Dear OpenMS users,

we are proud to announce the release of OpenMS 2.4.0. Grab it

Notable changes since version 2.3 are:


  • Switch to Qt 5 (>= 5.5)


  • New developer documentation to get started developing tools with OpenMS


  • Improved mass calculations for isotope distributions
  • Moved tool code from the tool to the library
  • BinnedSpectrum now also supports offsets
  • Improved peak type estimation
  • Improved adduct grouping
  • New EMG fitter for peak intensity imputation
  • Targeted / untargeted spectra extraction and matching
  • Spectra matching against a spectra library, using contrast angle similary function
  • More precise peak integration (trapezoid, simpson)

New tools:

  • AssayGeneratorMetabo — Assay library generation from DDA data (Metabolomics) (UTIL)
  • ClusterMassTraces — Creates pseudo spectra (UTIL)
  • ClusterMassTracesByPrecursor — Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile (UTIL)
  • CruxAdapter — Identifies MS/MS spectra using Crux (TOPP)
  • MSFraggerAdapter — Peptide Identification with MSFragger (UTIL)
  • MSstatsConverter — Converter to input for MSstats (UTIL)
  • MaRaClusterAdapter — Facilitate input to MaRaCluster and reintegrate (TOPP)
  • NovorAdapter — Template for Tool creation (UTIL)
  • RNADigestor — Digests an RNA sequence database in-silico (UTIL)

Deprecated and removed tools:

  • AdditiveSeries — Computes an additive series to quantify a peptide in a set of samples (TOPP)
  • IDEvaluator — Computes a ‘q-value vs. #PSM’ plot which is saved as an image to visualize the number entifications for a certain q-value (UTIL)
  • IDEvaluatorGUI — Computes a ‘q-value vs. #PSM’ plot to visualize the number identifications for a certain q-value (UTIL)
  • RNPxl — Tool for RNP cross linking experiment analysis (UTIL) (superseded by RNPxlSearch)

Changed Tools:

  • SiriusAdapter now supports several input data
  • FileFilter now supports filtering spectra by similarity
  • PeptideIndexer now supports automatic detection of decoy suffix/prefix string and position
  • PeakPickerHiRes now supports automatic detection and picking of profile spectra
  • Support for MSFragger search engine through MSFraggerAdapter
  • Support for Crux search engine through CruxAdapter
  • Support for Maracluster through MaraClusterAdapter
  • OpenPepXL was improved in efficiency and usability
  • IDFileConverter now supports the Cross-Linking MS specific xquest.xml format


  • Improved visualization of identification results and ion annotations
  • Support for visualization of Ion Mobility and DIA data

Major changes in functionality:

  • None

File formats:

  • Importer for MSP files


  • None


  • None

Third-party software:

  • New: maracluster (0.05)
  • Update: MS-GF+ to Release (2018.01.30)
  • Update: Sirius 4 for Windows 64bit, Linux 64bit, and MacOS 64bit
  • Update: Crux (crux-3.1.8b78546) on all 64bit platforms.