Derived from CPAS. LabKey Server incorporates a robust data pipeline for importing and processing mass spectrometry data from raw and mzXML data files. The pipeline manages the chain of processing steps needed to infer protein identifications and expression levels from the output of a mass spec machine. The pipeline integrates with leading search engines including X!Tandem?, Mascot?, and Sequest?. The pipeline also integrates PeptideProphet?, ProteinProphet? , and XPRESS?, all components of the Trans Proteomic Pipeline? from the Institute for Systems Biology.