[Open-ms-announcements] Announcement: OpenMS 2.2 source-only release

[Timo S. <sac...@gm...>]

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   - ITRAQAnalyzer -- superseded by IsobaricAnalyzer
   - TMTAnalyzer -- superseded by IsobaricAnalyzer
   - ConvertTSVToTraML - superseded by TargetedFileConverter
   - ConvertTraMLToTSV - superseded by TargetedFileConverter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 <https://github.com/OpenMS/OpenMS/pull/2449>,
   #2458 <https://github.com/OpenMS/OpenMS/pull/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