OpenMS

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

OpenMS 1.10 released

We are proud to announce the OpenMS 1.10 release with many major additions and bug fixes.

Much work has been put to make OpenMS 1.10 compatible to the KNIME (www.knime.org) workflow system which will in future extend the capabilities for down stream analysis. If you are interested in bleeding edge tools you can already try out OpenMS in KNIME (Note: That the integration is still in a beta.). A quick tutorial is given at the end of this overview.

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

Download: https://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-1.10/?

Installation process:
Search engines (OMSSA, X!Tandem, and MyriMatch) have been integrated into the Windows and Mac installers making the install process more convenient.

New tools:

  • OpenSWATH
  • QCCalculator
  • IDRipper
  • FeatureFinderMetabo
  • IDEvaluation
  • RNPxl
  • TMTAnalyzer

New file format support:

  • TraML 1.0.0
  • mzQuantML (experimental)
  • mzIdentML (experimental)
  • mzTab (experimental)

General:

  • Better chromatogram support
  • Decoy strings can now be prepended
  • Filtering of modified peptides
  • numerous memory and speed improvements
  • TMT-6plex support
  • EDTA conversion from feature and consensusXML in FileConverter
  • Filtering of MS2 spectra by identifications
  • FeatureFinderCentroided now supports non natural isotopic abundancies
  • and more …

New search engine support:

  • MyriMatch adapter

Fixed Bugs:

A full list of fixed bugs and new features in OpenMS 1.10 can be found in our issue tracker at Sourceforge. Just click on the link below to see the full list.

OpenMS 1.10 fixed bugs and added features

Installing OpenMS support in KNIME:
To do so, you need to download and install KNIME 2.7.2 available from www.knime.org. To add OpenMS to KNIME you first have to click on Help -> Install New Software and “Add” following installation source in the new window:

Name: KNIME Nightly Unstable
Location: http://tech.knime.org/update/community-contributions/nightly/

After clicking on “Ok” KNIME automatically checks the site. In “Community Contributions – Bioinformatics & NGS” you will now find OpenMS. Select it and click “Next”. After download and restart you will find under “Community Nodes” the “Generic KNIME Nodes” and OpenMS nodes.

The OpenMS Developers