/usr/bin/AccurateMassSearch
/usr/bin/AdditiveSeries
/usr/bin/BaselineFilter
/usr/bin/CompNovoCID
/usr/bin/CompNovo
/usr/bin/ConsensusID
/usr/bin/ConsensusMapNormalizer
/usr/bin/ConvertTraMLToTSV
/usr/bin/ConvertTSVToTraML
/usr/bin/CVInspector
/usr/bin/DBExporter
/usr/bin/DBImporter
/usr/bin/Decharger
/usr/bin/DecoyDatabase
/usr/bin/DeMeanderize
/usr/bin/Digestor
/usr/bin/DigestorMotif
/usr/bin/DTAExtractor
/usr/bin/EICExtractor
/usr/bin/ERPairFinder
/usr/bin/ExecutePipeline
/usr/bin/FalseDiscoveryRate
/usr/bin/FeatureFinderCentroided
/usr/bin/FeatureFinderIsotopeWavelet
/usr/bin/FeatureFinderMetabo
/usr/bin/FeatureFinderMRM
/usr/bin/FeatureFinderRaw
/usr/bin/FeatureFinderSuperHirn
/usr/bin/FeatureLinkerLabeled
/usr/bin/FeatureLinkerUnlabeled
/usr/bin/FeatureLinkerUnlabeledQT
/usr/bin/FFEval
/usr/bin/FileConverter
/usr/bin/FileFilter
/usr/bin/fileinfo
/usr/bin/FileMerger
/usr/bin/FuzzyDiff
/usr/bin/GenericWrapper
/usr/bin/HighResPrecursorMassCorrector
/usr/bin/IDConflictResolver
/usr/bin/IDDecoyProbability
/usr/bin/IDEvaluator
/usr/bin/IDEvaluatorGUI
/usr/bin/IDExtractor
/usr/bin/IDFileConverter
/usr/bin/idfilter
/usr/bin/IDMapper
/usr/bin/IDMassAccuracy
/usr/bin/IDMerger
/usr/bin/IDPosteriorErrorProbability
/usr/bin/IDRipper
/usr/bin/IDRTCalibration
/usr/bin/IDSplitter
/usr/bin/ImageCreator
/usr/bin/InclusionExclusionListCreator
/usr/bin/INIFileEditor
/usr/bin/INIUpdater
/usr/bin/InspectAdapter
/usr/bin/InternalCalibration
/usr/bin/IsobaricAnalyzer
/usr/bin/ITRAQAnalyzer
/usr/bin/LabeledEval
/usr/bin/MapAlignerIdentification
/usr/bin/MapAlignerPoseClustering
/usr/bin/MapAlignerSpectrum
/usr/bin/MapAlignmentEvaluation
/usr/bin/MapNormalizer
/usr/bin/MapRTTransformer
/usr/bin/MapStatistics
/usr/bin/MascotAdapter
/usr/bin/MascotAdapterOnline
/usr/bin/MassCalculator
/usr/bin/MassTraceExtractor
/usr/bin/MRMMapper
/usr/bin/MRMPairFinder
/usr/bin/MSSimulator
/usr/bin/MyriMatchAdapter
/usr/bin/MzTabExporter
/usr/bin/NoiseFilterGaussian
/usr/bin/NoiseFilterSGolay
/usr/bin/OMSSAAdapter
/usr/bin/OpenMSInfo
/usr/bin/OpenSwathAnalyzer
/usr/bin/OpenSwathChromatogramExtractor
/usr/bin/OpenSwathConfidenceScoring
/usr/bin/OpenSwathDecoyGenerator
/usr/bin/OpenSwathDIAPreScoring
/usr/bin/OpenSwathFeatureXMLToTSV
/usr/bin/OpenSwathMzMLFileCacher
/usr/bin/OpenSwathRewriteToFeatureXML
/usr/bin/OpenSwathRTNormalizer
/usr/bin/PeakPickerHiRes
/usr/bin/PeakPickerWavelet
/usr/bin/PepNovoAdapter
/usr/bin/PeptideIndexer
/usr/bin/PhosphoScoring
/usr/bin/PILISIdentification
/usr/bin/PILISModelCV
/usr/bin/PILISModelTrainer
/usr/bin/PILISSpectraGenerator
/usr/bin/PrecursorIonSelector
/usr/bin/PrecursorMassCorrector
/usr/bin/ProteinInference
/usr/bin/ProteinQuantifier
/usr/bin/ProteinResolver
/usr/bin/PTModel
/usr/bin/PTPredict
/usr/bin/QCCalculator
/usr/bin/QCEmbedder
/usr/bin/QCExporter
/usr/bin/QCExtractor
/usr/bin/QCImporter
/usr/bin/QCMerger
/usr/bin/QCShrinker
/usr/bin/Resampler
/usr/bin/RNPxl
/usr/bin/RNPxlXICFilter
/usr/bin/RTEvaluation
/usr/bin/RTModel
/usr/bin/RTPredict
/usr/bin/SeedListGenerator
/usr/bin/SemanticValidator
/usr/bin/SequenceCoverageCalculator
/usr/bin/SILACAnalyzer
/usr/bin/SpecLibCreator
/usr/bin/SpecLibSearcher
/usr/bin/SpectraFilterBernNorm
/usr/bin/SpectraFilterMarkerMower
/usr/bin/SpectraFilterNLargest
/usr/bin/SpectraFilterNormalizer
/usr/bin/SpectraFilterParentPeakMower
/usr/bin/SpectraFilterScaler
/usr/bin/SpectraFilterSqrtMower
/usr/bin/SpectraFilterThresholdMower
/usr/bin/SpectraFilterWindowMower
/usr/bin/SpectraMerger
/usr/bin/SvmTheoreticalSpectrumGeneratorTrainer
/usr/bin/TextExporter
/usr/bin/TMTAnalyzer
/usr/bin/TOFCalibration
/usr/bin/TOPPAS
/usr/bin/TOPPView
/usr/bin/TransformationEvaluation
/usr/bin/XMLValidator
/usr/bin/XTandemAdapter
You may install this package on Debian with
apt-get
install topp