Creates inclusion and/or exclusion lists. Web Documentation for InclusionExclusionListCreator

MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML) Web Documentation for MRMMapper

Picks peaks and finds features in an SWATH-MS or SRM experiment. Web Documentation for OpenSwathAnalyzer

Generates assays according to different models for a specific TraML Web Documentation for OpenSwathAssayGenerator

Extract chromatograms (XIC) from a MS2 map file. Web Documentation for OpenSwathChromatogramExtractor

Compute confidence scores for OpenSwath results Web Documentation for OpenSwathConfidenceScoring

Scoring spectra using the DIA scores. Web Documentation for OpenSwathDIAPreScoring

Generates decoys according to different models for a specific TraML Web Documentation for OpenSwathDecoyGenerator

Converts a featureXML to a mProphet tsv. Web Documentation for OpenSwathFeatureXMLToTSV

Splits SWATH files into n files, each containing one window. Web Documentation for OpenSwathFileSplitter

This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to…

Combines featureXML and mProphet tsv to FDR filtered featureXML. Web Documentation for OpenSwathRewriteToFeatureXML

PrecursorIonSelector Web Documentation for PrecursorIonSelector

Converts different transition files for targeted proteomics / metabolomics analysis. Web Documentation for TargetedFileConverter