OpenMS Changelog

What's new in OpenMS 2.0.0

• OpenMS 2.0 is the first release after the switch to git and a complete overhaul of the build system. It introduces a considerable number of new features and bug fixes.
• Furthermore, we removed the dependency to GSL and replaced the functionality using Eigen3 and Wildmagic. Thus, the OpenMS core and the full build are now under a more permissive non-GPL (e.g., Apache or BSD) license.
• FILE FORMATS:
• mzQuantML support (experimental)
• mzIdentML support (experimental)
• mzTab support (experimental)
• Indexed mzML support
• Support for numpress encoding in mzML
• Major speed improvement in mzML / mzXML parsing (up to 4x for some setups)
• TOPPVIEW:
• Support for visualizing mass fingerprinting hits from featureXML along with their raw spectra in MS1
• Improved “Tools” -> “Goto” dialog – Improved display of m/z, RT, and intensity values 1D and 2D view
• NEW TOOLS:
• FeatureFinderIdentification — Detects features in MS1 data based on peptide identifications (TOPP)
• FeatureFinderMultiplex — Determination of peak ratios in LC-MS data (TOPP) for e.g. SILAC or Dimethyl labeling
• FidoAdapter — Runs the protein inference engine Fido (TOPP)
• LowMemPeakPickerHiRes — Finds mass spectrometric peaks in profile mass spectra (UTIL)
• LowMemPeakPickerHiRes_RandomAccess — Finds mass spectrometric peaks in profile mass spectra (UTIL)
• MRMTransitionGroupPicker (UTIL)
• MSGFPlusAdapter — MS/MS database search using MS-GF+ (TOPP)
• MetaboliteSpectralMatcher — Find potential HMDB ids within the given mass error window (UTIL)
• OpenSwathWorkflow — Complete workflow to run OpenSWATH (UTIL)
• PeakPickerIterative — Finds mass spectrometric peaks in profile mass spectra (UTIL)
• RTAnnotator — Annotates identification files that are missing the RT field (UTIL)
• SimpleSearchEngine — Annotates MS/MS spectra using SimpleSearchEngine (UTIL)
• TopPerc — Facilitate input to Percolator and reintegrate (UTIL)
• DEPRECATED TOOLS:
• DBExporter — Exports data from an OpenMS database to a file (TOPP)
• DBImporter — Imports data to an OpenMS database (TOPP)
• FeatureFinderRaw — Determination of peak ratios in LC-MS data (TOPP)
• SILACAnalyzer — Determination of peak ratios in LC-MS data (TOPP)
• STATUS CHANGES:
• PhosphoScoring (UTIL -> TOPP)
• Tools with major changes:
• OpenSWATH now supports MS1 extraction and labelled workflows
• OpenSWATHWorkflow single binary (high performance integrated workflow)
• IsobaricAnalyzer now supports TMT 10-plex
• GENERAL:
• Removed GSL dependencies – Introduced low memory versions of various algorithms
• OpenMS now offers a single interface for different implementations to access mass spectrometric data
• in memory
• on disk with index
• – cached on disc for fast access
• as well as a chainable, low memory sequential processor of MS data (using a separate interface)
• pyOpenMS now supports python 3.x
• Refactored AASequence, major speed improvement (~40x) for construction of unmodified sequences
• THIRD PARTY SOFTWARE:
• Added Fido support
• Added MS-GF+ support
• CHANGES TO THE BUILD SYSTEM / PACKAGE SYSTEM:
• Restructured repository layout and build system
• Added support for Travis CI
• Simplified pyOpenMS build system
• Support for Visual Studio 2013