Open-source platform for the analysis of liquid chromatography-mass spectrometry (LC-MS) data.

The analysis of protein mixtures by liquid chromatography-mass spectrometry (LCMS) requires tools for viewing and navigating LC-MS data, locating peptides in LC-MS data, and eliminating low-quality peptides. msInspect, an open source platform, can carry out these steps for single experiments and can align and normalize peptide features in comparative studies with multiple LC-MS runs. In addition, msInspect can analyze quantitative studies with and without isotopic labels to generate peptide arrays.

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.