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 to 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 changed
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
Algorithm evaluation
- FFEval - Evaluation tool for feature detection algorithms.
- IDEvaluator - Evaluation tool, comparing peptide recovery at different q-value thresholds for multiple search engines (e.g., after ConsensusID). For interactive version use the IDEvaluatorGUI tool.
- LabeledEval - Evaluation tool for isotope-labeled quantitation experiments.
- MapAlignmentEvaluation - Evaluates alignment results against a ground truth.
- 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).
Peptide identification
- 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.
- DecoyDatabase - Create decoy peptide databases from normal ones.
- SequenceCoverageCalculator - Prints information about idXML files.
- 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.
- SpecLibCreator - Creates an MSP formated spectral library.
- RNPxl - Tool for RNP cross linking experiment analysis.
Quantitation
- ERPairFinder - Evaluate pair ratios on enhanced resolution (zoom) scans.
- MRMPairFinder - Evaluate labeled pair ratios on MRM features.
- FeatureFinderSuperHirn - Find Features using the SuperHirn Algorithm (it can handle centroided or profile data, see .ini file)
Misc
Metabolite identification
Quality control
Deprecated
- IDDecoyProbability - Estimates peptide probabilities using a decoy search strategy.
WARNING: This util is deprecated.