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.

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