UTILS documentation

Besides TOPP, OpenMS offers a range of other tools. They are not included in TOPP as they are not part of typical analysis pipelines, but they still might be very helpful to you.

Just as the TOPP tools, they can be found in the OpenMS/bin folder.

The UTILS tools are divided into several subgroups:

Maintenance

• INIUpdater - Update INI and TOPPAS files from previous versions of OpenMS as parameters and storage method might have change

Signal Processing and Preprocessing

• RNPxlXICFilter - Remove MS2 spectra from treatment based on the fold change between control and treatment for RNP cross linking experiments.

File Handling

• CVInspector - A tool for visualization and validation of PSI mapping and CV files.
• TargetedFileConverter - Converts targeted files (such as tsv or TraML files)
• FuzzyDiff - Compares two files, tolerating numeric differences.
• IDSplitter - Splits protein/peptide identifications off of annotated data files.
• MzMLSplitter - Splits an mzML file into multiple parts
• OpenSwathMzMLFileCacher - Caching of large mzML files
• SemanticValidator - SemanticValidator for analysisXML and mzML files.
• XMLValidator - Validates XML files against an XSD schema.

Algorithm Evaluation

• FFEval - Evaluation tool for feature detection algorithms.
• LabeledEval - Evaluation tool for isotope-labeled quantitation experiments.
• RTEvaluation - Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs.
• TransformationEvaluation - Simple evaluation of transformations (e.g. RT transformations produced by a MapAligner tool).

Protein/Peptide Identification

• DecoyDatabase - Create decoy peptide databases from normal ones.
• Digestor - Digests a protein database in-silico.
• DigestorMotif - Digests a protein database in-silico (optionally allowing only peptides with a specific motif) and produces statistical data for all peptides.
• 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.
• IDScoreSwitcher - Switches between different scores of peptide or protein hits in identification data.
• UTILS_RNPxl - Tool for RNP cross linking experiment analysis.
• SequenceCoverageCalculator - Prints information about idXML files.
• SpecLibCreator - Creates an MSP-formatted spectral library.
• SpectraSTSearchAdapter - An interface to the 'SEARCH' mode of the SpectraST program (external, beta).
• PSMFeatureExtractor - Creates search engine specific features for PercolatorAdapter input.
• MSFraggerAdapter - Peptide Identification with MSFragger.
• NovorAdapter - De novo sequencing from tandem mass spectrometry data.

Cross-linking

• OpenPepXL - Search for peptide pairs linked with a labeled cross-linker.
• OpenPepXLLF - Search for cross-linked peptide pairs in tandem MS spectra.
• XFDR - Calculates false discovery rate estimates on crosslink identifications.

Quantitation

• ERPairFinder - Evaluate pair ratios on enhanced resolution (zoom) scans.
• FeatureFinderSuperHirn - Find Features using the SuperHirn Algorithm (it can handle centroided or profile data, see .ini file).
• UTILS_MetaboliteAdductDecharger - Decharges and merges different feature charge variants of the same small molecule.
• MRMPairFinder - Evaluate labeled pair ratios on MRM features.
• OpenSwathWorkflow - Complete workflow to run OpenSWATH.

Metabolite Identification

• AccurateMassSearch - Find potential HMDB IDs within the given mass error window.
• MetaboliteSpectralMatcher - Identify small molecules from tandem MS spectra.
• SiriusAdapter - De novo metabolite identification.

Quality Control

• QCCalculator - Calculates basic quality parameters from MS experiments and compiles data for subsequent QC into a qcML file.
• QCEmbedder - This application is used to embed tables or plots generated externally as attachments to existing quality parameters in qcML files.
• QCExporter - Will extract several quality parameter from several run/sets from a qcML file into a tabular (text) format - counterpart to QCImporter.
• QCExtractor - Extracts a table attachment of a given quality parameter from a qcML file as tabular (text) format.
• QCImporter - Will import several quality parameter from a tabular (text) format into a qcML file - counterpart to QCExporter.
• QCMerger - Merges two qcML files together.
• QCShrinker - This application is used to remove extra verbose table attachments from a qcML file that are not needed anymore, e.g. for a final report.

Misc

• DeMeanderize - Orders the spectra of MALDI spotting plates correctly.
• ImageCreator - Creates images from MS1 data (with MS2 data points indicated as dots).
• MSSimulator - A highly configurable simulator for mass spectrometry experiments.
• MassCalculator - Calculates masses and mass-to-charge ratios of peptide sequences.
• OpenSwathDIAPreScoring - SWATH (data-independent acquisition) pre-scoring.
• OpenSwathRewriteToFeatureXML - Rewrites results from mProphet back into featureXML.
• OpenSwathFileSplitter - A tool for splitting a single SWATH / DIA file into a set of files, each containing one SWATH window.
• SvmTheoreticalSpectrumGeneratorTrainer - A trainer for SVM models as input for SvmTheoreticalSpectrumGenerator.
• PeakPickerIterative A tool for peak detection in profile data.
• DatabaseFilter - Filters a protein database in FASTA format according to one or multiple filtering criteria.
• TICCalculator - Calculates the TIC of a raw mass spectrometric file.
• MultiplexResolver - Resolves conflicts between identifications and quantifications in multiplex data.
• LowMemPeakPickerHiRes - A tool for peak detection on streamed profile data
• LowMemPeakPickerHiResRandomAccess - A tool for peak detection on streamed profile data
• MRMTransitionGroupPicker - Picks peaks in MRM chromatograms.
• ClusterMassTraces - Cluster mass traces occurring in the same map together.
• CorrelateMassTraces - Identifies precursor mass traces and tries to correlate them with fragment ion mass traces in SWATH maps.
• IDDecoyProbability - Estimate probability of peptide hits.
• RNADigestor - Digests an RNA sequence database in-silico.

Deprecated

• IDDecoyProbability - Estimates peptide probabilities using a decoy search strategy.
  WARNING: This utility is deprecated.