NAME¶
topp - library for LC/MS data management and analysis - tools
DESCRIPTION¶
This manual page documents briefly the
topp package that brings a set of
binary tools to build the OpenMS proteomics pipeline (topp). OpenMS offers an
infrastructure for the development of mass spectrometry-related software and
powerful 2D and 3D visualization solutions. OpenMS offers analyses for various
quantitation protocols, including label-free quantitation, SILAC, iTRAQ, SRM,
SWATH… It provides build-in algorithms for de-novo identification and
database search, as well as adapters to other state-of-the art tools like
X!Tandem, Mascot, OMSSA… OpenMS supports the Proteomics Standard
Initiative (PSI) formats for MS data and supports easy integration of tools
into workflow engines like Knime, Galaxy, WS-Pgrade, and TOPPAS via the
TOPPtools concept and a unified parameter handling.
AVAILABLE MODULES¶
AccurateMassSearch -- Find potential HMDB ids within the given mass error
window.
AdditiveSeries -- Computes an additive series to quantify a peptide in a
set of samples.
BaselineFilter -- Removes the baseline from profile spectra using a
top-hat filter.
CVInspector -- A tool for visualization and validation of PSI mapping and
CV files.
CompNovo -- Performs a de novo peptide identification using the CompNovo
engine.
CompNovoCID -- Performs a de novo peptide identification using the
CompNovo engine.
ConsensusID -- Computes a consensus identification from peptide
identifications of several identification engines.
ConsensusMapNormalizer -- Normalizes maps of one consensusXML file.
ConvertTSVToTraML -- Converts an OpenSWATH transition TSV file to a TraML
file.
ConvertTraMLToTSV -- Converts a TraML file to an OpenSWATH transition TSV
file.
DBExporter -- Exports data from an OpenMS database to a file.
DBImporter -- Imports data to an OpenMS database.
DTAExtractor -- Extracts spectra of an MS run file to several files in
DTA format.
DeMeanderize -- Orders the spectra of MALDI spotting plates correctly.
Decharger -- Decharges and merges different feature charge variants of
the same peptide.
DecoyDatabase -- Create decoy peptide databases from normal ones.
Digestor -- Digests a protein database in-silico.
DigestorMotif -- digests a protein database in-silico.
EICExtractor -- Extracts intensities from dedicates positions in a LC/MS
map.
ERPairFinder -- Util which can be used to evaluate pair ratios on
enhanced resolution (zoom) scans.
ExecutePipeline -- Executes workflows created by TOPPAS.
FFEval -- Evaluation tool for feature detection algorithms.
FalseDiscoveryRate -- Estimates the false discovery rate on peptide and
protein level using decoy searches.
FeatureFinderCentroided -- Detects two-dimensional features in LC-MS
data.
FeatureFinderIsotopeWavelet -- Detects two-dimensional features in LC-MS
data.
FeatureFinderMRM -- Detects two-dimensional features in LC-MS data.
FeatureFinderMetabo -- Assembles metabolite features from singleton mass
traces.
FeatureFinderRaw -- Determination of peak ratios in LC-MS data.
FeatureFinderSuperHirn -- Finds mass spectrometric features in mass
spectra.
FeatureLinkerLabeled -- Groups corresponding isotope-labeled features in
a feature map.
FeatureLinkerUnlabeled -- Groups corresponding features from multiple
maps.
FeatureLinkerUnlabeledQT -- Groups corresponding features from multiple
maps.
FileConverter -- Converts between different MS file formats.
FileFilter -- Extracts or manipulates portions of data from peak, feature
or consensus-feature files.
FileInfo -- Shows basic information about the file, such as data ranges
and file type.
FileMerger -- Merges several MS files into one file.
FuzzyDiff -- Compares two files, tolerating numeric differences.
GenericWrapper -- Allows the generic wrapping of external tools.
HighResPrecursorMassCorrector -- Corrects the precursor mz determined by
the instrument software.
IDConflictResolver -- Resolves ambiguous annotations of features with
peptide identifications.
IDDecoyProbability -- Estimates peptide probabilities using a decoy
search strategy.
IDEvaluatorGUI -- Computes a 'q-value vs. #PSM' plot to visualize the
number identifications for a certain q-value.
IDExtractor -- Extracts 'n' peptides randomly or best 'n' from idXML
files.
IDFileConverter -- Converts identification engine file formats.
IDFilter -- Filters results from protein or peptide identification
engines based on different criteria.
IDMapper -- Assigns protein/peptide identifications to features or
consensus features.
IDMassAccuracy -- Calculates a distribution of the mass error from given
mass spectra and IDs.
IDMerger -- Merges several protein/peptide identification files into one
file.
IDPosteriorErrorProbability -- Estimates probabilities for incorrectly
assigned peptide sequences and a set of search engine scores using a mixture
model.
IDRTCalibration -- Can be used to calibrate RTs of peptide hits linearly
to standards.
IDRipper -- Split protein/peptide identification file into several files
according annotated file origin.
IDSplitter -- Splits protein/peptide identifications off of annotated
data files.
INIFileEditor -- An editor for OpenMS configuration files.
INIUpdater -- Update INI and TOPPAS files to new OpenMS version.
ITRAQAnalyzer -- Calculates iTRAQ quantitative values for peptides.
ImageCreator -- Transforms an LC-MS map into an image.
InclusionExclusionListCreator -- Creates inclusion and/or exclusion
lists.
InspectAdapter -- Annotates MS/MS spectra using Inspect.
InternalCalibration -- Applies an internal calibration.
IsobaricAnalyzer -- Calculates isobaric quantitative values for peptides.
LabeledEval -- Evaluation tool for isotope-labeled quantitation
experiments.
MRMMapper -- MRMMapper maps measured chromatograms (mzML) and the
transitions used (TraML).
MRMPairFinder -- Util which can be used to evaluate labeled pair ratios
on MRM features.
MSSimulator -- A highly configurable simulator for mass spectrometry
experiments.
MapAlignerIdentification -- Corrects retention time distortions between
maps based on common peptide identifications.
MapAlignerPoseClustering -- Corrects retention time distortions between
maps using a pose clustering approach.
MapAlignerSpectrum -- Corrects retention time distortions between maps by
spectrum alignment.
MapAlignmentEvaluation -- Evaluates alignment results against a ground
truth.
MapNormalizer -- Normalizes peak intensities in an MS run.
MapRTTransformer -- Applies retention time transformations to maps.
MapStatistics -- Extract extended statistics on the features of a map for
quality control.
MascotAdapter -- Annotates MS/MS spectra using Mascot.
MascotAdapterOnline -- Annotates MS/MS spectra using Mascot.
MassCalculator -- Calculates masses and mass-to-charge ratios of peptide
sequences.
MassTraceExtractor -- Detects mass traces in centroided LC-MS data.
MyriMatchAdapter -- Annotates MS/MS spectra using MyriMatch.
MzTabExporter -- Exports various XML formats to an mzTab file.
NoiseFilterGaussian -- Removes noise from profile spectra by using
Gaussian filter (on uniform as well as non-uniform data).
NoiseFilterSGolay -- Removes noise from profile spectra by using a
Savitzky Golay filter. Requires uniform (equidistant) data.
OMSSAAdapter -- Annotates MS/MS spectra using OMSSA.
OpenSwathAnalyzer -- Picks peaks and finds features in an SRM experiment.
OpenSwathChromatogramExtractor -- Extract chromatograms (XIC) from a MS2
map file.
OpenSwathConfidenceScoring -- Compute confidence scores for OpenSwath
results.
OpenSwathDIAPreScoring -- Scoring spectra using the DIA scores.
OpenSwathDecoyGenerator -- Generates decoys according to different models
for a specific TraML.
OpenSwathFeatureXMLToTSV -- Converts a featureXML to a mProphet tsv.
OpenSwathMzMLFileCacher -- This tool caches the spectra and chromatogram
data of an mzML to disk.
OpenSwathRTNormalizer -- This tool will take a description of RT peptides
and their normalized retention time to write out a transformation file on how
to transoform the RT space into the normalized space.
OpenSwathRewriteToFeatureXML -- Combines featureXML and mProphet tsv to
FDR filtered featureXML.
PILISIdentification -- performs a peptide/protein identification with the
PILIS engine.
PILISModelCV -- Perform a cross validation of the PILIS model parameters.
PILISModelTrainer -- Train the PILIS model with a given set of spectra
and identifications.
PILISSpectraGenerator -- Generate spectra given a list of peptides and a
PILIS model.
PTModel -- Trains a model for the prediction of proteotypic peptides from
a training set.
PTPredict -- predicts the likelihood of peptides to be proteotypic via
svm_model which is trained by PTModel.
PeakPickerHiRes -- Finds mass spectrometric peaks in profile mass
spectra.
PeakPickerWavelet -- Finds mass spectrometric peaks in profile mass
spectra.
PepNovoAdapter -- Adapter to PepNovo supporting all PepNovo command line
parameters. The results are converted from the PepNovo text outfile format
into the idXML format.
PeptideIndexer -- Refreshes the protein references for all peptide hits.
PhosphoScoring -- Scores potential phosphorylation sites and therby tries
to localize the most probable sites.
PrecursorIonSelector -- PrecursorIonSelector.
PrecursorMassCorrector -- Corrects the precursor entries of MS/MS
spectra, by using MS1 information.
ProteinInference -- Protein inference based on the number of identified
peptides.
ProteinQuantifier -- Compute peptide and protein abundances.
ProteinResolver -- protein inference.
QCCalculator -- Calculates basic quality parameters from MS experiments
and subsequent analysis data as identification or feature detection.
QCEmbedder -- Attaches a table or an image to a given qc parameter.
QCExporter -- Will extract several qp from several run/sets in a tabular
format.
QCExtractor -- Extracts a table attachment to a given qc parameter.
QCImporter -- Imports tables with quality control parameters into qcml
files.
QCMerger -- Merges two qcml files together.
QCShrinker -- This application is used to remove the verbose table
attachments from a qcml file that are not needed anymore, e.g. for a final
report.
RNPxl -- Tool for RNP cross linking experiment analysis.
RNPxlXICFilter -- Remove MS2 spectra from treatment based on the fold
change between control and treatment.
RTEvaluation -- Application that evaluates TPs (true positives), TNs,
FPs, and FNs for an idXML file with predicted RTs.
RTModel -- Trains a model for the retention time prediction of peptides
from a training set.
RTPredict -- Predicts retention times for peptides using a model trained
by RTModel.
Resampler -- Transforms an LC/MS map into a resampled map or a PNG image.
SILACAnalyzer -- Determination of peak ratios in LC-MS data.
SeedListGenerator -- Generates seed lists for feature detection.
SemanticValidator -- SemanticValidator for analysisXML and mzML files.
SequenceCoverageCalculator -- Prints information about idXML files.
SpecLibCreator -- Creates an MSP formatted spectral library.
SpecLibSearcher -- Identifies peptide MS/MS spectra by spectral matching
with a searchable spectral library.
SpectraFilterBernNorm -- Applies thresholdfilter to peak spectra.
SpectraFilterMarkerMower -- Applies thresholdfilter to peak spectra.
SpectraFilterNLargest -- Applies thresholdfilter to peak spectra.
SpectraFilterNormalizer -- Applies thresholdfilter to peak spectra.
SpectraFilterParentPeakMower -- Applies thresholdfilter to peak spectra.
SpectraFilterScaler -- Applies thresholdfilter to peak spectra.
SpectraFilterSqrtMower -- Applies thresholdfilter to peak spectra.
SpectraFilterThresholdMower -- Applies thresholdfilter to peak spectra.
SpectraFilterWindowMower -- Applies thresholdfilter to peak spectra.
SpectraMerger -- Merges spectra (each MS level separately), increasing
S/N ratios.
SvmTheoreticalSpectrumGeneratorTrainer -- Trainer for SVM models as input
for SvmTheoreticalSpectrumGenerator.
TMTAnalyzer -- Calculates TMT quantitative values for peptides.
TOFCalibration -- Applies time of flight calibration.
TOPPAS -- An assistant for GUI-driven TOPP workflow design.
TOPPView -- A viewer for mass spectrometry data.
TextExporter -- Exports various XML formats to a text file.
TransformationEvaluation -- Applies a transformation to a range of
values.
XMLValidator -- Validates XML files against an XSD schema.
XTandemAdapter -- Annotates MS/MS spectra using XTandem.
BIBLIOGRAPHICAL REFERENCE TO BE CITED¶
Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene
Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut
Reinert, and Oliver Kohlbacher (2008) OpenMS – an Open-Source Software
Framework for Mass Spectrometry.
BMC Bioinformatics, 9:163.
doi:10.1186/1471-2105-9-163.
SEE ALSO¶
libopenms(3),
openms-common(7),
openms(7),
openms-doc(7).
The program is documented fully in the
Tutorials, that are packaged in
openms-doc.
AUTHOR¶
This manual page was written by Filippo Rusconi <lopippo@debian.org>.
Permission is granted to copy, distribute and/or modify this document under
the terms of the GNU General Public License, Version 3, published by the Free
Software Foundation.
On a Debian system the complete text of the GNU General Public License version
3 can be found in the file `
/usr/share/common-licenses/GPL-3'.