An open-source framework for mass spectrometry and TOPP – The OpenMS Proteomics Pipeline

OpenMS 2.0.1 released

We are proud to announce the next source-only OpenMS release (version 2.0.1) with major additions and bug fixes.


For up-to-date install instructions please refer to the documentation: documentation .


For details on resolved issues and merged features please see our GitHub page . A full list of changed tool parameters can be found in the released CHANGELOG .

OpenMS 2.0.1 is a source-only release of the core libraries and tools. This means that although we released the automatically generated installers for your convenience, we denote that these are not fully supported/tested. The same holds for the use of our provided tools in the third-party workflow systems for which we established integration (e.g. KNIME, ProteomeDiscoverer/CompoundDiscoverer). Our team of developers is happy to help you with any issues you might encounter. In such a case, please write to the mailing list  (open-ms-generalatlistsdotsourceforgedotnet)   or submit an issue on our GitHub issue tracker . Stabilization of the interaction with third-party tools and workflow systems is scheduled for the next major release.

Nonetheless, with over 300 merged pull requests, this source-only release introduces a considerable number of new features, bug fixes and speed improvements.

Notable changes are:

File formats:

* Improved mzIdentML support (experimental)
* Improved mzTab support (experimental)
* Comet pepXML file reading support (experimental)
* Search parameter units are retained through id files
* Faster base64 decoding in XML files


* HMDB has been updated to version 3.6


* Added slight margin around data range (%2) for improved visualization
* Added FeatureFinderMultiplex to the tools accessible from TOPPView
* Some fixes to the scrollbar behavior

Added tools:

* IDScoreSwitcher — Switches between different scores of peptide or protein hits in identification data (UTIL)
* LuciphorAdapter — Modification site localisation using LuciPHOr2 (TOPP)
* MetaProSIP — Performs proteinSIP on peptide features for elemental flux analysis (UTIL)
* MzMLSplitter — Splits an mzML file into multiple parts (UTIL)
* OpenSwathAssayGenerator — Generates assays according to different models for a specific TraML (TOPP)

Removed tools:

* RTAnnotator — Annotates identification files that are missing the RT field (UTIL)

Tools with major changes:

* OpenSWATH now outputs peak apices
* Improved iRT correction
* Assay generator
* UIS scoring
* Deuterium labeling in MetaProSIP (experimental)
* XTandemAdapter allows for external config file
* TextExporter can optionally export PeptideIdentification and PeptideHits meta-values
* FeatureLinkerUnlabeledQT speed improvements
* FileMerger allows to concatenate files in RT
* MzTabExporter supports protein IDs
* PeakPickerWavelet speedup
* HiResPrecursorMassCorrector supports correction of precursors to detected features
* FeatureFinderMultiplex speed improvements


* Support for user definable enzymes available in EnzymesDB.xml
* PeptideIndexing is now available as internal algorithm
* EnzymaticDigestion allows for minimum / maximum length constraints
* HyperScore and PScore implementations
* Fits allow extrapolation of data values
* QT clustering is now order independent
* Additional convinience functions to access the nearest spectrum peak in a mass tolerance window
* User defined averagine compositions
* A fast linear lowess implementation has been added
* MetaInfoInterface has been added to FeatureMap to store additional meta-values
* Calculation of Median Absolute Deviation


* OpenMS writes indexed mzML by default
* OpenMS home directory can be configured through OPENMS_HOME_DIR environment variable
* Updated GenericWrapper definitions for MS-GF+ and Mascot

Third-party software:

* LuciphorAdapter (experimental) PTM localization using the LuciPHOr2 algorithm ( )