Computational Proteomics Analysis System (CPAS): An Extensible, Open-Source Analytic System for Evaluating and Publishing Proteomic Data and High Throughput Biological Experiments

The open-source Computational Proteomics Analysis System (CPAS) contains an entire data analysis
and management pipeline for Liquid Chromatography Tandem Mass Spectrometry (LC−MS/MS)
proteomics, including experiment annotation, protein database searching and sequence management,
and mining LC−MS/MS peptide and protein identifications. CPAS architecture and features, such as a
general experiment annotation component, installation software, and data security management, make
it useful for collaborative projects across geographical locations and for proteomics laboratories without
substantial computational support.
Keywords: X! Tandem • FuGE • mzXML • pepXML • adenocarcinoma • proteomics