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<div class="title">TOPP documentation </div> </div>
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<div class="textblock"><p>'TOPP - The OpenMS Proteomics Pipeline' is a pipeline for the analysis of HPLC-MS data. It consists of several small applications that can be chained to create analysis pipelines tailored for a specific problem.</p>
<p><br/>
</p>
<p>The TOPP tools are divided into several subgroups:</p>
<p><b>Graphical Tools</b></p>
<ul>
<li><a class="el" href="TOPP_TOPPView.html">TOPPView</a> - A viewer for mass spectrometry data.</li>
<li><a class="el" href="TOPP_TOPPAS.html">TOPPAS</a> - An assistant for GUI-driven TOPP workflow design.</li>
<li><a class="el" href="TOPP_INIFileEditor.html">INIFileEditor</a> - An editor for OpenMS configuration files.</li>
</ul>
<p><b>File Handling</b></p>
<ul>
<li><a class="el" href="TOPP_DTAExtractor.html">DTAExtractor</a> - Extracts spectra of an MS run file to several files in DTA format.</li>
<li><a class="el" href="TOPP_FileConverter.html">FileConverter</a> - Converts between different MS file formats.</li>
<li><a class="el" href="TOPP_FileFilter.html">FileFilter</a> - Extracts or manipulates portions of data from peak, feature or consensus feature files.</li>
<li><a class="el" href="TOPP_FileInfo.html">FileInfo</a> - Shows basic information about the file, such as data ranges and file type.</li>
<li><a class="el" href="TOPP_FileMerger.html">FileMerger</a> - Merges several MS files into one file.</li>
<li><a class="el" href="TOPP_IDMerger.html">IDMerger</a> - Merges several protein/peptide identification files into one file.</li>
<li><a class="el" href="TOPP_IDRipper.html">IDRipper</a> - Splits protein/peptide identifications according their file-origin.</li>
<li><a class="el" href="TOPP_IDFileConverter.html">IDFileConverter</a> - Converts identification engine file formats.</li>
<li><a class="el" href="TOPP_MapStatistics.html">MapStatistics</a> - Extract extended statistics on the features of a map for quality control.</li>
<li><a class="el" href="TOPP_SpectraMerger.html">SpectraMerger</a> - Merges spectra from an LC-MS map, either by precursor or by RT blocks</li>
<li><a class="el" href="TOPP_TextExporter.html">TextExporter</a> - Exports various XML formats to a text file.</li>
<li><a class="el" href="TOPP_MzTabExporter.html">MzTabExporter</a> - Exports various XML formats to an mzTab file</li>
</ul>
<p><b>Signal Processing and Preprocessing</b></p>
<ul>
<li><a class="el" href="TOPP_BaselineFilter.html">BaselineFilter</a> - Removes the baseline from profile spectra using a top-hat filter.</li>
<li><a class="el" href="TOPP_InternalCalibration.html">InternalCalibration</a> - Applies an internal calibration.</li>
<li><a class="el" href="TOPP_MapNormalizer.html">MapNormalizer</a> - Normalizes peak intensities in an MS run.</li>
<li><a class="el" href="TOPP_MassTraceExtractor.html">MassTraceExtractor</a> - Annotates mass traces in centroided LC-MS maps.</li>
<li><a class="el" href="TOPP_NoiseFilterGaussian.html">NoiseFilterGaussian</a> - Removes noise from profile spectra by using different smoothing techniques.</li>
<li><a class="el" href="TOPP_NoiseFilterSGolay.html">NoiseFilterSGolay</a> - Removes noise from profile spectra by using different smoothing techniques.</li>
<li><a class="el" href="TOPP_PeakPickerHiRes.html">PeakPickerHiRes</a> - Finds mass spectrometric peaks in profile mass spectra.</li>
<li><a class="el" href="TOPP_PeakPickerWavelet.html">PeakPickerWavelet</a> - Finds mass spectrometric peaks in profile mass spectra.</li>
<li><a class="el" href="TOPP_PrecursorMassCorrector.html">PrecursorMassCorrector</a> - Correct the precursor entries of tandem MS scans.</li>
<li><a class="el" href="TOPP_HighResPrecursorMassCorrector.html">HighResPrecursorMassCorrector</a> - Correct the precursor entries of tandem MS scans.</li>
<li><a class="el" href="TOPP_Resampler.html">Resampler</a> - Transforms an LC-MS map into an equally-spaced (in RT and m/z) map.</li>
<li><a class="el" href="TOPP_SpectraFilterBernNorm.html">SpectraFilterBernNorm</a> - Applies a filter to peak spectra.</li>
<li><a class="el" href="TOPP_SpectraFilterMarkerMower.html">SpectraFilterMarkerMower</a> - Applies a filter to peak spectra.</li>
<li><a class="el" href="TOPP_SpectraFilterNLargest.html">SpectraFilterNLargest</a> - Applies a filter to peak spectra.</li>
<li><a class="el" href="TOPP_SpectraFilterNormalizer.html">SpectraFilterNormalizer</a> - Applies a filter to peak spectra.</li>
<li><a class="el" href="TOPP_SpectraFilterParentPeakMower.html">SpectraFilterParentPeakMower</a> - Applies a filter to peak spectra.</li>
<li><a class="el" href="TOPP_SpectraFilterScaler.html">SpectraFilterScaler</a> - Applies a filter to peak spectra.</li>
<li><a class="el" href="TOPP_SpectraFilterSqrtMower.html">SpectraFilterSqrtMower</a> - Applies a filter to peak spectra.</li>
<li><a class="el" href="TOPP_SpectraFilterThresholdMower.html">SpectraFilterThresholdMower</a> - Applies a filter to peak spectra.</li>
<li><a class="el" href="TOPP_SpectraFilterWindowMower.html">SpectraFilterWindowMower</a> - Applies a filter to peak spectra.</li>
<li><a class="el" href="TOPP_TOFCalibration.html">TOFCalibration</a> - Applies time of flight calibration.</li>
</ul>
<p><b>Quantitation</b></p>
<ul>
<li><a class="el" href="TOPP_AdditiveSeries.html">AdditiveSeries</a> - Computes an additive series to quantify a peptide in a set of samples.</li>
<li><a class="el" href="TOPP_Decharger.html">Decharger</a> - Decharges and merges different feature charge variants of the same chemical entity.</li>
<li><a class="el" href="TOPP_EICExtractor.html">EICExtractor</a> - Quantifies signals at given positions in (raw or picked) LC-MS maps.</li>
<li><a class="el" href="TOPP_FeatureFinderCentroided.html">FeatureFinderCentroided</a> - Detects two-dimensional features in centroided LC-MS data.</li>
<li><a class="el" href="TOPP_FeatureFinderRaw.html">FeatureFinderRaw</a> - Detects two-dimensional features in uncentroided (=raw) LC-MS data.</li>
<li><a class="el" href="TOPP_FeatureFinderIsotopeWavelet.html">FeatureFinderIsotopeWavelet</a> - Detects two-dimensional features in uncentroided (=raw) LC-MS data.</li>
<li><a class="el" href="TOPP_FeatureFinderMetabo.html">FeatureFinderMetabo</a> - Detects two-dimensional features in centroided LC-MS data of metabolites.</li>
<li><a class="el" href="TOPP_FeatureFinderMRM.html">FeatureFinderMRM</a> - Quantifies features LC-MS/MS MRM data.</li>
<li><a class="el" href="TOPP_IsobaricAnalyzer.html">IsobaricAnalyzer</a> - Extracts and normalizes TMT and iTRAQ information from a MS experiment.</li>
<li><a class="el" href="TOPP_ITRAQAnalyzer.html">ITRAQAnalyzer</a> - Extracts and normalizes iTRAQ information from an MS experiment.</li>
<li><a class="el" href="TOPP_ProteinQuantifier.html">ProteinQuantifier</a> - Computes protein abundances from annotated feature/consensus maps</li>
<li><a class="el" href="TOPP_ProteinResolver.html">ProteinResolver</a> - A peptide-centric algorithm for protein inference.</li>
<li><a class="el" href="TOPP_SILACAnalyzer.html">SILACAnalyzer</a> - Determines the ratio of peak pairs in LC-MS data.</li>
<li><a class="el" href="TOPP_SeedListGenerator.html">SeedListGenerator</a> - Generates seed lists for feature detection.</li>
<li><a class="el" href="TOPP_TMTAnalyzer.html">TMTAnalyzer</a> - Extracts and normalizes TMT information from an MS experiment.</li>
</ul>
<p><b>Map Alignment</b></p>
<ul>
<li><a class="el" href="TOPP_ConsensusMapNormalizer.html">ConsensusMapNormalizer</a> - Normalizes maps of one consensusXML file (after linking).</li>
<li><a class="el" href="TOPP_MapAlignerIdentification.html">MapAlignerIdentification</a> - Corrects retention time distortions between maps based on common peptide identifications.</li>
<li><a class="el" href="TOPP_MapAlignerPoseClustering.html">MapAlignerPoseClustering</a> - Corrects retention time distortions between maps using a pose clustering approach.</li>
<li><a class="el" href="TOPP_MapAlignerSpectrum.html">MapAlignerSpectrum</a> - Corrects retention time distortions between maps by spectrum alignment.</li>
<li><a class="el" href="TOPP_MapRTTransformer.html">MapRTTransformer</a> - Applies retention time transformations to maps.</li>
<li><a class="el" href="TOPP_FeatureLinkerLabeled.html">FeatureLinkerLabeled</a> - Groups corresponding isotope-labeled features in a feature map.</li>
<li><a class="el" href="TOPP_FeatureLinkerUnlabeled.html">FeatureLinkerUnlabeled</a> - Groups corresponding features from multiple maps.</li>
<li><a class="el" href="TOPP_FeatureLinkerUnlabeledQT.html">FeatureLinkerUnlabeledQT</a> - Groups corresponding features from multiple maps using a QT clustering approach.</li>
</ul>
<p><b>Protein/Peptide Identification</b></p>
<ul>
<li><a class="el" href="TOPP_CompNovo.html">CompNovo</a> - Performs a peptide/protein identification with the CompNovo engine.</li>
<li><a class="el" href="TOPP_CompNovoCID.html">CompNovoCID</a> - Performs a peptide/protein identification with the CompNovo engine in CID mode.</li>
<li><a class="el" href="TOPP_InspectAdapter.html">InspectAdapter</a> - Identifies MS/MS spectra using Inspect (external).</li>
<li><a class="el" href="TOPP_MascotAdapter.html">MascotAdapter</a> - Identifies MS/MS spectra using Mascot (external).</li>
<li><a class="el" href="TOPP_MascotAdapterOnline.html">MascotAdapterOnline</a> - Identifies MS/MS spectra using Mascot (external).</li>
<li><a class="el" href="TOPP_MyriMatchAdapter.html">MyriMatchAdapter</a> - Identifies MS/MS spectra using MyriMatch (external).</li>
<li><a class="el" href="TOPP_OMSSAAdapter.html">OMSSAAdapter</a> - Identifies MS/MS spectra using OMSSA (external).</li>
<li><a class="el" href="TOPP_PepNovoAdapter.html">PepNovoAdapter</a> - Identifies MS/MS spectra using PepNovo (external).</li>
<li><a class="el" href="TOPP_XTandemAdapter.html">XTandemAdapter</a> - Identifies MS/MS spectra using XTandem (external).</li>
<li><a class="el" href="TOPP_SpecLibSearcher.html">SpecLibSearcher</a> - Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.</li>
</ul>
<p><b>Protein/Peptide Processing</b></p>
<ul>
<li><a class="el" href="TOPP_ConsensusID.html">ConsensusID</a> - Computes a consensus identification from peptide identifications of several identification engines.</li>
<li><a class="el" href="TOPP_FalseDiscoveryRate.html">FalseDiscoveryRate</a> - Estimates the false discovery rate on peptide and protein level using decoy searches.</li>
<li><a class="el" href="TOPP_IDConflictResolver.html">IDConflictResolver</a> - Resolves ambiguous annotations of features with peptide identifications.</li>
<li><a class="el" href="TOPP_IDFilter.html">IDFilter</a> - Filters results from protein or peptide identification engines based on different criteria.</li>
<li><a class="el" href="TOPP_IDMapper.html">IDMapper</a> - Assigns protein/peptide identifications to feature or consensus features.</li>
<li><a class="el" href="TOPP_IDPosteriorErrorProbability.html">IDPosteriorErrorProbability</a> - Estimates posterior error probabilities using a mixture model.</li>
<li><a class="el" href="TOPP_IDRTCalibration.html">IDRTCalibration</a> - Can be used to calibrate RTs of peptide hits linearly to standards.</li>
<li><a class="el" href="TOPP_PeptideIndexer.html">PeptideIndexer</a> - Refreshes the protein references for all peptide hits.</li>
<li><a class="el" href="TOPP_ProteinInference.html">ProteinInference</a> - Infer proteins from a list of (high-confidence) peptides.</li>
</ul>
<p><b>Targeted Experiments</b></p>
<ul>
<li><a class="el" href="TOPP_InclusionExclusionListCreator.html">InclusionExclusionListCreator</a> - Creates inclusion and/or exclusion lists for LC-MS/MS experiments.</li>
<li><a class="el" href="TOPP_PrecursorIonSelector.html">PrecursorIonSelector</a> - A tool for precursor ion selection based on identification results.</li>
<li><a class="el" href="TOPP_MRMMapper.html">MRMMapper</a> - MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</li>
<li><a class="el" href="TOPP_OpenSwathDecoyGenerator.html">OpenSwathDecoyGenerator</a> - Generates decoys according to different models for a specific TraML</li>
<li><a class="el" href="TOPP_OpenSwathChromatogramExtractor.html">OpenSwathChromatogramExtractor</a> - Extract chromatograms (XIC) from a MS2 map file.</li>
<li><a class="el" href="TOPP_OpenSwathAnalyzer.html">OpenSwathAnalyzer</a> - Picks peaks and finds features in an SRM experiment.</li>
<li><a class="el" href="TOPP_OpenSwathRTNormalizer.html">OpenSwathRTNormalizer</a> - This tool will align an SRM / SWATH run to a normalized retention time space.</li>
<li><a class="el" href="TOPP_OpenSwathFeatureXMLToTSV.html">OpenSwathFeatureXMLToTSV</a> - Converts a featureXML to a tsv.</li>
<li><a class="el" href="TOPP_OpenSwathConfidenceScoring.html">OpenSwathConfidenceScoring</a> - Computes confidence scores for <a class="el" href="namespaceOpenSwath.html">OpenSwath</a> results.</li>
</ul>
<p><b>Peptide Property Prediction</b></p>
<ul>
<li><a class="el" href="TOPP_PTModel.html">PTModel</a> - Trains a model for the prediction of proteotypic peptides from a training set.</li>
<li><a class="el" href="TOPP_PTPredict.html">PTPredict</a> - Predicts the likelihood of peptides to be proteotypic using a model trained by PTModel.</li>
<li><a class="el" href="TOPP_RTModel.html">RTModel</a> - Trains a model for the retention time prediction of peptides from a training set.</li>
<li><a class="el" href="TOPP_RTPredict.html">RTPredict</a> - Predicts retention times for peptides using a model trained by RTModel.</li>
</ul>
<p><b>Misc</b></p>
<ul>
<li><a class="el" href="TOPP_GenericWrapper.html">GenericWrapper</a> - Allows the generic wrapping of external tools.</li>
<li><a class="el" href="TOPP_ExecutePipeline.html">ExecutePipeline</a> - Executes workflows created by TOPPAS. </li>
</ul>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:25 using doxygen 1.8.5</font></TD>
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