OpenMS 2.2 is a source-only release. It introduces a considerable number of new features and bug fixes.
We recommend checking out the Release2.2.0 git tag
(https://github.com/OpenMS/
Alternatively, you can download the full source code at https://sourceforge.
Notable changes since version 2.1 are:
Databases:
- By default, decoy sequences are now denoted by the prefix “DECOY_”
New tools:
- FeatureLinkerUnlabeledKD — Fast feature linking using a KD tree (TOPP)
- SpectraSTSearchAdapter — Interface to the SEARCH Mode of the SpectraST executable (UTIL)
- DatabaseFilter — Filters a protein database (FASTA format) based on identified proteins (UTIL)
- TargetedFileConverter — Conversion of multiple targeted file formats (CSV, TraML, etc.)
- RNPxlSearch — Annotate RNA to peptide crosslinks in MS/MS spectra (UTIL)
Deprecated and removed tools:
- ITRAQAnalyzer — superseded by IsobaricAnalyzer
- TMTAnalyzer — superseded by IsobaricAnalyzer
- ConvertTSVToTraML – superseded by TargetedFileConverter
- ConvertTraMLToTSV – superseded by TargetedFileConverter
- MapAlignmentEvaluation — removed as deprecated
Major changes in functionality:
- OpenSWATH analysis
- Support for metabolomics workflows
- Support for scanning SWATH (SONAR)
- Support for SQL-based file formats
- XTandemAdapter
- Simplified usage
- Improved support for PTMs and newer X! Tandem versions (“Vengeance”, “Alanine”)
- IsobaricAnalyzer
- Support for TMT10plex
- Support for quantification in MS3 data
- IDMapper
- Allows to map unidentified tandem mass spectra to features
- FeatureFinderIdentification
- Advanced multi-sample support using machine learning
- FileFilter
- Allows users to enable zlib and lossy compression (see “-lossy_compression”)
- Allows users to set desired mass accuracy
- IDFilter
- Added option to filter for valid digestion products
- FalseDiscoveryRate
- Allow filtering by q-value in the tool (no need for IDFilter with “score:pep” option)
Library:
- Averagine approximation for fragment isotope distributions
- Precursor mass correction supports correction to highest intensity peak in tolerance window
- Functionality for resampling and adding of spectra
- Protein-protein cross-link spectrum generator
- Terminal modifications are now separated by “.” in text output
- SQLite support in OpenSWATH
- TheoreticalSpectrumGenerator speed-up and removal of RichPeak code
- Removal of template parameters from MSExperiment (reduced compile time and binary size)
- Allow estimation of isotope distributions with predefined numbers of sulfur atoms
- Improved handling of bracket notation for modified residues (e.g. N[2457.877]VSVK)
- Improved handling of terminal and residue specificity of modifications
- Improved annotation of peptide identifications with spectrum references
- Improved handling of unknown amino acids (“X”) in sequences
File formats:
- Improved mzML support for SONAR data and mzML with drift time (experimental)
- Improved support for cross-link data and unknown modifications in mzIdentML
- mzXML writer able to write MaxQuant-compatible files
- mzML files now routinely support substantial compression (up to 5x compression, see #2449, #2458)
- Support for Percolator result files based on X! Tandem searches
Scripts:
- New R script for visualizing RT transformations (trafoXML)
Known Build Issues:
You might encounter build issues on recent compilers. We recommend using Visual Studio Version 2015 and GCC 5.0 or older.
The OpenMS Developers