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OpenMS
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Functions | |
| subpage TOPP_TargetedFileConverter Converts targeted | files (such as tsv or TraML files). - @subpage TOPP_TextExporter - Exports various XML formats to a text file. - @subpage TOPP_TriqlerConverter - Convert to Triqler input file format.< b >File Filtering/Extraction/Merging</b > - @subpage TOPP_DatabaseFilter - Filter protein databases. - @subpage TOPP_DecoyDatabase - Creates decoy peptide databases from normal ones. - @subpage TOPP_DTAExtractor - Extracts spectra of an MS run file to several files in DTA format. - @subpage TOPP_FileFilter - Extracts or manipulates portions of data from peak |
| subpage TOPP_TargetedFileConverter Converts targeted feature or consensus feature files subpage TOPP_FileInfo Shows basic information about the such as data ranges and file type subpage TOPP_FileMerger Merges several MS files into one file subpage TOPP_IDFilter Filters results from protein or peptide identification engines based on different criteria subpage TOPP_IDMerger Merges several protein peptide identification files into one file subpage TOPP_IDRipper Splits protein peptide identifications according their file origin subpage TOPP_IDSplitter Splits protein peptide identifications off of annotated data files subpage TOPP_IonMobilityBinning Merges spectra with similar IM values and creates p N output mzML s by discretizing the IM range subpage TOPP_MapStatistics Extract extended statistics on the features of a map for quality control subpage TOPP_MzMLSplitter Splits an mzML file into multiple parts< b > Spectrum either by precursor or by RT blocks< b > Mass Correction and Calibration</b > subpage TOPP_InternalCalibration Applies an internal mass | calibration (using PSMs or fixed masses). - @subpage TOPP_ExternalCalibration - Applies an external mass calibration. - @subpage TOPP_HighResPrecursorMassCorrector - Correct the precursor entries of tandem MS scans for high resolution data. - @subpage TOPP_IDRTCalibration - Can be used to calibrate RTs of peptide hits linearly to standards.< b >Quantitation</b > - @subpage TOPP_ConsensusMapNormalizer - Normalizes maps of one consensusXML file(after linking). - @subpage TOPP_Decharger - Decharges and merges different feature charge variants of the same chemical entity. - @subpage TOPP_EICExtractor - Quantifies signals at given positions in(raw or picked) LC-MS maps. - @subpage TOPP_FeatureFinderCentroided - Detects two-dimensional features in centroided LC-MS data. - @subpage TOPP_FeatureFinderIdentification - Detects two-dimensional features in MS1 data based on peptide identifications. - @subpage TOPP_FeatureFinderMetabo - Detects two-dimensional features in centroided LC-MS data of metabolites. - @subpage TOPP_FeatureFinderMetaboIdent - Detects features in MS1 data corresponding to small molecule identifications. - @subpage TOPP_FeatureFinderMultiplex - Identifies peptide multiplets(pairs |
| subpage TOPP_TargetedFileConverter Converts targeted feature or consensus feature files subpage TOPP_FileInfo Shows basic information about the such as data ranges and file type subpage TOPP_FileMerger Merges several MS files into one file subpage TOPP_IDFilter Filters results from protein or peptide identification engines based on different criteria subpage TOPP_IDMerger Merges several protein peptide identification files into one file subpage TOPP_IDRipper Splits protein peptide identifications according their file origin subpage TOPP_IDSplitter Splits protein peptide identifications off of annotated data files subpage TOPP_IonMobilityBinning Merges spectra with similar IM values and creates p N output mzML s by discretizing the IM range subpage TOPP_MapStatistics Extract extended statistics on the features of a map for quality control subpage TOPP_MzMLSplitter Splits an mzML file into multiple parts< b > Spectrum either by precursor or by RT blocks< b > Mass Correction and Calibration</b > subpage TOPP_InternalCalibration Applies an internal mass triplets e g for SILAC or Dimethyl labeling and determines their relative abundance subpage TOPP_IsobaricAnalyzer Extracts and normalizes TMT and iTRAQ information from an MS experiment subpage TOPP_IsobaricWorkflow Complete workflow for quantification with isobaric | labeling (TMT, iTRAQ) combining several OpenMS tools. - @subpage TOPP_MassTraceExtractor - Annotates mass traces in centroided LC-MS maps. - @subpage TOPP_MetaboliteAdductDecharger - Decharges and merges different feature charge variants of the same small molecule. - @subpage TOPP_MetaProSIP - Detect labeled peptides from protein-SIP experiments. - @subpage TOPP_MultiplexResolver - Resolves conflicts between identifications and quantifications in multiplex data. - @subpage TOPP_ProteinQuantifier - Computes protein abundances from annotated feature/consensus maps. - @subpage TOPP_ProteomicsLFQ - Perform label-free quantification in a single tool. - @subpage TOPP_SeedListGenerator - Generates seed lists for feature detection.< b >Identification of Proteins/Peptides(SearchEngines)</b > - @subpage TOPP_CometAdapter - Identifies MS/MS spectra using Comet(external). - @subpage TOPP_LuciphorAdapter - Scores potential phosphorylation sites in order to localize the most probable sites. - @subpage TOPP_MascotAdapterOnline - Identifies MS/MS spectra using Mascot(external). - @subpage TOPP_MSFraggerAdapter - Peptide Identification with MSFragger. - @subpage TOPP_MSGFPlusAdapter - Identifies MS/MS spectra using MSGFPlus(external). - @subpage TOPP_NovorAdapter - De novo sequencing from tandem mass spectrometry data. - @subpage TOPP_SageAdapter - Identifies MS/MS spectra using Sage(external). - @subpage TOPP_SimpleSearchEngine - A simple database search engine for annotating MS/MS spectra. - @subpage TOPP_SpectraSTSearchAdapter - An interface to the 'SEARCH' mode of the SpectraST program(external |
Variables | |
| subpage TOPP_TargetedFileConverter Converts targeted feature or consensus feature files subpage TOPP_FileInfo Shows basic information about the | file |
| subpage TOPP_TargetedFileConverter Converts targeted feature or consensus feature files subpage TOPP_FileInfo Shows basic information about the such as data ranges and file type subpage TOPP_FileMerger Merges several MS files into one file subpage TOPP_IDFilter Filters results from protein or peptide identification engines based on different criteria subpage TOPP_IDMerger Merges several protein peptide identification files into one file subpage TOPP_IDRipper Splits protein peptide identifications according their file origin subpage TOPP_IDSplitter Splits protein peptide identifications off of annotated data files subpage TOPP_IonMobilityBinning Merges spectra with similar IM values and creates p N output mzML s by discretizing the IM range subpage TOPP_MapStatistics Extract extended statistics on the features of a map for quality control subpage TOPP_MzMLSplitter Splits an mzML file into multiple parts< b > Spectrum | processing |
| subpage TOPP_TargetedFileConverter Converts targeted feature or consensus feature files subpage TOPP_FileInfo Shows basic information about the such as data ranges and file type subpage TOPP_FileMerger Merges several MS files into one file subpage TOPP_IDFilter Filters results from protein or peptide identification engines based on different criteria subpage TOPP_IDMerger Merges several protein peptide identification files into one file subpage TOPP_IDRipper Splits protein peptide identifications according their file origin subpage TOPP_IDSplitter Splits protein peptide identifications off of annotated data files subpage TOPP_IonMobilityBinning Merges spectra with similar IM values and creates p N output mzML s by discretizing the IM range subpage TOPP_MapStatistics Extract extended statistics on the features of a map for quality control subpage TOPP_MzMLSplitter Splits an mzML file into multiple parts< b > Spectrum either by precursor or by RT blocks< b > Mass Correction and Calibration</b > subpage TOPP_InternalCalibration Applies an internal mass triplets | etc |
| subpage TOPP_TargetedFileConverter Converts targeted feature or consensus feature files subpage TOPP_FileInfo Shows basic information about the such as data ranges and file type subpage TOPP_FileMerger Merges several MS files into one file subpage TOPP_IDFilter Filters results from protein or peptide identification engines based on different criteria subpage TOPP_IDMerger Merges several protein peptide identification files into one file subpage TOPP_IDRipper Splits protein peptide identifications according their file origin subpage TOPP_IDSplitter Splits protein peptide identifications off of annotated data files subpage TOPP_IonMobilityBinning Merges spectra with similar IM values and creates p N output mzML s by discretizing the IM range subpage TOPP_MapStatistics Extract extended statistics on the features of a map for quality control subpage TOPP_MzMLSplitter Splits an mzML file into multiple parts<b> Spectrum either by precursor or by RT blocks<b> Mass Correction and Calibration</b> subpage TOPP_InternalCalibration Applies an internal mass calibration | ( | using PSMs or fixed | masses | ) |
| subpage TOPP_TargetedFileConverter Converts targeted files | ( | such as tsv or TraML | files | ) |
Referenced by TOPPViewBase::metadataFileDialog(), and TOPPASBase::openFilesInTOPPView().
| subpage TOPP_TargetedFileConverter Converts targeted feature or consensus feature files subpage TOPP_FileInfo Shows basic information about the such as data ranges and file type subpage TOPP_FileMerger Merges several MS files into one file subpage TOPP_IDFilter Filters results from protein or peptide identification engines based on different criteria subpage TOPP_IDMerger Merges several protein peptide identification files into one file subpage TOPP_IDRipper Splits protein peptide identifications according their file origin subpage TOPP_IDSplitter Splits protein peptide identifications off of annotated data files subpage TOPP_IonMobilityBinning Merges spectra with similar IM values and creates p N output mzML s by discretizing the IM range subpage TOPP_MapStatistics Extract extended statistics on the features of a map for quality control subpage TOPP_MzMLSplitter Splits an mzML file into multiple parts<b> Spectrum either by precursor or by RT blocks<b> Mass Correction and Calibration</b> subpage TOPP_InternalCalibration Applies an internal mass triplets e g for SILAC or Dimethyl labeling and determines their relative abundance subpage TOPP_IsobaricAnalyzer Extracts and normalizes TMT and iTRAQ information from an MS experiment subpage TOPP_IsobaricWorkflow Complete workflow for quantification with isobaric labeling | ( | TMT | , |
| iTRAQ | |||
| ) |
| subpage TOPP_TargetedFileConverter Converts targeted feature or consensus feature files subpage TOPP_FileInfo Shows basic information about the such as data ranges and file type subpage TOPP_FileMerger Merges several MS files into one file subpage TOPP_IDFilter Filters results from protein or peptide identification engines based on different criteria subpage TOPP_IDMerger Merges several protein peptide identification files into one file subpage TOPP_IDRipper Splits protein peptide identifications according their file origin subpage TOPP_IDSplitter Splits protein peptide identifications off of annotated data files subpage TOPP_IonMobilityBinning Merges spectra with similar IM values and creates p N output mzML s by discretizing the IM range subpage TOPP_MapStatistics Extract extended statistics on the features of a map for quality control subpage TOPP_MzMLSplitter Splits an mzML file into multiple parts<b> Spectrum either by precursor or by RT blocks<b> Mass Correction and Calibration</b> subpage TOPP_InternalCalibration Applies an internal mass triplets etc |
| subpage TOPP_TargetedFileConverter Converts targeted feature or consensus feature files subpage TOPP_FileInfo Shows basic information about the file |
| subpage TOPP_TargetedFileConverter Converts targeted feature or consensus feature files subpage TOPP_FileInfo Shows basic information about the such as data ranges and file type subpage TOPP_FileMerger Merges several MS files into one file subpage TOPP_IDFilter Filters results from protein or peptide identification engines based on different criteria subpage TOPP_IDMerger Merges several protein peptide identification files into one file subpage TOPP_IDRipper Splits protein peptide identifications according their file origin subpage TOPP_IDSplitter Splits protein peptide identifications off of annotated data files subpage TOPP_IonMobilityBinning Merges spectra with similar IM values and creates p N output mzML s by discretizing the IM range subpage TOPP_MapStatistics Extract extended statistics on the features of a map for quality control subpage TOPP_MzMLSplitter Splits an mzML file into multiple parts<b> Spectrum processing |
1.9.1 
