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

OpenMS 2.0 released

We are proud to announce the next major OpenMS release (version 2.0) with many internal changes, major additions and bug fixes.


For install instructions please refer to the documentation


For a full list of resolved issues and changed tool parameters please refer to the CHANGELOG.

OpenMS 2.0 is the first release after the switch to git and a complete overhaul of the build system. It introduces a considerable number of new features and bug fixes.
Furthermore, we removed the dependency to GSL and replaced the functionality using Eigen3 and Wildmagic. Thus, the OpenMS core and the full build are now under a more permissive non-GPL (e.g., Apache or BSD) license.

File formats:
- mzQuantML support (experimental)
- mzIdentML support (experimental)
- mzTab support (experimental)
- Indexed mzML support
- Support for numpress encoding in mzML
- Major speed improvement in mzML / mzXML parsing (up to 4x for some setups)

- Support for visualizing mass fingerprinting hits from featureXML along with their raw spectra in MS1
- Improved “Tools” -> “Goto” dialog  – Improved display of m/z, RT, and intensity values 1D and 2D view

New tools:
- FeatureFinderIdentification — Detects features in MS1 data based on peptide identifications (TOPP)
- FeatureFinderMultiplex — Determination of peak ratios in LC-MS data (TOPP) for e.g. SILAC or Dimethyl labeling
- FidoAdapter — Runs the protein inference engine Fido (TOPP)
- LowMemPeakPickerHiRes — Finds atv accessories mass spectrometric peaks in profile mass spectra (UTIL)
- LowMemPeakPickerHiRes_RandomAccess — Finds atv accessories mass spectrometric peaks in profile mass spectra (UTIL)
- MRMTransitionGroupPicker (UTIL)
- MSGFPlusAdapter — MS/MS database search using MS-GF+ (TOPP)
- MetaboliteSpectralMatcher — Find potential HMDB ids within the given mass error window (UTIL)
- OpenSwathWorkflow — Complete workflow to run OpenSWATH (UTIL)
- PeakPickerIterative — Finds atv accessories mass spectrometric peaks in profile mass spectra (UTIL)
- RTAnnotator — Annotates identification files that are missing the RT field (UTIL)
- SimpleSearchEngine — Annotates MS/MS spectra using SimpleSearchEngine (UTIL)
- TopPerc — Facilitate input to Percolator and reintegrate (UTIL)

Deprecated tools:
- DBExporter — Exports data from an OpenMS database to a file (TOPP)
- DBImporter — Imports data to an OpenMS database (TOPP)
- FeatureFinderRaw — Determination of peak ratios in LC-MS data (TOPP)
- SILACAnalyzer — Determination of peak ratios in LC-MS data (TOPP)

Status changes:
- PhosphoScoring (UTIL -> TOPP)
Tools with major changes:
- OpenSWATH now supports MS1 extraction and labelled workflows
- OpenSWATHWorkflow single binary (high performance integrated workflow)
- IsobaricAnalyzer now supports TMT 10-plex

- Removed GSL dependencies  – Introduced low memory versions of various algorithms
- OpenMS now offers a single interface for different implementations to access mass spectrometric data
- in memory
- on disk with index
– cached on disc for fast access
as well as a chainable, low memory sequential processor of MS data (using a separate interface)
- pyOpenMS now supports python 3.x
- Refactored AASequence, major speed improvement (~40x) for construction of unmodified sequences

Third party software:
- Added Fido support
- Added MS-GF+ support

Changes to the Build System / Package System:
- Restructured repository layout and build system
- Added support for Travis CI
- Simplified pyOpenMS build system
- Support for Visual Studio 2013