MRMPairFinder 

Util which can be used to evaluate labeled pair ratios on MRM features.

OpenSwathAssayGenerator 

Generates assays according to different models for a specific TraML

FeatureFinderMetabo 

Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.

OpenSwathRTNormalizer 

Generate a transformation file on how to transform the RT space into the normalized space given a description of RT peptides and their normalized retention […]

Structure Sketcher 

Sketch a molecular structure

IDFilter 

Filters results from protein or peptide identification engines based on different criteria.