The data pipeline searches and processes LC-MS/MS data and displays the results for analysis. For an environment where multiple users may be processing large runs, it also handles queueing and workflow of jobs.

The pipeline is used for file upload and processing throughout LabKey Server, not just the MS2 tools. For general information on the LabKey Pipeline and links to how it is used by other features, see Data Processing Pipeline. This topic covers additional MS2-specific information on the pipeline.

You can also use the pipeline to import existing analysis results.

Pipeline Searches

You can use the LabKey Server data pipeline to search and process MS/MS run data that's stored in an mzXML file. You can also process pepXML files, which are stored results from a search for peptides on an mzXML file against a protein database. The LabKey Server data pipeline incorporates a number of tools developed as part of the Trans Proteomic Pipeline (TPP) by the Institute for Systems Biology. The data pipeline includes the following tools:

  • The X! Tandem search engine, which searches tandem mass spectra for peptide sequences. You can configure X! Tandem search parameters from within LabKey Server to specify how the search is run.
  • PeptideProphet, which validates peptide assignments made by the search engine, assigning a probability that each result is correct. - ProteinProphet, which validates protein identifications made by the search engine on the basis of peptide assignments.
  • XPRESS, which performs protein quantification.
Using the Pipeline

To experiment with a sample data set, see the Proteomics Tutorial guide and the proteomics demo project.

Additional Pipeline Features

For those who wish to take advantage of the power of a computing cluster, LabKey Server provides the Enterprise Pipeline. Please see the Enterprise Pipeline page for further details.

Note: Please contact LabKey for information about support.

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