OpenMS 2.2 source-only release

03.07.2017

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  • ITRAQAnalyzer — superseded by IsobaricAnalyzer
  • TMTAnalyzer — superseded by IsobaricAnalyzer
  • ConvertTSVToTraML – superseded by TargetedFileConverter
  • ConvertTraMLToTSV – superseded by TargetedFileConverter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

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