Computes a consensus of peptide identifications of several identification engines. Web Documentation for ConsensusID

Estimates the false discovery rate on peptide and protein level using decoy searches. Web Documentation for FalseDiscoveryRate

Runs the protein inference engine Fido. Web Documentation for FidoAdapter

Resolves ambiguous annotations of features with peptide identifications Web Documentation for IDConflictResolver

Converts identification engine file formats. Web Documentation for IDFileConverter

Filters results from protein or peptide identification engines based on different criteria. Web Documentation for IDFilter

Assigns protein/peptide identifications to features or consensus features. Web Documentation for IDMapper

Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. Web D…

Can be used to calibrate RTs of peptide hits linearly to standards. Web Documentation for IDRTCalibration

Modification site localisation using LuciPHOr2. Web Documentation for LuciphorAdapter

Facilitate input to MaRaCluster and reintegrate. Web Documentation for MaRaClusterAdapter

Refreshes the protein references for all peptide hits. Web Documentation for PeptideIndexer

Facilitate input to Percolator and reintegrate. Web Documentation for PercolatorAdapter

Scores potential phosphorylation sites in order to localize the most probable sites. Web Documentation for PhosphoScoring

Calculates false discovery rate estimates on crosslink identifications Web Documentation for XFDR