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CHANGELOG
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Glossary:
OpenMS - Name of the project and our C++ library
TOPP - "The OpenMS Proteomics Pipeline", collection of chainable tools for flexible HPLC/MS workflows
TOPPAS - "The OpenMS Proteomics Pipeline Assistant", graphical tool to interactively build and run HPLC/MS workflows
TOPPView - Versatile viewer for HPLC/MS data
INI file - parameter configuration file, holding custom parameter settings for TOPP tools
INIFileEditor - graphical parameter editor for INI files
Parameters - list of algorithm or TOPP tool parameters that changed in this release
PR - Pull Request (on GitHub), i.e. integration of a new feature or bugfix
UTIL - An executable, just like a TOPP tool, but usually experimental or of lesser importance to common pipelines
#<number>, e.g. #4957 - a reference to an issue or pull request on GitHub, visit https://github.com/OpenMS/OpenMS/pull/4957 for details
------------------------------------------------------------------------------------------
---- OpenMS 3.0 (releases 4/2022) ----
------------------------------------------------------------------------------------------
- full release
- OpenSwath: Add support for diaPASEF data with overlapping m/z and IM windows, and add new outputs on ion mobility features (delta_im)
- OpenSwath: Fix duplicated transition error when multiple genes map to a single peptide (#5653)
- TOPPView: TheoreticalSpectrumGenerationDialog now supports generation of isotope patterns for metabolites
- pyopenms: pyopenms-extra is renamed to pyopenms-docs.
- Add extractSpectra to TargetedSpectraExtractor with support of MS1 features
- TargetedSpectraExtractor::searchSpectrum added an option to add unknown features to the result featureMap
- Fixed race condition when logging messages.
- Added the support for 'no cleavage' for XTandemAdapter and CometAdapter (#6133).
- ParamEditor with more convenient StringList editing (#5135)
- TOPPAS: add a `recent files` submenu
- removed InspectAdapter
- removed OMSSAAdapter
- removed MyriMatchAdapter
- removed Crux
- OpenMS documentation is moved to openms.readthedocs.io/en/latest. OpenMS API
reference and advanced developer documentation remains inside OpenMS doxygen
documentation.
- Add support for user defined ribonucleotides with phosphorothioate linkages
New Tools:
- FLASHDeconv -- Ultra-fast high-quality deconvolution enables online processing of top-down MS data (TOPP)
------------------------------------------------------------------------------------------
---- OpenMS 2.8 (released 2/2022) ----
------------------------------------------------------------------------------------------
- source + conda release only
- Restructuring of Imported CMake targets and pyOpenMS CMake
- Reduce exposition of third-party libraries to interface
- greatly improved pyOpenMS documentation and extra functions (in the pyopenms-extra submodule)
- Fixes IDMapper for isobaric labelling experiments (will lead to much more identifications)
- Deisotoping algorithm using KL
- PeptideIndexer supports ambiguous AA's in Peptide sequence (as reported by recent Mascot versions) (#5776)
- SeqAn external library removed from source tree (not needed anymore)
- Resolve compatibility issues between IDRipper and IDMerger (#4957)
- Basic MzTabM support for AccurateMassSearch
- Changed default parameter keep_unidentified_masses to "true" (AccurateMassSearch/AccurateMassSearchEngine)
- Added parameter allow_nterm_protein_cleavage to PeptideIndexer to support no cleavage.
- Fixes and improves TheoreticalSpectrumGenerationDialog in TOPPView (closes #5787) (#5883)
------------------------------------------------------------------------------------------
---- OpenMS 2.7 (released 9/2021) ----
------------------------------------------------------------------------------------------
General:
- OpenMS now expects a compiler that supports C++17
- Config storage path on linux changed to ~/.config/
- Some documentation improvements to pyOpenMS https://pyopenms.readthedocs.io/en/latest/
- PyOpenMS checks if `OPENMS_DATA_PATH` environment variable is set, before setting to default value
Adapters/Third-party support:
- Added support for SIRIUS 4.9.0
- Added basic Triqler export
- Improved NOVOR support
- Improved MSFragger support
- Removed Inspect support
- Easier 15N-labeling support for XTandemAdapter by shipping the required AA mass modification file (#5026)
What's new:
- Add some support for integrating spectral information when conducting DDA metabolomics experiments
- SimpleSearchEngine and algorithm: Additional spectrum features for percolator added
- FeatureFinderMetaboIdent: Targeted feature extraction is now also available from pyOpenMS
- AssayGeneratorMetabo: Added SIRIUS 4.9.0 support, allowing internal decoy generation and added internal feature linking support
- QCCalculator: export in mzQC file format is now available
New Tools:
- OpenMSDatabasesInfo -- Prints the content of OpenMS' enzyme and modification databases to TSV (UTIL)
- TriqlerConverter -- Converter to input for Triqler (UTIL)
Removed Tools:
- FeatureFinderSuperHirn -- Finds mass spectrometric features in mass spectra (TOPP)
- InspectAdapter -- Annotates MS/MS spectra using Inspect (TOPP)
Further fixes:
- Support for GLPK 5.x (#5127)
- IPF (identification of peptidoforms): add a check for terminal residue modification when generating theoretical peptidoforms
- Reduced build times on Windows
- Reduced AddressSanitizer warnings
File formats:
- Exporter for MSP files
- Improved support for reading NIST MSP files
Dependencies:
- Promoted SeqAn v1 to C17. Moved Seqan from contrib to main source tree (as it is not officially maintained anymore).
Library:
- Removed Elements.xml and Residues.xml. Hard-coded elements and residues for better performance/startup times.
- Moved algorithm of FeatureFinderMetaboIdent into library
- Added support for isotopic labelling experiments (MDV)
- Removed SuperHirn library
GUI tools:
- TOPPView: Various bug fixes
- TOPPView: Dynamic detection of tools in TOPPView upon startup
- TOPPView: Improved DIA data browsing
- TOPPAS: add a `recent files` submenu
- ParamEditor: with more convenient StringList editing
- SwathWizard: Allow opening in TOPPView
------------------------------------------------------------------------------------------
---- OpenMS 2.6 (released 10/2020) ----
------------------------------------------------------------------------------------------
We now create nightly pyopenms wheels (https://pypi.org/project/pyopenms-nightly/) and conda packages (https://anaconda.org/OpenMS/)
Adapters/Third-party support:
- LuciphorAdapter now stores which modifications were used for localization (#4771) and localization scores are reported in mzTab #4772
- Added Percolator3.0 support, fixed ConsensusID reading from wrong (Percolator-overwritten) meta data (#4829), and adapted the Regex parsing of XTandem Percolator output files #4849
- Added options introduced in new MSGF versions #4713
- Updated IsoSpec fine structure isotopic calculator sources to v 2.1.0 #4733
- Updated other third-party tools
What's new:
- Introduced a Wizard for Swath data (#4647 #4706 #4758 #4769 #4773 #4837), which also reports summary statistics about Swath TargetedExperiments #4788 #4790
- UTIL StaticModification: Applies a set of modifications to all PeptideIDs in an idXML file (UTIL)
- TOPP DatabaseSuitability: Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra. #4791 #4781 #4814
- Added support for QC of labeled experiments (iTRAQ/TMT)
- Added automated QC computations for MRM (#4637)
- Adapted consensusXML and mzTab to support protein groups (#4630)
- Consensus/IDMerger: Introduced use of merge idx to ensure keeping track of primaryRuns
- Epifany: Added calculation of protein group FDR, ID filtering for protein group scores (#4802) and support for inference on not just individual samples but also consensusXML files
- FeatureFinderCentroided/FeatureFinderAlgorithmPicked: Improved runtime performance #4652 #4701
- FeatureFinderIdentification: Improved SLIM-labeling experiment support
- FileConverter: Improved runtime performance when producing mzML output #4750
- FeatureLinkerQT: Introduced Fibonacci heaps for large runtime optimization (#4721) and fixed related preconditions/segfaults #4756 #4760 #4778
- IDFilter: added support for consensusXMLs #4798 #4799
- MapAlignerIdentification: New option to use an "identity" transformation when data is too sparse to determine alignment model #4628
- MzTabExporter: changed to only export one main score, and to derive nativeIDs from data (#4767). Now ensures that all output rows contain the same number of columns #4801
- MzTabExporter on LFQ consensusXMLs produces 100% PRIDE validated mzTabs now
- ProteomicsLFQ: Added spectral counting as quantification method (#4726). Introduced performance improvements for AASequence and string parsing, especially for modified sequences. Various further improvements (e.g. #4669)
- SimpleSearchEngine (multithreaded), TheoreticalSpectrumGenerator, MSSpectrum: Runtime optimization #4709
- Further introduction of more file streaming to address possible memory consumption issues #4682 #4694
Further fixes:
- We now limit double precision to 17 digits during file writes #4636
- Ensure that CometAdapter always writes indexed mzML fixes for CometAdapter (#4653), fixed the writing of terminal modifications with specific origin in Comet (#4742), the writing of protein terminal mods in Comet and MSGF adapter #4710, and the Comet pepXML modification parsing #4755
- Removed secondary search engine settings duplication in mzTab MTD section. #4720
- Improved XTandem output protein parsing #4789 to fix Issue #4770
- Increased (partial) support for parsing mzid with nonstandard, non-CV-term scores, fixes #4859
- Fixes to NucleicAcidSearchEngine mzTab output #4692
- ConsensusID now passes spectrum reference meta values along #4703
- Fix to LFQ requantification #4633
- Improved MapAlignerTreeGuided memory usage (#4704) and fixed segfault when featureXML contains no IDs #4665
- TOPPAS fixes #4780
Various:
- OMMSAAdapter now writes out native ids and spectrum references #4852
- FileInfo: Report more charge distribution and MS2 activation-method information for Raw files #4836
- Added sum formula output in RNAMassCalculator #4677
- Added automatic OpenMS tool reporting of peak memory usage #4712
- Some extra tools documentation outputs #4822 #4823
- Extended mapping of filetypes and mimetypes for knime output formats documentation #4839
- RTEvaluation: fixed output formats #4533
- Some further clarifications, standardization/consolidation of outputs formats/consistency
- Continued fixes/improvement of documentation
- Removed deprecated version of PeakPickerHiRes (LowMemPeakPickerHiResRandomAccess and LowMemPeakPickerHiRes). Their functionality can be accessed through options of PeakPickerHiRes
- moved the config storage location for unix installations to comply with X Display Group (freedesktop.org) guidelines.
-------------------------------------------------------------------------------------------
---- OpenMS 2.5 (released 2/2020) ----
-------------------------------------------------------------------------------------------
OpenMS 2.5 ships exciting new tools and improvements.
General:
- support for RNA mass spectrometry
- TMT16plex support for IsobaricAnalyzer (see PR #4295)
- improved MsStats/MsStatsTMT output support (see PR #4181, #4207)
- extended MaxQuant-compatible mzXML support (via FileConverter) (see PR #4432, #4423)
- QualityControl Workflow (all in the QC folder)
- OpenMS and pyOpenMS support for oligonucleotides
- OpenSWATH support for ion mobility extraction and scoring
- OpenSWATH support for metabolite assay library building through SIRIUS (and metabolite extraction and scoring)
- OpenSWATH support for PRM
- TOPPAS improvements (see PR #4100, #4121, #4266, #4497)
- fixes to PeptideIndexer for X!Tandem special cutting rules and ambiguous amino acids (see PR #4356)
- support for HDF5
- support for hyperfine isotopic distributions (through IsoSpec)
- JSON support (see PR #3786)
- speed improvements (loading/storing files, handling peptide sequences)
- support for VS2019 and GCC 9.1 (see PR #4211)
- support for outlier removal in IDPosteriorErrorProbability
- reduced memory footprint of FeatureFinderIdentification through batch processing
New Tools:
- Epifany -- Runs a Bayesian protein inference (UTIL)
- FeatureFinderMetaboIdent -- Detects features in MS1 data based on metabolite identifications (UTIL)
- GNPSExport -- Tool to export consensus features into MGF format (TOPP)
- NucleicAcidSearchEngine -- Annotate nucleic acid identifications to MS/MS spectra (UTIL)
- ProteomicsLFQ -- A standard proteomics LFQ pipeline (TOPP) (experimental)
- QualityControl -- Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get (TOPP)
- RNAMassCalculator -- Calculates masses and mass-to-charge ratios of RNA sequences (UTIL)
- MapAlignerTreeGuided -- Aligns maps through hierarchical clustering based on distances computed between shared IDs.
Deprecated and removed Tools:
Changed Tools:
- OpenPepXL and OpenPepXLLF runtime and memory efficiency improved by orders of magnitude
- IDFilter can now filter by using all MetaValues available in the ID files
- ImageCreator uses updated gradients and has gained RT and m/z filtering options (PR #4188)
Status changed:
- OpenPepXL (UTIL -> TOPP)
- OpenPepXLLF (UTIL -> TOPP)
- XFDR (UTIL -> TOPP)
-------------------------------------------------------------------------------------------
---- OpenMS 2.4 (released 9/2021) ----
-------------------------------------------------------------------------------------------
OpenMS 2.4 introduces changes from 322 pull requests including new features and bug fixes.
Notable changes since version 2.3 are:
Dependencies:
- Switch to Qt 5 (>= 5.5)
Documentation:
- New developer documentation to get started developing tools with OpenMS
Library:
- Improved mass calculations for isotope distributions
- Moved tool code from the tool to the library
- BinnedSpectrum now also supports offsets
- Improved peak type estimation
- Improved adduct grouping
- New EMG fitter for peak intensity imputation
- Targeted / untargeted spectra extraction and matching
- Spectra matching against a spectra library, using contrast angle similary function
- More precise peak integration (trapezoid, simpson)
New tools:
- AssayGeneratorMetabo -- Assay library generation from DDA data (Metabolomics) (UTIL)
- ClusterMassTraces -- Creates pseudo spectra (UTIL)
- ClusterMassTracesByPrecursor -- Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile (UTIL)
- CruxAdapter -- Identifies MS/MS spectra using Crux (TOPP)
- MSFraggerAdapter -- Peptide Identification with MSFragger (UTIL)
- MSstatsConverter -- Converter to input for MSstats (UTIL)
- MaRaClusterAdapter -- Facilitate input to MaRaCluster and reintegrate (TOPP)
- NovorAdapter -- Template for Tool creation (UTIL)
- RNADigestor -- Digests an RNA sequence database in-silico (UTIL)
Deprecated and removed tools:
- AdditiveSeries -- Computes an additive series to quantify a peptide in a set of samples (TOPP)
- IDEvaluator -- Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value (UTIL)
- IDEvaluatorGUI -- Computes a 'q-value vs. #PSM' plot to visualize the number identifications for a certain q-value (UTIL)
- RNPxl -- Tool for RNP cross linking experiment analysis (UTIL) (superseded by RNPxlSearch)
Changed Tools:
- SiriusAdapter now supports several input data
- FileFilter now supports filtering spectra by similarity
- PeptideIndexer now supports automatic detection of decoy suffix/prefix string and position
- PeakPickerHiRes now supports automatic detection and picking of profile spectra
- Support for MSFragger search engine through MSFraggerAdapter
- Support for Crux search engine through CruxAdapter
- Support for Maracluster through MaraClusterAdapter
- OpenPepXL was improved in efficiency and usability
- IDFileConverter now supports the Cross-Linking MS specific xquest.xml format
TOPPView:
- Improved visualization of identification results and ion annotations
- Support for visualization of Ion Mobility and DIA data
Major changes in functionality:
- None
File formats:
- Importer for MSP files
Scripts:
- None
Databases:
- None
Third-party software:
- New: maracluster (0.05)
- Update: MS-GF+ to Release (2018.01.30)
- Update: Sirius 4 for Windows 64bit, Linux 64bit, and MacOS 64bit
- Update: Crux (crux-3.1.8b78546) on all 64bit platforms.
-------------------------------------------------------------------------------------------
---- OpenMS 2.3 (released 1/18) ----
-------------------------------------------------------------------------------------------
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
- Support for TMT11plex (https://www.thermofisher.com/order/catalog/product/A34808)
- 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
- Support for C++11 (requires a compiler that supports C++11)
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)
-------------------------------------------------------------------------------------------
---- OpenMS 2.2 (released 11/2016) ----
-------------------------------------------------------------------------------------------
OpenMS 2.2 introduces a considerable number of new features and bug fixes.
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 IsobaricAanalyzer
- TMTAnalyzer -- superseded by IsobaricAanalyzer
- 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_"
Third-party software:
-------------------------------------------------------------------------------------------
---- OpenMS 2.1 (released 11/2016) ----
-------------------------------------------------------------------------------------------
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 64-bit X!Tandem VENGEANCE (2015.12.15) NOTE: 32-bit version kept at SLEDGEHAMMER (2013.09.01)
- update for MS-GF+ Release v2016.10.14, released October 14, 2016
- update for pwiz 3.0.9935
-------------------------------------------------------------------------------------------
---- OpenMS 2.0.1 (released 4/2016) ----
-------------------------------------------------------------------------------------------
OpenMS 2.0.1 is a source only release of the core libraries and tools.
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:
- LuciphorAdapter (experimental) PTM localization using the LuciPHOr2 algorithm (http://luciphor2.sourceforge.net/)
-------------------------------------------------------------------------------------------
---- OpenMS 2.0 (released 4/2015) ----
-------------------------------------------------------------------------------------------
Release date: February 2015
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)
- 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
Resolved issues and merged pull requests:
#644 Fix header macros
#649 Fix ms numpress
#651 [INTERNAL,API] Removal of the GSL
#656 Repository layout restructuring
#657 [FIX, INTERNAL]
#658 [FIX] PeptideIndexer crashes on empty idXML (#653)
#659 [NOP] replaced c like file ending C with cpp
#660 [FIX] fix Cython 0.20 compatibility issue
#661 [BUILD,PYOPENMS] simplify pyOpenMS build system
#662 CMake and docu cleanups w.r.t. to the new layout
#664 [BUILD] build system fixes / cleanups
#665 Fix coverity errors
#666 [FEATURE] ib spectra format export
#667 [BUILD] improved handling of boost in OpenMS build system
#668 [NOP] added support for travis-ci to OpenMS
#669 [FIX] fixed AccurateMassSearch_test
#673 [FEATURE,FIX] Added min/max values to go-to dialog
#675 Checker/Test fixes and adds test for CTD writing
#677 [PYOPENMS] setup.py as minimal as possible + other improvements
#678 [FIX] fix how swath files are annotated
#679 [FIX,TEST] fixed OpenSwathDecoyGenerator / MRMDecoy
#680 [INTERNAL] Feature/CachedMzML fixes
#684 [FIX] Bugfix for threading issue in MascotGenericFile
#685 Typo fixes in documentation and licence files
#688 Fix/file size limit
#689 [FIX] disable OpenMP again for ILPDCWrapper
#690 Fix/misc
#691 further improvements to MGF::load()
#693 Major speedup of String --> Double conversion
#694 added missing index file for OMSSA test, which gets recreated when runni...
#696 [FIX] fix RAM usage when adding dataprocessing to chromatograms
#697 [FIX] proper usage of map in ControlledVocabulary
#698 Updates to FeatureFinderIdentification and the ...TraceFitter classes
#702 Feature/parallel reader
#703 Feature/aa sequence tpp
#705 [FIX] Propagate metadata in OpenSwathWorkflow
#707 [FEATURE] variable stylesheet support for qcml
#708 [BUILD] fix build system bug
#711 [FEATURE,BUILD] fix install target
#713 Fix for pepXML loading bug (#710)
#715 Feature/pyopenms wrapping improvements neu
#716 [NOP,TEST] clean up MRMDecoy, add more tests
#717 fixed 32bit memory limitation of OMSSA by chunking input data
#718 [FIX] fixed misleading warning ("Removed x peptide identifications...
#719 [CI,FIX] fix travis contrib clone problems
#721 [INTERNAL] cleanup of iostream includes
#722 Feature/mz xml consumer
#724 Feature/pyopenms mzxml consumer
#725 Fix/misc
#726 IDPosteriorErrorProbability fix
#729 Fix/coverity
#730 Feature/peak picker sn performance
#734 Feature/more pyopenms improvements
#735 [FEATURE] clang warning level
#737 [FIX] several minor fixes
#739 Feature/uids fileconverter
#741 ProteinResolver fix
#742 svn cleanup
#743 [FIX] fixed compilation error on vs2013
#747 Speedup OMSSA-XML parsing and some stats for OMSSA&XTandem
#749 Feature/python3
#750 [PYOPENMS,FIX] fixed streampos->long conversion
#751 [FEATURE] track base name when reading pep.xml files
#752 [FIX] fixed missing adaption PeptideIdentification::empty()
#754 [PYOPENMS] changed extra methods on MSSpectrum
#755 [FIX] fixed shadow warning
#756 Unity Builds
#760 [FIX-#618] fix spelling errors in headers
#761 Feature/header fixes
#764 [FEATURE] lib superhirn
#765 Feature/db removal
#768 [FIX] fixed warnings in CONCEPTS
#770 [FIX] fixed some clang warnings in stream manipulation
#771 New warnings
#773 [BUILD,PYOPENMS] fix pyOpenMS build
#775 [FIX] typos in the CMake file
#776 Fix for IDPosteriorErrorProbability on Mascot search results (#740)
#777 Memory profiling class
#779 [FIX] replaced DoubleReal and Real by double and float.
#780 [FIX] fix Swath window estimation
#781 Fix/open swath fixes
#784 [FEATURE] fix macosx pyopenms errors
#785 [FIX] VS2013 compile fixes
#786 [FEATURE] added openms_add_library function
#787 [FEATURE,BUILD] move pyOpenMS to src
#789 small fix to Win install doc for VS2013
#790 Remove "RT"; and "MZ"; metavalues from PeptideIdentification
#791 [FIX] forgot writtenDigits fixes in tests VS2013
#792 [FIX] AASequence refactoring
#794 Generic Wrapping of R scripts using GenericWrapper
#797 [NOP,DOC] removed all remaining references to FeatureFinderRaw and SILAC...
#798 Fix/py open ms testfix
#799 [DOC] removed migrated pages from doxygen. replaced by link to wiki
#800 spline interpolation of MS1 spectra
#801 RTPredict: fixed order of parameters and doc
#802 [FIX] fixed copy-paste mistake in error message
#804 [FIX] MRMDecoy: Fix neutral losses for higher charge states
#805 [PYOPENMS] added getters/setters for MZ and RT in PeptideIdentification....
#807 cubic spline implementation
#810 cubic spline interpolation
#811 [NOP] add better debug information and error handling
#812 [FIX] per cppcheck
#813 Fix/openswath
#814 [FEATURE] ConvertTSVToTraML: Support for SpectraST MRM Transition Lists
#816 Feature/cached mz ml format change
#817 [FIX] fix spline derivative for cubic spline
#819 Feature/custom i rt
#820 Fix/warnings
#821 [FIX] suppress clang warnings
#823 Feature/update numpress
#824 Fix/coverity
#826 Feature/funny pictures
#827 [FIX] fixes export macro warnings
#831 [FEATURE] fix all gcc warnings and turn warnings into errors
#832 several pyopenms fixes + updates
#833 Feature/visibility hidden
#834 Fix/fix werror
#835 Fix spline spectrum
#836 [FIX,TEST] MRMRTNormalizer_test: Windows compatibility
#838 [FIX] fixed uninitialized pointer warning
#840 [FIX] fix pyOpenMS test
#841 [BUILD] disable -Werror by default
#842 [FIX] fix dereference of iterator
#843 [FIX] fixes tests failing win debug mode
#844 [FIX] evaluation at m/z in first package now possible
#845 [FEATURE] replace String classes with StringUtils
#846 Fix/fixes from822
#847 peak boundaries and new cubic splines for PeakPickerHiRes
#850 [FEATURE] modified tests to reflect X!Tandem SLEDGEHAMMER as default
#851 Fix and tests for a bug in reading Mascot XML files
#852 [FIX] fix windows compile error
#854 [FIX] ConsensusID doesn't sort peptide hits before processing (idXML)
#855 [FIX] FalseDiscoveryRate "target+decoy"; hits should be considered as targets
#856 [FEATURE] KNIME package generation updates
#857 Fix/py open ms fix
#858 [FEATURE] ~40x speedup for constructions of unmodified AASequence
#859 Feature/SystemWildMagic
#863 [BUILD] added test for x!tandem version to enable tests only with newer ...
#865 Work-around for special modifications in Mascot (fixes #864)
#866 [FEATURE] git version embedding
#867 [FIX-#861,DOC] fixed eigen 3.2.1 problems with GammaDistributionFitter
#868 multiplex filtering
#869 [FIX] fixed problems with negative sizeof values in CachedMzML
#870 [FIX,DOC] doxygen 1.8.7 fixes
#873 [FIX] fixed macosx version query
#875 Rewrite of 'AASequence::parseString_', increasing robustness of parsing (fixes #818)
#876 [DOC] added new doc_class_only target
#880 PeakPickerHiRes peak boundaries fixed
#881 [FEATURE] mzTab 1.0
#882 [FEATURE] coding style improvements
#884 [FIX] Convert XTandem search results into .pepXML by IDFileConverter
#885 [NOP] added moc files to gitignore
#888 [FIX-#887] IDFilter errornousely removed peptidhits in multiple run files
#889 multiplex clustering
#891 [FIX] converting uniform distributed generators with normal distributions
#892 Enable loading of some pepXML files that used to cause crashes
#894 [FEATURE] improved 3rd party lib finding
#895 [FEATURE] simple search engine
#896 added scan-polarity filter to FileFilter ...
#897 (feature for Windows developers) added a small Windows .reg file
#898 More compact format for MGF files (fixes #890)
#899 [DOC] some minor documentation addition
#901 [FIX] fix MS level for DTA file reader
#902 [FIX,PYOPENMS] fix pyOpenMS after #875
#903 [FIX] mzXML fix (filterLine, basePeakMz)
#904 Feature/fix peak boundaries
#910 [FIX] fixed unity build error introduced in #845
#911 [FIX] FFCentroided replace exception handling with proper check
#914 fix index in CubicSpline2d
#916 IDMapper extension for featureMaps
#917 AccurateMassSearchEngine annotation of input map (not only mzTab output)
#919 [FIX] libc++ test fixes
#920 [FIX] fixed minor problem with knime package generation and cmake versions >2.8.11
#921 MS1 annotation in TOPPView
#922 [FIX] build system improvements
#923 EmpiricalFormula: fix (negative counts were casted away)
#924 Switch to disable tracking of Git version within OpenMS
#925 Fix/small docu improvement
#926 Feature/spellcheck
#927 PeptideIndexer: support for treating isoleucine/leucine as equivalent (resolves #872)
#928 Build System
#929 TextFile feature (skip empty lines) and docu fix
#930 check for missing peaks
#931 fix for evaluation at last node
#936 [FIX] fixed the 'variable' consumption of xslt files for a QcML file.
#938 [FEATURE] precursor scoring
#939 [FIX] fix compile error
#940 coding convention violations in MultiplexClustering fixed
#943 [FIX,PYOPENMS] fix pyOpenMS after #889
#944 [FIX,TOOLS] pyopenms parser fix
#945 [FEATURE] pyopenms wrap improved
#946 OPENMS_DLLAPI removed from GridBasedClustering
#947 [FEATURE] FeatureFinderMultiplex
#949 Fix/xml escape
#950 Feature/traml heavylight
#951 [FIX] add setOptions method for FileHandler
#955 Fix/xml escape
#958 [FIX] disallow concurrent access to the static PRNG
#959 Feature/pyopenms copyconstr
#960 [FEATURE] peptide group label new
#962 [FIX] QCCalculator now computes TIC only on MS1 spectra (fixes #96)
#964 [FIX] check for invalid charge ranges in search engine adapters (see #963)
#965 [FEATURE] tmt 10plex support
#966 [FEATURE] chaining consumer
#967 [FEATURE,TEST] mssim more ground truth in id xml
#968 [FEATURE] export PT value analogous to predicted rt value in TextExporte...
#969 [FEATURE] add a low memory FileConverter option
#970 [FEATURE] test if java can be executed
#972 Fix/file cleanup
#973 [FIX] validate presence of input file before starting executable
#977 [FEATURE] replaced pphires ms1_only flag with ms_levels parameter
#981 Feature/TextExporter_mzML
#983 [FEATURE] add library check on Windows for correct lib arch
#984 [NOP] add heavy methyl SILAC labels to unimod.xml
#985 [FEATURE] bspline support using eol bsplines implementation
#988 [FIX] simplified EmpiricalFormula
#990 [FIX,FEATURE] TransformationModelInterpolated readded
#993 Feature/sort on load (mzML, mzXML)
#994 fixes mass traces in featureXML output
#995 fixes CubicSpline2d constructor exceptions
#996 allow for SplinePackages based on just two data points
#1000 fixes problems with ">>" generated in nested C++ templates
#1001 Fix/py open ms test
#1002 [pyOPENMS] features
#1003 [FIX] fixes random fails of MSSim_test
#1006 [FEATURE] enable gui less OpenMS
#1009 update unimod.xml with newest version from unimod.org
#1010 [FIX] external code tests updated/fixed
#1011 [FIX] external project doc
#1012 [FEATURE] decreased memory footprint of Feature class by up to 44%
#1014 TOPPView: group separator for mz,rt and int values in 1D and 2D canvas
#1019 [FIX] fixed unitybuild problem on win32 with eol-bsplines
#1020 [NOP] updated copyright/license header to 2014
#1021 Feature/py open ms fixes and wraps
#1024 sorting mass shifts in FeatureFinderMultiplex
#1025 Fix/checker fixes
#1026 additional example in SplineSpectrum test
#1027 Adapter for Fido (protein inference engine), solves #808
#1029 [FIX-#184] remove public vector/map inheritance
#1032 fixes peak boundaries in PeakPickerHiRes (resolves #1022)
#1034 [FIX] improve set_peaks documentation
#1035 B-spline interpolation for peak width estimation in MultiplexClustering class
#1036 [FEATURE,API] Removed template parameter from FeatureMap
#1037 Fix/ TraML load/store
#1038 Feature/py open ms wraps
#1039 Fix/debug fix
#1040 Fix/spellcheck
#1044 [FIX:#1043]fixed featureXML reading spectrum_reference as String
#1045 [FIX] fix compile issue on win32 systems
#1046 Fix/py open ms wrap
#1047 [FIX] first probe install path, then the build path for share/OpenMS
#1048 Feature/peptide hit protein locations
#1050 Re-added B-spline transformation for non-linear RT alignment in MapAlignerIdentification
#1051 [FIX] made arguments and functions in BSpline2d const (if possible)
#1055 [FEATURE] improved purity computation for IsobaricAnalyzer
#1056 [FIX] UniqueIdGenerator susceptible to identical RNG seeds
#1057 GenericWrapper doc has minor quirks
#1058 Feature/openswathwf add
#1059 Switch to version 2.0
#1061 FeatureFinderIdentification: documentation, tests, parameter improvements
#1063 Fix/accession nr
#1065 PeakPickerHiRes docu updated
#1067 Testing/mzid
#1069 Fix and test for issue #1068 (bug in "AASequence::operator<" involving N-terminal modifications)
#1070 removing zeros in profile data caused by Thermo bug
#1072 PeakPickerHiRes: disable spacing constraints for chromatograms (fixes #1060)
#1074 'intensity weighted mean'; averaging added to ProteinQuantifier, solves #830
#1076 Adapter for MS-GF+ search engine
#1077 [TESTING] download and add MSGFPlus in travis-ci
#1078 [FEATURE] export aabefore and aaafter in peptideindexer
#1079 Linear extrapolation (and other options) for B-spline transformation
#1080 [NOP] refactored PeptideHit protein accession extraction to true member
#1082 [NOP] removed index file as these are recreated by MSGF+ anyways
#1083 Feature/mz tab fixes
#1084 [FIX] compile fixes
#1086 Update (indistinguishable) protein groups when filtering protein identifications (fixes #748)
#1087 centroided input data for FeatureFinderMultiplex
#1088 Fix FileConverter's "write_mzML_index" flag
#1089 Fix/mzid
#1090 Enable mzIdentML input in IDFileConverter
#1091 Feature/mz tab cleanup
#1092 [NOP] removed unnecessary index files
#1094 [FIX] fixed small bugs preventing a build on windows
#1097 [FIX] consistent use of wildmagic
#1098 Revert "[FIX] consistent use of wildmagic"
#1099 [FIX,BUILD] fix Windows build
#1100 Fix/windows fix
#1101 optimisation for knockout searches in FeatureFinderMultiplex
#1102 Fix/fix spellcheck
#1104 [FIX] fix compile warning from unused variables
#1108 [FIX] fix compile warnings and increase QT min version to 4.6
#1109 [FIX] removed support for multiple id formats in tools without
#1115 fix some windows compile warnings
#1116 fix segfaults in XTandemXMLFile and IsobaricChannelExtractor
#1118 Feature/swath window loader
#1121 [FIX] some VC 2013 static tests fixed
#1122 Fix PeakPicker Wavelet
#1123 [FEATURE] remove PeakType template argument from FeatureFinder
#1124 [NOP] addendum to #1123
#1125 optimisations in FeatureFinderMultiplex
#1126 [FIX] intermediate fix for win32 systems
#1127 [FEATURE] create uncrustify branch
#1128 Fix/RT meta value related bug, removed unused comment
#1131 Make BuildSystem's LibCheck fail-safe
#1135 Fix/ams mz tab export
#1136 [NOP] uncrustified
#1137 [FIX] added -b option to create new branch
#1140 [FIX] fixed bugs in AScore implementation and added deisotoping as
#1141 Fix AccurateMassSearch and visualization
#1145 Fix/spellchecks
#1147 Fix/copyright update
#1150 Added PhosphoScoring tool to TOPP documentation
#1151 Changelog 2.0
#1152 [FIX,PYOPENMS] fix and adopt pyOpenMS
#1153 minor amendmend to last fix (better console output)
#1154 [TEST] fix test
#1156 [FIX-#618] fix spelling errors
#1157 [NOP] correct version in LICENSE file
#1158 [FIX] make identifier of multiple identification runs unique
#1161 pyOpenMS 2.0 features
#1162 [FIX] fixed study variable index start at 1. Added global identifiert to
#1164 [FIX] pepXML does on some occassion contain very small fixed
#1165 Added minimal test cases for checker.php Missing test errors
#1169 [FIX] fixed segfault if searchparam requested on empty proteinids
#1170 [FIX,TEST] FidoAdapter test
#1172 [FIX] fix for the write out of mzid
#1173 [FIX] changed path String parameter to input files
#1174 [TRAVIS] added Fido executables and adapted to new directory structure
#1175 [FEATURE] add ConsensusMap push_back
#1176 [BUILD] added support for new thirdparty executables in KNIME
#1179 [FIX] added missing option to apply e-value filtering
#1180 [FIX] fix toolnames for KNIME packaging
#1181 fixed minor typo in error message
#1184 [FIX] we decided to add the missing struct mapping file and in the
#1185 [FIX] added missing elements and spike ins
#1186 Fix/docu qc mzid
#1187 [FIX] AMS: export observed-Mass in mzTab as well
#1188 [Build] Added support for new third party binaries for dmg packaging. Adapted Li...
#1189 Feature/sn
#1190 [TEST] fix test
#1192 [FIX] HMDB: removed duplicates introduced by including spike ins
#1194 [NOP] removed deprecated qc toppas workflow
#1195 [STYLE] Changed header guards mentioned by checker.php
#1196 [FIX] XTandemAdapter added option to disable isotope error flag
#1198 [TEST] fix