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

Signal Processing and Preprocessing

• PeakPickerIterative - A tool for peak detection in profile data.

File Handling

• CVInspector - A tool for visualization and validation of PSI mapping and CV 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.
• 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 true positives (TP), true negatives (TN), false positives (FP), and false negatives (FN) for an idXML file with predicted RTs.
• TransformationEvaluation - Simple evaluation of transformations (e.g. RT transformations produced by a MapAligner tool).

Protein/Peptide Identification

• DatabaseFilter - Filters a protein database in FASTA format according to one or multiple filtering criteria.
• DecoyDatabase - Creates 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.
• Epifany - Bayesian protein inference based on PSM probabilities.
• 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.
• MSFraggerAdapter - Peptide Identification with MSFragger.
• NovorAdapter - De novo sequencing from tandem mass spectrometry data.
• PSMFeatureExtractor - Creates search engine specific features for PercolatorAdapter input.
• 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).
• StaticModification - Allows to attach a set of fixed modifications to an idXML file (MS/MS search results), e.g. to add 15N (N15) labeling post-hoc.

Cross-linking

• RNPxlSearch - Annotates RNA-to-peptide cross-links in MS/MS spectra.
• RNPxlXICFilter - Removes MS2 spectra from treatment based on the fold change between control and treatment for RNA-to-peptide cross-linking experiments.

Quantitation

• ERPairFinder - Evaluates pair ratios on enhanced resolution (zoom) scans.
• FeatureFinderMetaboIdent - Detects features in MS1 data corresponding to small molecule identifications.
• FeatureFinderSuperHirn - Finds features using the SuperHirn algorithm (can handle centroided or profile data, see .ini file).
• ProteomicsLFQ - A standard Proteomics LFQ pipeline.
• MetaboliteAdductDecharger - Decharges and merges different feature charge variants of the same small molecule.
• MultiplexResolver - Resolves conflicts between identifications and quantifications in multiplex data.

Metabolite Identification

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

Targeted Experiments and OpenSWATH

• ClusterMassTracesByPrecursor - Identifies precursor mass traces and tries to correlate them with fragment ion mass traces in SWATH maps.
• MRMPairFinder - Evaluates labeled pair ratios on MRM features.
• OpenSwathDIAPreScoring - SWATH (data-independent acquisition) pre-scoring.
• OpenSwathFileSplitter - A tool for splitting a single SWATH / DIA file into a set of files, each containing one SWATH window.
• OpenSwathMzMLFileCacher - Caching of large mzML files.
• OpenSwathRewriteToFeatureXML - Rewrites results from mProphet back into featureXML.

RNA

• NucleicAcidSearchEngine - Search MzML files for oligonucleotides and their modifications.
• RNADigestor - Digests an RNA sequence database in-silico.
• RNAMassCalculator - Calculates masses and mass-to-charge ratios of RNA sequences.

Quality Control

• QCCalculator - Calculates basic quality parameters from MS experiments and compiles data for subsequent QC into a qcML file.
• QCEmbedder - Embeds tables or plots generated externally as attachments to existing quality parameters in qcML files.
• QCExporter - Extracts several quality parameter from several runs/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 - Imports several quality parameters from a tabular (text) format into a qcML file - counterpart to QCExporter.
• QCMerger - Merges two qcML files together.
• QCShrinker - Removes extra verbose table attachments from a qcML file that are not needed anymore, e.g. for a final report.

Misc

• ClusterMassTraces - Cluster mass traces occurring in the same map together.
• DeMeanderize - Orders the spectra of MALDI spotting plates correctly.
• ImageCreator - Creates images from MS1 data (with MS2 data points indicated as dots).
• MassCalculator - Calculates masses and mass-to-charge ratios of peptide sequences.
• MetaProSIP - Performs proteinSIP on peptide features for elemental flux analysis.
• MSSimulator - A highly configurable simulator for mass spectrometry experiments.
• SvmTheoreticalSpectrumGeneratorTrainer - A trainer for SVM models as input for SvmTheoreticalSpectrumGenerator.
• TICCalculator - Calculates the TIC of a raw mass spectrometric file.
• MSstatsConverter - Converter to input for MSstats.

Deprecated

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