Dear OpenMS-Users,

we are proud to announce the release of OpenMS 2.3.0. Grab it here

In the following you find all important changes to the previous version:

OpenMS – Name of the project and our C++ library
TOPP – “The OpenMS Proteomics Pipeline”, collection of chainable tools for flexible HPLC/MS workflows
TOPPAS – “The OpenMS Proteomics Pipeline Assistant”, graphical tool to interactively build and run HPLC/MS workflows
TOPPView – Versatile viewer for HPLC/MS data
INI file – parameter configuration file, holding custom parameter settings for TOPP tools
INIFileEditor – graphical parameter editor for INI files
Parameters – list of algorithm or TOPP tool parameters that changed in this release

—- OpenMS 2.3 —-
OpenMS 2.3 introduces a considerable number of new features and bug fixes.

Notable changes since version 2.2 are:

– Deletion of selections of Peak Annotations is reflected in the Peptide Hit
– Buttons for saving ID files were merged to one single button. Format is determined by file extension or selected filter
– Clicking on a data point in 2D view, the search range for close fragment ion spectra is extended if no spectra are found initially

New tools:
– CometAdapter — Annotates MS/MS spectra using Comet (TOPP)
– MetaboliteAdductDecharger — Decharges and merges different feature charge variants of the same metabolite (UTIL)
– OpenPepXL — Tool for protein-protein cross-linking identification using labeled linkers (UTIL)
– OpenPepXLLF — Tool for protein-protein cross linking with label-free linkers (UTIL)
– PSMFeatureExtractor — Computes extra features for each input PSM (UTIL)
– SiriusAdapter — Tool for metabolite identification using single and tandem mass spectrometry (UTIL)
– XFDR — Calculates false discovery rate estimates on protein-protein-crosslink identifications (UTIL)

Deprecated and removed tools:
– None

Renamed tool:
– LowMemPeakPickerHiRes_RandomAccess was renamed to LowMemPeakPickerHiResRandomAccess

Major changes in functionality:
– Experimental design
– Add support for fractions
– FeatureLinkerUnlabeledKD
– m/z and retention time tolerances for warping and linking are now separate parameters
– IsobaricAnalyzer
– Support for TMT11plex (
– FileInfo
– For idXML files, the tool computes the average length of contained peptides
– TopPerc
– Renamed in PercolatorAdapter (still experimental)
– OpenSWATH:
– RT normalization now allows more models
– Add S/N ratio for each ion trace

– TOPP tools report their peak memory usage when using -debug 1 (or higher)
– idXML files can now be written faster (about 10%)
– pyOpenMS bindings for DataArrayByName getters
– Python build are now split in compilation units and can thus run in parallel
– FASTA files can now be written
– Allow String values to be passed to EnzymaticDigestion::isValidProduct

File formats:
– consensusXML now supports both channels and MS runs. Information will also be exported in mzTab

– None

– None

Third-party software:
– New: Comet “2016.01 rev. 3” for Windows 32bit/64bit, Linux 64bit, and MacOS 64bit
– New: Percolator 3.1.2 for Windows 32bit/64bit, Linux 64bit, and MacOS 64bit (still experimental)
– New: Sirius 3.5.1 for Windows 64bit, Linux 64bit, and MacOS 64bit
– New: SpectraST 5.0 for Windows 64bit, Linux 64bit, and MacOS 64bit
– Update MS-GF+ to Release (v2017.07.21)