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| 16 | Initiative·(PSI)·formats·for·MS·data·and·supports·easy·integration·of | 16 | Initiative·(PSI)·formats·for·MS·data·and·supports·easy·integration·of |
| 17 | tools·into·workflow·engines·like·Knime,·Galaxy,·WS-Pgrade,·and·TOPPAS | 17 | tools·into·workflow·engines·like·Knime,·Galaxy,·WS-Pgrade,·and·TOPPAS |
| 18 | via·the·TOPPtools·concept·and·a·unified·parameter·handling. | 18 | via·the·TOPPtools·concept·and·a·unified·parameter·handling. |
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| 19 | .SH·"AVAILABLE·MODULES" | 19 | .SH·"AVAILABLE·MODULES" |
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| 20 | \fBAccurateMassSearch\fR·--·Match·MS·signals·to·molecules·from·a·database·by·mass. | 20 | \\fBAccurateMassSearch\\fR·--·Match·MS·signals·to·molecules·from·a·database·by·mass. |
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| 21 | \fBAssayGeneratorMetabo\fR·--·Assay·library·generation·from·DDA·data·(Metabolomics). | 21 | \\fBAssayGeneratorMetabo\\fR·--·Assay·library·generation·from·DDA·data·(Metabolomics). |
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| 22 | \fBBaselineFilter\fR·--·Removes·the·baseline·from·profile·spectra·using·a·top-hat·filter. | 22 | \\fBBaselineFilter\\fR·--·Removes·the·baseline·from·profile·spectra·using·a·top-hat·filter. |
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| 23 | \fBCVInspector\fR·--·A·tool·for·visualization·and·validation·of·PSI·mapping·and·CV·files. | 23 | \\fBCVInspector\\fR·--·A·tool·for·visualization·and·validation·of·PSI·mapping·and·CV·files. |
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| 24 | \fBClusterMassTraces\fR·--·Creates·pseudo·spectra. | 24 | \\fBClusterMassTraces\\fR·--·Creates·pseudo·spectra. |
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| 25 | \fBClusterMassTracesByPrecursor\fR·--·Correlate·precursor·masstraces·with·fragment·ion·masstraces·in·SWATH·maps·based·on·their·elution·profile. | 25 | \\fBClusterMassTracesByPrecursor\\fR·--·Correlate·precursor·masstraces·with·fragment·ion·masstraces·in·SWATH·maps·based·on·their·elution·profile. |
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| 26 | \fBCometAdapter\fR·--·Annotates·MS/MS·spectra·using·Comet. | 26 | \\fBCometAdapter\\fR·--·Annotates·MS/MS·spectra·using·Comet. |
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| 27 | \fBCompNovo\fR·--·Performs·a·de·novo·peptide·identification·using·the·CompNovo·engine. | 27 | \\fBCompNovo\\fR·--·Performs·a·de·novo·peptide·identification·using·the·CompNovo·engine. |
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| 28 | \fBCompNovoCID\fR·--·Performs·a·de·novo·peptide·identification·using·the·CompNovo·engine. | 28 | \\fBCompNovoCID\\fR·--·Performs·a·de·novo·peptide·identification·using·the·CompNovo·engine. |
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| 29 | \fBConsensusID\fR·--·Computes·a·consensus·of·peptide·identifications·of·several·identification·engines. | 29 | \\fBConsensusID\\fR·--·Computes·a·consensus·of·peptide·identifications·of·several·identification·engines. |
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| 30 | \fBConsensusMapNormalizer\fR·--·Normalizes·maps·of·one·consensusXML·file. | 30 | \\fBConsensusMapNormalizer\\fR·--·Normalizes·maps·of·one·consensusXML·file. |
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| 31 | \fBCruxAdapter\fR·--·Identifies·MS/MS·spectra·using·Crux. | 31 | \\fBCruxAdapter\\fR·--·Identifies·MS/MS·spectra·using·Crux. |
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| 32 | \fBDTAExtractor\fR·--·Extracts·spectra·of·an·MS·run·file·to·several·files·in·DTA·format. | 32 | \\fBDTAExtractor\\fR·--·Extracts·spectra·of·an·MS·run·file·to·several·files·in·DTA·format. |
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| 33 | \fBDatabaseFilter\fR·--·Filters·a·protein·database·(FASTA·format)·based·on·identified·proteins. | 33 | \\fBDatabaseFilter\\fR·--·Filters·a·protein·database·(FASTA·format)·based·on·identified·proteins. |
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| 34 | \fBDatabaseSuitability\fR·--·Computes·a·suitability·score·for·a·database·which·was·used·for·a·peptide·identification·search.·Also·reports·the·quality·of·LC-MS·spectra. | 34 | \\fBDatabaseSuitability\\fR·--·Computes·a·suitability·score·for·a·database·which·was·used·for·a·peptide·identification·search.·Also·reports·the·quality·of·LC-MS·spectra. |
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| 35 | \fBDeMeanderize\fR·--·Orders·the·spectra·of·MALDI·spotting·plates·correctly. | 35 | \\fBDeMeanderize\\fR·--·Orders·the·spectra·of·MALDI·spotting·plates·correctly. |
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| 36 | \fBDecharger\fR·--·Decharges·and·merges·different·feature·charge·variants·of·the·same·peptide. | 36 | \\fBDecharger\\fR·--·Decharges·and·merges·different·feature·charge·variants·of·the·same·peptide. |
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| 37 | \fBDecoyDatabase\fR·--·Create·decoy·sequence·database·from·forward·sequence·database. | 37 | \\fBDecoyDatabase\\fR·--·Create·decoy·sequence·database·from·forward·sequence·database. |
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| 38 | \fBDigestor\fR·--·Digests·a·protein·database·in-silico. | 38 | \\fBDigestor\\fR·--·Digests·a·protein·database·in-silico. |
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| 39 | \fBDigestorMotif\fR·--·digests·a·protein·database·in-silico. | 39 | \\fBDigestorMotif\\fR·--·digests·a·protein·database·in-silico. |
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| 40 | \fBEICExtractor\fR·--·Extracts·intensities·from·dedicates·positions·in·a·LC/MS·map. | 40 | \\fBEICExtractor\\fR·--·Extracts·intensities·from·dedicates·positions·in·a·LC/MS·map. |
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| 41 | \fBERPairFinder\fR·--·Util·which·can·be·used·to·evaluate·pair·ratios·on·enhanced·resolution·(zoom)·scans. | 41 | \\fBERPairFinder\\fR·--·Util·which·can·be·used·to·evaluate·pair·ratios·on·enhanced·resolution·(zoom)·scans. |
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| 42 | \fBEpifany\fR·--·Runs·a·Bayesian·protein·inference. | 42 | \\fBEpifany\\fR·--·Runs·a·Bayesian·protein·inference. |
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| 43 | \fBExecutePipeline\fR·--·Executes·workflows·created·by·TOPPAS. | 43 | \\fBExecutePipeline\\fR·--·Executes·workflows·created·by·TOPPAS. |
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| 44 | \fBExternalCalibration\fR·--·Applies·an·external·mass·recalibration. | 44 | \\fBExternalCalibration\\fR·--·Applies·an·external·mass·recalibration. |
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| 45 | \fBFFEval\fR·--·Evaluation·tool·for·feature·detection·algorithms. | 45 | \\fBFFEval\\fR·--·Evaluation·tool·for·feature·detection·algorithms. |
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| 46 | \fBFalseDiscoveryRate\fR·--·Estimates·the·false·discovery·rate·on·peptide·and·protein·level·using·decoy·searches. | 46 | \\fBFalseDiscoveryRate\\fR·--·Estimates·the·false·discovery·rate·on·peptide·and·protein·level·using·decoy·searches. |
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| 47 | \fBFeatureFinderCentroided\fR·--·Detects·two-dimensional·features·in·LC-MS·data. | 47 | \\fBFeatureFinderCentroided\\fR·--·Detects·two-dimensional·features·in·LC-MS·data. |
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| 48 | \fBFeatureFinderIdentification\fR·--·Detects·features·in·MS1·data·based·on·peptide·identifications. | 48 | \\fBFeatureFinderIdentification\\fR·--·Detects·features·in·MS1·data·based·on·peptide·identifications. |
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| 49 | \fBFeatureFinderIsotopeWavelet\fR·--·Detects·two-dimensional·features·in·LC-MS·data. | 49 | \\fBFeatureFinderIsotopeWavelet\\fR·--·Detects·two-dimensional·features·in·LC-MS·data. |
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| 50 | \fBFeatureFinderMRM\fR·--·Detects·two-dimensional·features·in·LC-MS·data. | 50 | \\fBFeatureFinderMRM\\fR·--·Detects·two-dimensional·features·in·LC-MS·data. |
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| 51 | \fBFeatureFinderMetabo\fR·--·Assembles·metabolite·features·from·centroided·(LC-)MS·data·using·the·mass·trace·approach. | 51 | \\fBFeatureFinderMetabo\\fR·--·Assembles·metabolite·features·from·centroided·(LC-)MS·data·using·the·mass·trace·approach. |
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| 52 | \fBFeatureFinderMetaboIdent\fR·--·Detects·features·in·MS1·data·based·on·metabolite·identifications. | 52 | \\fBFeatureFinderMetaboIdent\\fR·--·Detects·features·in·MS1·data·based·on·metabolite·identifications. |
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| 53 | \fBFeatureFinderMultiplex\fR·--·Determination·of·peak·ratios·in·LC-MS·data. | 53 | \\fBFeatureFinderMultiplex\\fR·--·Determination·of·peak·ratios·in·LC-MS·data. |
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| 54 | \fBFeatureFinderSuperHirn\fR·--·Finds·mass·spectrometric·features·in·mass·spectra. | 54 | \\fBFeatureFinderSuperHirn\\fR·--·Finds·mass·spectrometric·features·in·mass·spectra. |
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| 55 | \fBFeatureLinkerLabeled\fR·--·Groups·corresponding·isotope-labeled·features·in·a·feature·map. | 55 | \\fBFeatureLinkerLabeled\\fR·--·Groups·corresponding·isotope-labeled·features·in·a·feature·map. |
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| 56 | \fBFeatureLinkerUnlabeled\fR·--·Groups·corresponding·features·from·multiple·maps. | 56 | \\fBFeatureLinkerUnlabeled\\fR·--·Groups·corresponding·features·from·multiple·maps. |
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| 57 | \fBFeatureLinkerUnlabeledKD\fR·--·Groups·corresponding·features·from·multiple·maps. | 57 | \\fBFeatureLinkerUnlabeledKD\\fR·--·Groups·corresponding·features·from·multiple·maps. |
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| 58 | \fBFeatureLinkerUnlabeledQT\fR·--·Groups·corresponding·features·from·multiple·maps. | 58 | \\fBFeatureLinkerUnlabeledQT\\fR·--·Groups·corresponding·features·from·multiple·maps. |
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| 59 | \fBFidoAdapter\fR·--·Runs·the·protein·inference·engine·Fido. | 59 | \\fBFidoAdapter\\fR·--·Runs·the·protein·inference·engine·Fido. |
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| 60 | \fBFileConverter\fR·--·Converts·between·different·MS·file·formats. | 60 | \\fBFileConverter\\fR·--·Converts·between·different·MS·file·formats. |
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| 61 | \fBFileFilter\fR·--·Extracts·or·manipulates·portions·of·data·from·peak,·feature·or·consensus-feature·files. | 61 | \\fBFileFilter\\fR·--·Extracts·or·manipulates·portions·of·data·from·peak,·feature·or·consensus-feature·files. |
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| 62 | \fBFileInfo\fR·--·Shows·basic·information·about·the·file,·such·as·data·ranges·and·file·type. | 62 | \\fBFileInfo\\fR·--·Shows·basic·information·about·the·file,·such·as·data·ranges·and·file·type. |
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| 63 | \fBFileMerger\fR·--·Merges·several·MS·files·into·one·file. | 63 | \\fBFileMerger\\fR·--·Merges·several·MS·files·into·one·file. |
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| 64 | \fBFuzzyDiff\fR·--·Compares·two·files,·tolerating·numeric·differences. | 64 | \\fBFuzzyDiff\\fR·--·Compares·two·files,·tolerating·numeric·differences. |
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| 65 | \fBGNPSExport\fR·--·Tool·to·export·consensus·features·into·MGF·format. | 65 | \\fBGNPSExport\\fR·--·Tool·to·export·consensus·features·into·MGF·format. |
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| 66 | \fBGenericWrapper\fR·--·Allows·the·generic·wrapping·of·external·tools. | 66 | \\fBGenericWrapper\\fR·--·Allows·the·generic·wrapping·of·external·tools. |
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| 67 | \fBHighResPrecursorMassCorrector\fR·--·Corrects·the·precursor·mass·and·charge·determined·by·the·instrument·software. | 67 | \\fBHighResPrecursorMassCorrector\\fR·--·Corrects·the·precursor·mass·and·charge·determined·by·the·instrument·software. |
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| 68 | \fBIDConflictResolver\fR·--·Resolves·ambiguous·annotations·of·features·with·peptide·identifications. | 68 | \\fBIDConflictResolver\\fR·--·Resolves·ambiguous·annotations·of·features·with·peptide·identifications. |
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| 69 | \fBIDDecoyProbability\fR·--·Estimates·peptide·probabilities·using·a·decoy·search·strategy. | 69 | \\fBIDDecoyProbability\\fR·--·Estimates·peptide·probabilities·using·a·decoy·search·strategy. |
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| 70 | \fBIDExtractor\fR·--·Extracts·'n'·peptides·randomly·or·best·'n'·from·idXML·files. | 70 | \\fBIDExtractor\\fR·--·Extracts·'n'·peptides·randomly·or·best·'n'·from·idXML·files. |
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| 71 | \fBIDFileConverter\fR·--·Converts·identification·engine·file·formats. | 71 | \\fBIDFileConverter\\fR·--·Converts·identification·engine·file·formats. |
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| 72 | \fBIDFilter\fR·--·Filters·results·from·protein·or·peptide·identification·engines·based·on·different·criteria. | 72 | \\fBIDFilter\\fR·--·Filters·results·from·protein·or·peptide·identification·engines·based·on·different·criteria. |
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| 73 | \fBIDMapper\fR·--·Assigns·protein/peptide·identifications·to·features·or·consensus·features. | 73 | \\fBIDMapper\\fR·--·Assigns·protein/peptide·identifications·to·features·or·consensus·features. |
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| 74 | \fBIDMassAccuracy\fR·--·Calculates·a·distribution·of·the·mass·error·from·given·mass·spectra·and·IDs. | 74 | \\fBIDMassAccuracy\\fR·--·Calculates·a·distribution·of·the·mass·error·from·given·mass·spectra·and·IDs. |
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| 75 | \fBIDMerger\fR·--·Merges·several·protein/peptide·identification·files·into·one·file. | 75 | \\fBIDMerger\\fR·--·Merges·several·protein/peptide·identification·files·into·one·file. |
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| 76 | \fBIDPosteriorErrorProbability\fR·--·Estimates·probabilities·for·incorrectly·assigned·peptide·sequences·and·a·set·of·search·engine·scores·using·a·mixture·model. | 76 | \\fBIDPosteriorErrorProbability\\fR·--·Estimates·probabilities·for·incorrectly·assigned·peptide·sequences·and·a·set·of·search·engine·scores·using·a·mixture·model. |
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| 77 | \fBIDRTCalibration\fR·--·Can·be·used·to·calibrate·RTs·of·peptide·hits·linearly·to·standards. | 77 | \\fBIDRTCalibration\\fR·--·Can·be·used·to·calibrate·RTs·of·peptide·hits·linearly·to·standards. |
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| 78 | \fBIDRipper\fR·--·Split·protein/peptide·identification·file·into·several·files·according·to·annotated·file·origin. | 78 | \\fBIDRipper\\fR·--·Split·protein/peptide·identification·file·into·several·files·according·to·annotated·file·origin. |
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| 79 | \fBIDScoreSwitcher\fR·--·Switches·between·different·scores·of·peptide·or·protein·hits·in·identification·data. | 79 | \\fBIDScoreSwitcher\\fR·--·Switches·between·different·scores·of·peptide·or·protein·hits·in·identification·data. |
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