Proteome Discoverer (v2.0)

Software package for the interpretation and evaluation of mass spectometry-based proteomics data. Within the Proteome Discoverer suite different search engines can be used in combination for more comprehensive sequence database searches. We have integrated the Mascot, Sequest HT and MS Amanda search engines. Besides sequence database-dependent search engines Proteome Discoverer also provides spectral library search options using the MSPepSearch and SpectraST programs. Workflows for quantification by peptide/protein labelling such as iTRAQ, ICAT, TMT or SILAC are supported. Label-free semi-quantitative proteomics can be performed using the Top3 approach or spectrum counts. The Proteome Discoverer software reads RAW, mgf, mzML, mzXML and DTA formats and can convert raw data into different MS data formats.