OpenMS 2.2 source-only release

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/OpenMS/releases/tag/Release2.2.0).
Alternatively, you can download the full source code at https://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-2.2.

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• ITRAQAnalyzer — superseded by IsobaricAnalyzer
• TMTAnalyzer — superseded by IsobaricAnalyzer
• ConvertTSVToTraML – superseded by TargetedFileConverter
• ConvertTraMLToTSV – superseded by TargetedFileConverter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)