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

OpenMS 1.11 released

We are proud to announce the OpenMS 1.11 release with many major additions and bug fixes.

OpenMS 1.11 is the first release with fully integrated Python bindings (termed pyOpenMS). For further details, please refer to

Important: Please note that currently there is no working installer for Mac OS X 10.6. We will provide one as soon as possible.

Please find below the list of changes from 1.10 to 1.11:

File formats:

  • QcML support
  • pepXML exported from Mascot (added support)
  • mzTab updated to 1.0RC3
  • ParamXML updated to v 1.6.2
  • support for CTD schema 0.3
  • full support of sourceFile tag in mzML (all source files are written, SHA1 support)


  • handle .mzML file with mixed spectra and chromatograms (prefer spectra)
  • chromatograms of all types can be displayed (not just SRM)
  • link to documentation and webpage fixed
  • fix a segfault when loading empty chromatograms into TOPPView


  • link to documentation and webpage fixed

TOPP tools:


  • FeatureLinkerUnlabeledQT: performance (speed and memory) improvement
  • FeatureLinkerUnlabeled: performance (memory) improvement (now constant in number of input maps)
  • MapAlignerPoseClustering: performance (memory) improvement (now constant in number of input maps)
  • EICExtractor: critical bugfix if the input map was not sorted
  • PeptideIndexer: by default now demands that the peptide is fully tryptic (“-enzyme:specificity none” restores the old behavior)
  • FileFilter: filter MS2 spectra by consensus map feature overlap, collision energy, isolation window width
  • ProteinResolver: documentation and interface improvements
  • QCCalculator/QCEmbedder/QCExtractor: multiple improvements
  • WindowMower: speed improvement (movetype either slide or jump [faster])


  • AccurateMassSearch: AccurateMassSearch assembles metabolite features from singleton mass traces.
  • IsobaricAnalyzer: Extracts and normalizes isobaric labeling information from an MS experiment. This merges the previous TMTAnalyzer and ITRAQAnalyzer functionality
  • QCExtractor: Extracts a table attachment to a given qc parameter
  • QCImporter: Embed tables or pictures in QcML


  • Python bindings allow full access to the OpenMS API from Python
  • TOPPTools now support passing of all parameters on the command line (use –helphelp)
  • Better chromatogram support (for NoiseFilterGaussian, NoiseFilterSGolay, PeakPickerHiRes)

Search engine support:

  • Mascot 2.4 is now supported
  • OMSSAAdapter with improved memory footprint
  • N-terminal modifications work now with X!Tandem

Changes to the Build System / Package System:

  • shared linking works for all contrib packages with automated detection using CMake find modules
  • upgrade of xerces to version 3.1.1
  • upgrade of libsvm to version 3.12


  • public inheritance from std::vector and std::set has been reduced in the OpenMS codebase (removed from ConsensusFeature, FeatureMap, ConsensusMap, MSExperiment)
  • addition of the OpenMS/INTERFACES folder which contains proposed OpenMS interfaces for reading/writing spectra


  • TMTAnalyzer, ITRAQAnalyzer -> please use IsobaricAnalyzer instead
  • Several functions provided by std::vector in the MSSpectrum interface are now deprecated (e.g. push_back, reserve etc.)

Resolved issues:
A full list of fixed bugs and new features in OpenMS 1.11 can be found in our issue tracker at Sourceforge.

The OpenMS Developers