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The codebase of the OpenMS project

Release2.0.1

8 years ago

---- OpenMS 2.0.1 ----

OpenMS 2.0.1 is a source only release of the core libraries and tools. This means that although we release the automatically generated installers, we denote that these are not fully supported/tested. The same holds for the use of the provided tools in the third-party workflow systems for which we established integration (e.g. KNIME). With over 300 merged pull requests, it introduces a considerable number of new features, bug fixes and speed improvements.

Notable changes are:

File formats:

  • Improved mzIdentML support (experimental)
  • Improved mzTab support (experimental)
  • Comet pepXML file reading support (experimental)
  • Search parameter units are retained through id files
  • Faster base64 decoding in XML files

Databases:

  • HMDB has been updated to version 3.6

TOPPView:

  • Added slight margin around data range (%2) for improved visualization
  • Added FeatureFinderMultiplex to the tools accessible from TOPPView
  • Some fixes to the scrollbar behaviour

Added tools:

  • IDScoreSwitcher -- Switches between different scores of peptide or protein hits in identification data (UTIL)
  • LuciphorAdapter -- Modification site localisation using LuciPHOr2 (TOPP)
  • MetaProSIP -- Performs proteinSIP on peptide features for elemental flux analysis (UTIL)
  • MzMLSplitter -- Splits an mzML file into multiple parts (UTIL)
  • OpenSwathAssayGenerator -- Generates assays according to different models for a specific TraML (TOPP)

Removed tools:

  • RTAnnotator -- Annotates identification files that are missing the RT field (UTIL)

Tools with major changes:

  • OpenSWATH now outputs peak apices
    • Improved iRT correction
    • Assay generator
    • UIS scoring
  • Deuterium labeling in MetaProSIP (experimental)
  • XTandemAdapter allows for external config file
  • TextExporter can optionally export PeptideIdentification and PeptideHits meta-values
  • FeatureLinkerUnlabeledQT speed improvements
  • FileMerger allows to concatenate files in RT
  • MzTabExporter supports protein IDs
  • PeakPickerWavelet speedup
  • HiResPrecursorMassCorrector supports correction of precursors to detected features
  • FeatureFinderMultiplex speed improvements

Library:

  • Support for user definable enzymes available in EnzymesDB.xml
  • PeptideIndexing is now available as internal algorithm
  • EnzymaticDigestion allows for minimum / maximum length constraints
  • HyperScore and PScore implementations
  • Fits allow extrapolation of data values
  • QT clustering is now order independent
  • Additional convinience functions to access the nearest spectrum peak in a mass tolerance window
  • User defined averagine compositions
  • A fast linear lowess implementation has been added
  • MetaInfoInterface has been added to FeatureMap to store additional meta-values
  • Calculation of Median Absolute Deviation

General:

  • OpenMS writes indexed mzML by default
  • OpenMS home directory can be configured through OPENMS_HOME_DIR environment variable
  • Updated GenericWrapper definitions for MS-GF+ and Mascot

Third party software: