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ABI Tools & Packages using GKN/CTD

A summary of our tools and packages using GKN/CTD

OpenMS

In File Handling:

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.
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.
IDMerger:
Merges several protein/peptide identification files into one file.
IDRipper:
Split protein/peptide identification file into several files according annotated file origin.
MapStatistics:
Extract extended statistics on the features of a map for quality control.
MzTabExporter:
Exports various XML formats to an mzTab file.
SpectraMerger:
Merges spectra (each MS level separately), increasing S/N ratios.
TextExporter:
Exports various XML formats to a text file.

In ID Processing:

ConsensusID:
Computes a consensus identification from peptide identifications of several identification engines.
FalseDiscoveryRate:
Estimates the false discovery rate on peptide and protein level using decoy searches.
IDConflictResolver:
Resolves ambiguous annotations of features with peptide identifications
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.
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.
PeptideIndexer:
Refreshes the protein references for all peptide hits.

In Identification:

CompNovo:
Performs a de novo peptide identification using the CompNovo engine.
CompNovoCID:
Performs a de novo peptide identification using the CompNovo engine.
MascotAdapterOnline:
Annotates MS/MS spectra using Mascot.
MyriMatchAdapter:
Annotates MS/MS spectra using MyriMatch.
OMSSAAdapter:
Annotates MS/MS spectra using OMSSA.
ProteinInference:
Protein inference based on the number of identified peptides.
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.
XTandemAdapter:
Annotates MS/MS spectra using XTandem.

In Map Alignment:

ConsensusMapNormalizer:
Normalizes maps of one consensusXML file
FeatureLinkerLabeled:
Groups corresponding isotope-labeled features in a feature map.
FeatureLinkerUnlabeled:
Groups corresponding features from multiple maps.
FeatureLinkerUnlabeledQT:
Groups corresponding features from multiple maps.
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.
MapRTTransformer:
Applies retention time transformations to maps.

In Misc:

ExecutePipeline:
Executes workflows created by TOPPAS.

In Peptide property prediction:

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
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.

In QCFileHandling:

QCFeatureReader:
QCIDReader:
Reads ID tsv files from QCExporter
QCIonInjectionTimeReader:
Reads an ion injection time summary file into a KNIME table.
QCPrecursorReader:
Read the precursor file created by the QCCalculator
QCSetIdReader:
Read the set id file created by the QCCalculator
QCTICReader:

In Quantitation:

AdditiveSeries:
Computes an additive series to quantify a peptide in a set of samples.
Decharger:
Decharges and merges different feature charge variants of the same peptide.
EICExtractor:
Extracts intensities from dedicates positions in a LC/MS map
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.
ITRAQAnalyzer:
Calculates iTRAQ quantitative values for peptides
ProteinQuantifier:
Compute peptide and protein abundances
ProteinResolver:
protein inference
SILACAnalyzer:
Determination of peak ratios in LC-MS data
SeedListGenerator:
Generates seed lists for feature detection.
TMTAnalyzer:
Calculates TMT quantitative values for peptides

In Signal processing and preprocessing:

BaselineFilter:
Removes the baseline from profile spectra using a top-hat filter.
HighResPrecursorMassCorrector:
Corrects the precursor mz determined by the instrument software.
InternalCalibration:
Applies an internal calibration.
MapNormalizer:
Normalizes peak intensities in an MS run.
MassTraceExtractor:
Detects mass traces in centroided LC-MS data.
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.
PeakPickerHiRes:
Finds mass spectrometric peaks in profile mass spectra.
PeakPickerWavelet:
Finds mass spectrometric peaks in profile mass spectra.
PrecursorMassCorrector:
Corrects the precursor entries of MS/MS spectra, by using MS1 information.
Resampler:
Transforms an LC/MS map into a resampled map or a PNG image.
TOFCalibration:
Applies time of flight calibration.

In Targeted Experiments:

ConvertTSVToTraML:
Converts an OpenSWATH transition TSV file to a TraML file
ConvertTraMLToTSV:
Converts a TraML file to an OpenSWATH transition TSV file
InclusionExclusionListCreator:
Creates inclusion and/or exclusion lists.
MRMMapper:
MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
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.
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.
PrecursorIonSelector:
PrecursorIonSelector

In Utilities:

CVInspector:
A tool for visualization and validation of PSI mapping and CV files.
DeMeanderize:
Orders the spectra of MALDI spotting plates correctly.
DecoyDatabase:
Create decoy peptide databases from normal ones.
Digestor:
Digests a protein database in-silico.
DigestorMotif:
digests a protein database in-silico
ERPairFinder:
Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans.
FFEval:
Evaluation tool for feature detection algorithms.
IDDecoyProbability:
Estimates peptide probabilities using a decoy search strategy. WARNING: This util is deprecated.
IDEvaluator:
Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value.
IDExtractor:
Extracts 'n' peptides randomly or best 'n' from idXML files.
IDMassAccuracy:
Calculates a distribution of the mass error from given mass spectra and IDs.
IDSplitter:
Splits protein/peptide identifications off of annotated data files
INIUpdater:
Update INI and TOPPAS files to new OpenMS version.
ImageCreator:
Transforms an LC-MS map into an image.
LabeledEval:
Evaluation tool for isotope-labeled quantitation experiments.
MRMPairFinder:
Util which can be used to evaluate labeled pair ratios on MRM features.
MSSimulator:
A highly configurable simulator for mass spectrometry experiments.
MapAlignmentEvaluation:
Evaluates alignment results against a ground truth.
MassCalculator:
Calculates masses and mass-to-charge ratios of peptide sequences
QCCalculator:
produces table data dedicted for R import. These data is produced based on mzML, featureXMl and/ or idXML files
QCEmbedder:
produces qcml files
QCExporter:
produces qcml files
QCMerger:
produces qcml files
QCShrinker:
produces qcml files
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.
SemanticValidator:
SemanticValidator for analysisXML and mzML files.
SequenceCoverageCalculator:
Prints information about idXML files.
SpecLibCreator:
Creates an MSP formatted spectral library.
TransformationEvaluation:
Applies a transformation to a range of values
XMLValidator:
Validates XML files against an XSD schema.