MetaProSIP 

Performs proteinSIP on peptide features for elemental flux analysis.

MetaboliteAdductDecharger 

Decharges and merges different feature charge variants of the same metabolite.

OrientationJ Measurement Streamable

Extracts the features energy, orientation and coherency from images.

OpenSwathAnalyzer 

Picks peaks and finds features in an SWATH-MS or SRM experiment.

MRMPairFinder 

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

FeatureFinderMetabo 

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

Stereoizer Deprecated

Labels stereochemical features or generates structures based upon the chiral properties of the chiral atoms in the structure.

QCCalculator 

Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.

SeeSAR Interactive GUI 

Use SeeSAR interactively, taking advantage of all its features, namely Inspirator, Molecule Editor, Docking and Analyzer.