - Working with protein express assays.
• Link Protein Expression Data with Annotations - Join protein expression data with gene and protein annotations.
• Spectra Counts - Export summarized MS2 data from multiple runs.