ProteinScape uses Mascot as search engine (other engines are supported via mzIdentML) together with expert algorithms that increase the quality and reliability of protein identifications.
Compiling protein lists for improved search results
The ProteinExtractor compiles multiple peptide lists from a number of different techniques and instruments, significantly improving overall search results and increasing confidence in identifications.
Decoy validation approaches
ProteinScape supports decoy-database approaches to generate protein lists based on defined false-discovery rates.
Posttranslational modifications (PTMs)
Labile modifications like phosphorylation require special fragmentation techniques for optimum analysis. Electron Transfer Dissociation (ETD) fragments peptide backbones, leaving labile PTMs intact. ETD specific annotation in the Spectrum and Sequence viewers enables fast and easy interpretation of ETD analyses.
If the protein sequence is known the database search can be skipped, and a theoretical digest is performed instead with subsequent matching of the theoretical peptide masses to the spectraof an LC-MS/MS dataset. Using theintegrated Sequence Editor, modificationcan be varied in a highly flexible way.