Proteome Discoverer Software 2.0
Proteome Discoverer Software 2.0 is proteomics analysis software for analyzing qualitative and quantitative proteomics data. It combines spectral library searching with classical database searching for fast, highly reliable identification of true positive peptide spectrum matches. The software also includes a multi-threaded SEQUEST search engine that takes advantage of the latest computer architecture to accelerate database searches. The software’s peptide and protein false discovery rate and probability (PFDRP) feature provides high-confidence identification of proteins and peptides. High-confidence measurement of phosphorylation sites is provided by PhosphoRS 2.0, included in Proteome Discoverer 2.0. It also generates reports automatically, which is especially useful for large studies where hundreds of files are interpreted.