Dear OpenMS users,
we are proud to announce the release of OpenMS 2.4.0. Grab it
here
Notable changes since version 2.3 are:
Dependencies:
- Switch to Qt 5 (>= 5.5)
Documentation:
- New developer documentation to get started developing tools with OpenMS
Library:
- 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- RNPxl — Tool for RNP cross linking experiment analysis (UTIL) (superseded by RNPxlSearch)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
TOPPView:
- 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
Scripts:
- None
Databases:
- 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.