OpenMS for proteomics
OpenMS provides a large amount of tools to analyse your proteomics datasets.
Starting from input files in either vendor-specific raw formats (convertible with the integrated ProteoWizard) or a number of open HUPO-compliant formats (mzML, mzXML), you can process your data by simply combining a set of our almost 200 ready-made tools from „The OpenMS proteomics pipeline (TOPP)”. These tools are available on the command line, from within workflow engines (e.g. KNIME and Galaxy) and a subset of them was packaged as ProteomeDiscoverer 2.x plugin.
These TOPP tools can roughly be categorised based on their applicability to certain common tasks of a proteomics pipeline:
- Import, export and conversion of vendor formats and several open community-driven XML formats (LINK and make a list somewhere)
- Preprocessing of spectra
- Filtering based on various properties
- Peak picking
- Baseline and noise filtering
- MS2 spectrum identification
- Support for third-party peptide search engines (OMSSA, Mascot, Myrimatch, XTandem, MSGF+)
- Own customisable and extensible basic search engine
- Indexing of peptides in custom protein databases with SeqAn
- Statistical validation via posterior error probability and FDR/q-value calculation
- Combining results of different peptide search engines with ConsensusID
- Working with MS1 maps
- Feature finding algorithms
- Retention time and full map alignment
- Creating a consensus over multiple replicates
- Feature-based quantification (labelled and unlabelled)
- Protein inference with Fido
- Visualisation of spectra (on all MS levels), features and peptide identifications in our TOPPView
- Finding RNA and protein-protein crosslinks
- Identification of phosphorylation sites with Luciphor
- Support for data independent acquisition via OpenSWATH integration
A full list of the tools can be found in our documentation here.
If you do not find what you are looking for and you have some experience in developing C++, you can adapt, extend as well as add new tools by contributing to our library or using the library in your own project (see our “Getting Started for developers”).