@openms-jenkins-bot openms-jenkins-bot released this Jan 3, 2018 · 3797 commits to develop since this release

Assets 6

Dear OpenMS-Users,

we are proud to announce the release of OpenMS 2.3.0. Grab it here

In the following you find all important changes to the previous version:


OpenMS 2.3 introduces a considerable number of new features and bug fixes.

Notable changes since version 2.2 are:

TOPPView:

  • Deletion of selections of Peak Annotations is reflected in the Peptide Hit
  • Buttons for saving ID files were merged to one single button. Format is determined by file extension or selected filter
  • Clicking on a data point in 2D view, the search range for close fragment ion spectra is extended if no spectra are found initially

New tools:

  • CometAdapter -- Annotates MS/MS spectra using Comet (TOPP)
  • MetaboliteAdductDecharger -- Decharges and merges different feature charge variants of the same metabolite (UTIL)
  • OpenPepXL -- Tool for protein-protein cross-linking identification using labeled linkers (UTIL)
  • OpenPepXLLF -- Tool for protein-protein cross linking with label-free linkers (UTIL)
  • PSMFeatureExtractor -- Computes extra features for each input PSM (UTIL)
  • SiriusAdapter -- Tool for metabolite identification using single and tandem mass spectrometry (UTIL)
  • XFDR -- Calculates false discovery rate estimates on protein-protein-crosslink identifications (UTIL)

Deprecated and removed tools:

  • None

Renamed tool:

  • LowMemPeakPickerHiRes_RandomAccess was renamed to LowMemPeakPickerHiResRandomAccess

Major changes in functionality:

  • Experimental design
    • Add support for fractions
  • FeatureLinkerUnlabeledKD
    • m/z and retention time tolerances for warping and linking are now separate parameters
  • IsobaricAnalyzer
  • FileInfo
    • For idXML files, the tool computes the average length of contained peptides
  • TopPerc
    • Renamed in PercolatorAdapter (still experimental)
  • OpenSWATH:
    • RT normalization now allows more models
    • Add S/N ratio for each ion trace

Library:

  • TOPP tools report their peak memory usage when using -debug 1 (or higher)
  • idXML files can now be written faster (about 10%)
  • pyOpenMS bindings for DataArrayByName getters
  • Python build are now split in compilation units and can thus run in parallel
  • FASTA files can now be written
  • Allow String values to be passed to EnzymaticDigestion::isValidProduct

File formats:

  • consensusXML now supports both channels and MS runs. Information will also be exported in mzTab

Scripts:

  • None

Databases:

  • None

Third-party software:

  • New: Comet "2016.01 rev. 3" for Windows 32bit/64bit, Linux 64bit, and MacOS 64bit
  • New: Percolator 3.1.2 for Windows 32bit/64bit, Linux 64bit, and MacOS 64bit (still experimental)
  • New: Sirius 3.5.1 for Windows 64bit, Linux 64bit, and MacOS 64bit
  • New: SpectraST 5.0 for Windows 64bit, Linux 64bit, and MacOS 64bit
  • Update MS-GF+ to Release (v2017.07.21)

Best regards,
The OpenMS-Developers

@jpfeuffer jpfeuffer released this Nov 13, 2017 · 2619 commits to master since this release

Assets 5

OpenMS 2.2 is a source-only release. It introduces a considerable number of new features and bug fixes.
For using new versions of the dependencies we included a new source package below, called OpenMS-2.2.0-bugfixNewContrib.tar.gz.

Notable changes since version 2.1 are:

New tools:

  • RNPxlSearch -- Annotate RNA to peptide crosslinks in MS/MS spectra (UTIL)
  • SpectraSTSearchAdapter -- Interface to the SEARCH Mode of the SpectraST executable (UTIL)
  • FeatureLinkerUnlabeledKD -- Feature linking using a KD tree (TOPP)
  • DatabaseFilter -- Filters a protein database (FASTA format) based on identified proteins (UTIL)
  • TargetedFileConverter -- Conversion of multiple targeted file formats (CSV, TraML etc)

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)

Databases:

  • By default, decoy sequences are now denoted by the prefix "DECOY_"

@timosachsenberg timosachsenberg released this Nov 21, 2016 · 4374 commits to master since this release

Assets 5

---- OpenMS 2.1 ----

OpenMS 2.1 introduces a considerable number of new features and bug fixes.

Notable changes since version 2.0.1 are:

New tools:

  • ExternalCalibration -- Applies an external mass recalibration (TOPP)
  • OpenSwathFileSplitter -- Splits SWATH files into n files, each containing one window (TOPP)
  • MultiplexResolver -- Completes peptide multiplets and resolves conflicts within them (UTIL)
  • TICCalculator -- Calculates the TIC from a mass spectrometric raw file (useful for benchmarking) (UTIL)

Deprecated and removed tools:

  • PILISIdentification -- performs a peptide/protein identification with the PILIS engine (TOPP)
  • PILISModelCV -- Perform a cross validation of the PILIS model parameters (TOPP)
  • PILISModelTrainer -- Train the PILIS model with a given set of spectra and identifications (TOPP)
  • PILISSpectraGenerator -- Generate spectra given a list of peptides and a PILIS model (TOPP)

Major changes in functionality:

  • Update notification: starting with OpenMS 2.1 all TOPP tools will check for updated versions of the tools
    online and will print an information message if a newer version is available. This version check occurs only
    once per day and tool. Information on which tools are executed will be collected anonymously to identify which
    tools are no longer used and to optimally distribute development resources. If the feature causes problems or
    concerns, it can be disabled through a command line switch or environment variable (see the documentation).
  • InternalCalibration:
    • supports calibration using a table of lock masses and peptide ids.
    • global or RT-chunked calibration
    • linear & quadratic models (with intensity weighting)
    • outlier removal via RANSAC
    • reoccurring calibrations can be quickly applied to other files using the novel ExternalCalibration tool
  • OpenSwathWorkflow
    • support for metabolites / small molecules
  • MapAlignerIdentification
    • support for "lowess" transformation model
  • AccurateMassSearch:
    • support for multiple databases
  • FeatureFinderMetabo
    • isotope spacing model for carbon rich molecules (e.g. lipids)
  • PeakPickerHiRes and MassTraceExtractor:
    • support for FWHM annotation

File formats:

  • Improved mzIdentML support (experimental)
  • Improved pepXML support
  • Improved support for indexed mzML files
  • Improved TraML support

Databases:

  • By default, decoy sequences are now denoted by a prefix 'DECOY_'.

Third-party software:

  • update for X!Tandem VENGEANCE (2015.12.15)
  • update for MS-GF+ Release v2016.10.14, released October 14, 2016
  • update for pwiz 3.0.9935
Assets 6

---- 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: