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2 ·09492b3ccb638ace8f786fc56ddff8f9·880308·libdevel·optional·libopenms-dev_2.6.0+cleaned1-3_amd64.deb2 ·09492b3ccb638ace8f786fc56ddff8f9·880308·libdevel·optional·libopenms-dev_2.6.0+cleaned1-3_amd64.deb
3 ·ccd85a1a320c91047804a49e8286c62a·230656320·debug·optional·libopenms2.6.0-dbgsym_2.6.0+cleaned1-3_amd64.deb3 ·ccd85a1a320c91047804a49e8286c62a·230656320·debug·optional·libopenms2.6.0-dbgsym_2.6.0+cleaned1-3_amd64.deb
4 ·cad7d3cb4d7c17bbbe7a21440ecc6308·8004824·libs·optional·libopenms2.6.0_2.6.0+cleaned1-3_amd64.deb4 ·cad7d3cb4d7c17bbbe7a21440ecc6308·8004824·libs·optional·libopenms2.6.0_2.6.0+cleaned1-3_amd64.deb
5 ·7c8823ac90482fa1dcfcbf64ed689035·4291440·science·optional·openms-common_2.6.0+cleaned1-3_all.deb5 ·7c8823ac90482fa1dcfcbf64ed689035·4291440·science·optional·openms-common_2.6.0+cleaned1-3_all.deb
6 ·78ae9ae76a5a3e4db93e0e2703d6f293·42967712·doc·optional·openms-doc_2.6.0+cleaned1-3_all.deb6 ·78ae9ae76a5a3e4db93e0e2703d6f293·42967712·doc·optional·openms-doc_2.6.0+cleaned1-3_all.deb
7 ·a02db9284ab511463b401504c3cf6c2c·53520·science·optional·openms_2.6.0+cleaned1-3_all.deb7 ·a02db9284ab511463b401504c3cf6c2c·53520·science·optional·openms_2.6.0+cleaned1-3_all.deb
8 ·32d5d88738ccb3610cab51835de1ece7·88756244·debug·optional·topp-dbgsym_2.6.0+cleaned1-3_amd64.deb8 ·32d5d88738ccb3610cab51835de1ece7·88756244·debug·optional·topp-dbgsym_2.6.0+cleaned1-3_amd64.deb
9 ·37dfec745a2c245396eb9a3991a94bfb·3119656·science·optional·topp_2.6.0+cleaned1-3_amd64.deb9 ·07f8e9409364b62fc2dcec7dfd50fd72·3119664·science·optional·topp_2.6.0+cleaned1-3_amd64.deb
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topp_2.6.0+cleaned1-3_amd64.deb
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190 -rw-r--r--···0·root·········(0)·root·········(0)····38745·2020-10-01·13:46:20.000000·./usr/share/doc/topp/changelog.gz190 -rw-r--r--···0·root·········(0)·root·········(0)····38745·2020-10-01·13:46:20.000000·./usr/share/doc/topp/changelog.gz
191 -rw-r--r--···0·root·········(0)·root·········(0)····31665·2021-03-02·07:20:17.000000·./usr/share/doc/topp/copyright191 -rw-r--r--···0·root·········(0)·root·········(0)····31665·2021-03-02·07:20:17.000000·./usr/share/doc/topp/copyright
192 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-02·07:20:17.000000·./usr/share/lintian/192 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-02·07:20:17.000000·./usr/share/lintian/
193 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-02·07:20:17.000000·./usr/share/lintian/overrides/193 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-02·07:20:17.000000·./usr/share/lintian/overrides/
194 -rw-r--r--···0·root·········(0)·root·········(0)·······26·2021-03-02·07:20:17.000000·./usr/share/lintian/overrides/topp194 -rw-r--r--···0·root·········(0)·root·········(0)·······26·2021-03-02·07:20:17.000000·./usr/share/lintian/overrides/topp
195 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-02·07:20:17.000000·./usr/share/man/195 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-02·07:20:17.000000·./usr/share/man/
196 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-02·07:20:17.000000·./usr/share/man/man1/196 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-02·07:20:17.000000·./usr/share/man/man1/
197 -rw-r--r--···0·root·········(0)·root·········(0)·····5917·2021-03-02·07:20:17.000000·./usr/share/man/man1/topp.1.gz197 -rw-r--r--···0·root·········(0)·root·········(0)·····5940·2021-03-02·07:20:17.000000·./usr/share/man/man1/topp.1.gz
198 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-02·07:20:17.000000·./usr/share/metainfo/198 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-02·07:20:17.000000·./usr/share/metainfo/
199 -rw-r--r--···0·root·········(0)·root·········(0)·····1413·2020-10-01·13:46:20.000000·./usr/share/metainfo/TOPPAS.appdata.xml199 -rw-r--r--···0·root·········(0)·root·········(0)·····1413·2020-10-01·13:46:20.000000·./usr/share/metainfo/TOPPAS.appdata.xml
200 -rw-r--r--···0·root·········(0)·root·········(0)·····1709·2020-10-01·13:46:20.000000·./usr/share/metainfo/TOPPView.appdata.xml200 -rw-r--r--···0·root·········(0)·root·········(0)·····1709·2020-10-01·13:46:20.000000·./usr/share/metainfo/TOPPView.appdata.xml
201 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-02·07:20:17.000000·./usr/share/pixmaps/201 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-02·07:20:17.000000·./usr/share/pixmaps/
202 -rw-r--r--···0·root·········(0)·root·········(0)·····5833·2021-03-02·07:20:17.000000·./usr/share/pixmaps/TOPPAS.xpm202 -rw-r--r--···0·root·········(0)·root·········(0)·····5833·2021-03-02·07:20:17.000000·./usr/share/pixmaps/TOPPAS.xpm
203 -rw-r--r--···0·root·········(0)·root·········(0)·····6142·2021-03-02·07:20:17.000000·./usr/share/pixmaps/TOPPView.xpm203 -rw-r--r--···0·root·········(0)·root·········(0)·····6142·2021-03-02·07:20:17.000000·./usr/share/pixmaps/TOPPView.xpm
204 lrwxrwxrwx···0·root·········(0)·root·········(0)········0·2021-03-02·07:20:17.000000·./usr/share/man/man1/AccurateMassSearch.1.gz·->·topp.1.gz204 lrwxrwxrwx···0·root·········(0)·root·········(0)········0·2021-03-02·07:20:17.000000·./usr/share/man/man1/AccurateMassSearch.1.gz·->·topp.1.gz
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16 Initiative·(PSI)·formats·for·MS·data·and·supports·easy·integration·of16 Initiative·(PSI)·formats·for·MS·data·and·supports·easy·integration·of
17 tools·into·workflow·engines·like·Knime,·Galaxy,·WS-Pgrade,·and·TOPPAS17 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.
  
19 .SH·"AVAILABLE·MODULES"19 .SH·"AVAILABLE·MODULES"
  
  
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.
  
21 \fBAssayGeneratorMetabo\fR·--·Assay·library·generation·from·DDA·data·(Metabolomics).21 \\fBAssayGeneratorMetabo\\fR·--·Assay·library·generation·from·DDA·data·(Metabolomics).
  
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.
  
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.
  
24 \fBClusterMassTraces\fR·--·Creates·pseudo·spectra.24 \\fBClusterMassTraces\\fR·--·Creates·pseudo·spectra.
  
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.
  
26 \fBCometAdapter\fR·--·Annotates·MS/MS·spectra·using·Comet.26 \\fBCometAdapter\\fR·--·Annotates·MS/MS·spectra·using·Comet.
  
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.
  
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.
  
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.
  
30 \fBConsensusMapNormalizer\fR·--·Normalizes·maps·of·one·consensusXML·file.30 \\fBConsensusMapNormalizer\\fR·--·Normalizes·maps·of·one·consensusXML·file.
  
31 \fBCruxAdapter\fR·--·Identifies·MS/MS·spectra·using·Crux.31 \\fBCruxAdapter\\fR·--·Identifies·MS/MS·spectra·using·Crux.
  
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.
  
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.
  
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.
  
35 \fBDeMeanderize\fR·--·Orders·the·spectra·of·MALDI·spotting·plates·correctly.35 \\fBDeMeanderize\\fR·--·Orders·the·spectra·of·MALDI·spotting·plates·correctly.
  
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.
  
37 \fBDecoyDatabase\fR·--·Create·decoy·sequence·database·from·forward·sequence·database.37 \\fBDecoyDatabase\\fR·--·Create·decoy·sequence·database·from·forward·sequence·database.
  
38 \fBDigestor\fR·--·Digests·a·protein·database·in-silico.38 \\fBDigestor\\fR·--·Digests·a·protein·database·in-silico.
  
39 \fBDigestorMotif\fR·--·digests·a·protein·database·in-silico.39 \\fBDigestorMotif\\fR·--·digests·a·protein·database·in-silico.
  
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.
  
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.
  
42 \fBEpifany\fR·--·Runs·a·Bayesian·protein·inference.42 \\fBEpifany\\fR·--·Runs·a·Bayesian·protein·inference.
  
43 \fBExecutePipeline\fR·--·Executes·workflows·created·by·TOPPAS.43 \\fBExecutePipeline\\fR·--·Executes·workflows·created·by·TOPPAS.
  
44 \fBExternalCalibration\fR·--·Applies·an·external·mass·recalibration.44 \\fBExternalCalibration\\fR·--·Applies·an·external·mass·recalibration.
  
45 \fBFFEval\fR·--·Evaluation·tool·for·feature·detection·algorithms.45 \\fBFFEval\\fR·--·Evaluation·tool·for·feature·detection·algorithms.
  
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.
  
47 \fBFeatureFinderCentroided\fR·--·Detects·two-dimensional·features·in·LC-MS·data.47 \\fBFeatureFinderCentroided\\fR·--·Detects·two-dimensional·features·in·LC-MS·data.
  
48 \fBFeatureFinderIdentification\fR·--·Detects·features·in·MS1·data·based·on·peptide·identifications.48 \\fBFeatureFinderIdentification\\fR·--·Detects·features·in·MS1·data·based·on·peptide·identifications.
  
49 \fBFeatureFinderIsotopeWavelet\fR·--·Detects·two-dimensional·features·in·LC-MS·data.49 \\fBFeatureFinderIsotopeWavelet\\fR·--·Detects·two-dimensional·features·in·LC-MS·data.
  
50 \fBFeatureFinderMRM\fR·--·Detects·two-dimensional·features·in·LC-MS·data.50 \\fBFeatureFinderMRM\\fR·--·Detects·two-dimensional·features·in·LC-MS·data.
  
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.
  
52 \fBFeatureFinderMetaboIdent\fR·--·Detects·features·in·MS1·data·based·on·metabolite·identifications.52 \\fBFeatureFinderMetaboIdent\\fR·--·Detects·features·in·MS1·data·based·on·metabolite·identifications.
  
53 \fBFeatureFinderMultiplex\fR·--·Determination·of·peak·ratios·in·LC-MS·data.53 \\fBFeatureFinderMultiplex\\fR·--·Determination·of·peak·ratios·in·LC-MS·data.
  
54 \fBFeatureFinderSuperHirn\fR·--·Finds·mass·spectrometric·features·in·mass·spectra.54 \\fBFeatureFinderSuperHirn\\fR·--·Finds·mass·spectrometric·features·in·mass·spectra.
  
55 \fBFeatureLinkerLabeled\fR·--·Groups·corresponding·isotope-labeled·features·in·a·feature·map.55 \\fBFeatureLinkerLabeled\\fR·--·Groups·corresponding·isotope-labeled·features·in·a·feature·map.
  
56 \fBFeatureLinkerUnlabeled\fR·--·Groups·corresponding·features·from·multiple·maps.56 \\fBFeatureLinkerUnlabeled\\fR·--·Groups·corresponding·features·from·multiple·maps.
  
57 \fBFeatureLinkerUnlabeledKD\fR·--·Groups·corresponding·features·from·multiple·maps.57 \\fBFeatureLinkerUnlabeledKD\\fR·--·Groups·corresponding·features·from·multiple·maps.
  
58 \fBFeatureLinkerUnlabeledQT\fR·--·Groups·corresponding·features·from·multiple·maps.58 \\fBFeatureLinkerUnlabeledQT\\fR·--·Groups·corresponding·features·from·multiple·maps.
  
59 \fBFidoAdapter\fR·--·Runs·the·protein·inference·engine·Fido.59 \\fBFidoAdapter\\fR·--·Runs·the·protein·inference·engine·Fido.
  
60 \fBFileConverter\fR·--·Converts·between·different·MS·file·formats.60 \\fBFileConverter\\fR·--·Converts·between·different·MS·file·formats.
  
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.
  
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.
  
63 \fBFileMerger\fR·--·Merges·several·MS·files·into·one·file.63 \\fBFileMerger\\fR·--·Merges·several·MS·files·into·one·file.
  
64 \fBFuzzyDiff\fR·--·Compares·two·files,·tolerating·numeric·differences.64 \\fBFuzzyDiff\\fR·--·Compares·two·files,·tolerating·numeric·differences.
  
65 \fBGNPSExport\fR·--·Tool·to·export·consensus·features·into·MGF·format.65 \\fBGNPSExport\\fR·--·Tool·to·export·consensus·features·into·MGF·format.
  
66 \fBGenericWrapper\fR·--·Allows·the·generic·wrapping·of·external·tools.66 \\fBGenericWrapper\\fR·--·Allows·the·generic·wrapping·of·external·tools.
  
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.
  
68 \fBIDConflictResolver\fR·--·Resolves·ambiguous·annotations·of·features·with·peptide·identifications.68 \\fBIDConflictResolver\\fR·--·Resolves·ambiguous·annotations·of·features·with·peptide·identifications.
  
69 \fBIDDecoyProbability\fR·--·Estimates·peptide·probabilities·using·a·decoy·search·strategy.69 \\fBIDDecoyProbability\\fR·--·Estimates·peptide·probabilities·using·a·decoy·search·strategy.
  
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.
  
71 \fBIDFileConverter\fR·--·Converts·identification·engine·file·formats.71 \\fBIDFileConverter\\fR·--·Converts·identification·engine·file·formats.
  
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.
  
73 \fBIDMapper\fR·--·Assigns·protein/peptide·identifications·to·features·or·consensus·features.73 \\fBIDMapper\\fR·--·Assigns·protein/peptide·identifications·to·features·or·consensus·features.
  
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.
  
75 \fBIDMerger\fR·--·Merges·several·protein/peptide·identification·files·into·one·file.75 \\fBIDMerger\\fR·--·Merges·several·protein/peptide·identification·files·into·one·file.
  
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.
  
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.
  
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.
  
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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