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CHANGELOG
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Glossary:
OpenMS - Name of the project and our C++ library
TOPP - "The OpenMS PiPeline", a collection of chainable tools for flexible HPLC/MS workflows. Formerly known as "The OpenMS Proteomics Pipeline"
TOPPAS - "The OpenMS PiPeline Assistant", a 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
#<number>, e.g. #4957 - a reference to an issue or pull request on GitHub, visit e.g. https://github.com/OpenMS/OpenMS/pull/XXXX (replace XXXX with number of interest) for details
------------------------------------------------------------------------------------------
---- OpenMS 3.4.0 (under development) ----
------------------------------------------------------------------------------------------
General:
- OpenMS now expects a compiler that supports C++20
OpenSwath:
- Changes to -out_features (# 7793)
- Deprecate .tsv feature output
- Deprecate -out_osw, -out_tsv. -out_features is used for outputting .osw or .featureXML files and file format is autodetected.
- Enable outputting any feature file (.osw or .featureXML) from a .tsv library
- Add warning message if irt_im_extraction_window not set and im_window is set (#7813)
Misc:
- pyOpenMS: improve developer experience (installation/compilation) (#7735)
- TOPP tools and TOPPAS/ExecutePipeline return exit code 14 when external third-party tools (such as Comet or Sage) are not found (#7758)
- ProteinInference tool: Algorithm:score_type allows switching the main score (e.g., "RAW", "PEP") for BasicProteinInference. (#7769)
Library:
- IDScoreSwitcherAlgorithm: Added switchToScoreType and switchBackScoreType methods for score switching and reversion. (#7769)
------------------------------------------------------------------------------------------
---- OpenMS 3.3.0 ----
------------------------------------------------------------------------------------------
What's new:
- Changes breaking backward compatibility:
- the QualityControl TOPP tool has some renamed parameters and supports output directories (#7497)
- Low-level peak extraction helper for MSExperiments (#7628)
- pyOpenMS: use Numpy2 (#7539)
- Docker files are now part of the main OpenMS repo (#7303)
- Added new functionality to SageAdapter + compatibility with new Sage versions (#7577)
Library:
- TOPPView:
- offer Ion mobility view from 2D spectra view (#7423)
- view ion mobility frames, irrespective of its MS level (formerly only MS1 was supported) (#7427)
- OpenSwath:
- Add output on peak shape metrics to .osw file (#7222)
- Update IonMobilityScoring to use Mobilogram Kernel datastructure (#7587)
Misc:
- FileInfo:
- support MzTab files (#7568)
- TOPPAS
- supports writing results to output directories (for TOPP tools that have such parameters) (#7497)
- TOPPAS tutorial enhanced (#7497)
- TOPPAS & TOPPView: new splash screen with new OpenMS logo (#7712)
- FeatureFinderMetabo
- added report_smoothed_intensities parameter (#7594)
- Write out percolator features in search engine adapters (by default, no PSMFeatureExtractor is needed)
- Add isobaric correction defaults for tmt6plex and 11plex (#7601)
- Decoy phosho added to unimod.xml (#7612)
- Add additional convenience functions for MSExperiment (#7630)
- Improve file list comparison (#7645)
- pyOpenMS: Add more convenient constructor for AASequence (#7650)
- Add annotate_features param in Deisotoper.cpp (#7643)
- internal enhancements (#7652)
Fixes:
- OpenMS does not compile when using GLPK (instead of COINOR) (#7626)
- fix MassCalculator error ('residue type has no name') (#7698)
- pyOpenMS
- get_feature_df() in MRMTransitionGroupCP, output is now as expected (#7646)
- Fix scan number extraction for merged spectra (#7599)
- Cmake fix (#7625)
- use Boost config instead of find module (new policy of CMake)
- escape quotes in whitespace strings
- remove invalid PRE_BUILD option (in combination with OUTPUT)
- update diff regex and actual results (which seem to have changed with recent Sage versions...)
- MzTab: preallocate enough memory instead of allocating in the loops (#7624)
- add check that otherwise will result in out of memory error
- reduce memory fragmentation on huge files
- KNIME Plugin: Fix categories (#7622)
------------------------------------------------------------------------------------------
---- OpenMS 3.2.0 (released 09/2024) ----
------------------------------------------------------------------------------------------
What's new:
- Changes breaking backwards compatibility:
- Rename of parameters for TOPP tool FeatureFinderCentroided (debug -> advanced), and PeakPickerWavelet/TOFCalibration (optimization -> optimization:type) (#7154)
- Rename of parameters for TOPP tool IDFilter (score:pep -> score:psm; score:prot -> score:protein; score:protgroup -> score:proteingroup) with 'nan' as new default (#7541)
- 3.2.0 KNIME package requires KNIME 5.3 or later
- Support for SubsetNeighborSearch (SNS) via DecoyDatabase (#7565)
- SageAdapter received large updates including added functionality for PTM discovery + enabling features such as chimera seach, RT prediction, filtering by q-value, etc.
Library:
- Extend FileHandler to support load and store operations for our major datastructures (spectra, features, identifications, etc.). Replaced file type specific code with the more generic FileHandler calls to decouple the IO code from other parts of the library.
- SiriusAdapter reworked to SiriusExport: Instead of running SIRIUS directly, this reworked tool takes multiple mzML and feautureXML (optional) files exporting a single SIRIUS .ms input file as well as an input table with compound info from features for the new AssayGeneratorMetaboSirius tool. (#7234)
- Splitting AssayGeneratorMetabo into two tools: In line with the changes to SiriusExport this tool has been split into two separate workflows. AssayGeneratorMetabo generates an assay library from mzML and feautreXML files using an heuristic approach picking the highest intensity MS2 peaks (like before). AssayGeneratorMetaboSirius takes an existing SIRIUS project directory as input to generate an assay library based on fragmentation trees. (#7234)
- better documentation for all SpectraFilter... tools (#7183)
- TOPPView: offer Ion mobility view from 2D spectra view (#7423)
- TOPPView: view ion mobility frames, irrespective of its MS level (formerly only MS1 was supported) (#7427)
- OpenSwath: Add output on peak shape metrics to .osw file (#7222)
New Tools:
- IonMobilityBinning - Merges spectra with similar IM values and creates @p N output mzML's by discretizing the IM range (#7459)
- AssayGeneratorMetaboSirius -- Assay library generation from a SIRIUS project directory (Metabolomics)
- SiriusExport -- Metabolite identification using single and tandem mass spectrometry
Fixes:
- FileConverter: more robust (#7176)
- MSFragger: allow relative path to database (#7155)
- MSGFPlusAdapter: allow concurrent creation of indexed database (#7272)
- CometAdapter: work around bug in Comet 2024.01 rev. 0 to avoid empty results (#7540)
- ParamEditor: fixed error for the subsection parameter (ParamNode) to go through store function (#7180)
- TOPPView:
- fix crash when viewing certain Chromatograms (#7220)
- in 2D view, show correct adjacent layers in context menu, if user clicked to the right of the last MS1 scan (now shows the 4 rightmost MS1 scans, used to show the 4 leftmost scans) (#7423)
- fix glitches in 1D view and layer names (#7549)
- Show prefix ions (e.g. b1) when generating theoretical spectra (#7567)
- TOPPAS: open files in TOPPView (#7213)
- pyOpenMS: Log warnings in pure Python code with warnings.warn instead of print (#7418)
- more robust parsing of mzIdentML (#7153)
- SageAdapter now works with sage v0.15.0 and beyond
- OpenSwath: Fix bug in diaPASEF window determination (#7546)
Misc:
- FileInfo: Report ion mobility ranges (if any) (#7459)
- OpenMSInfo reports the ILP solver (CoinOr or glpk) (#7156)
- add citation information for OpenMS 3.0 (Nat. Methods) (#7383)
- Add export for Common Workflow Language (CWL) (#6156)
- Add tool description lib (TDL) dependency (#6156)
- Docker containers have been optimized (#7303)
Changed/new parameters: see CHANGELOG_PARAMS for details
Note: The goal of our library is to provide useful, reusable code in a way that’s easy to understand and use.
To make OpenMS simpler, more focused and more accessible we gradually remove potentially outdated tools and algorithms.
If you, as a user, are negatively affected by this step please contact us. We listen to our users and will try to find
an alternative solution or reverse a particular decision for removal.
Cleanup/Removal:
- removed tools:
- SpectraFilterMarkerMower -- Applies thresholdfilter to peak spectra (#7183)
- FeatureFinderIsotopeWavelet -- Detects two-dimensional features in LC-MS data
- PeakPickerWavelet -- Finds mass spectrometric peaks in profile mass spectra
- PrecursorMassCorrector -- Corrects the precursor entries of MS/MS spectra, by using MS1 information
- TOFCalibration -- Applies time of flight calibration
- ERPairFinder -- Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans
- RNPxlSearch -- Annotate RNA/DNA-peptide cross-links in MS/MS spectra
- SpectraFilterSqrtMower -- Applies thresholdfilter to peak spectra
- FeatureFinderMRM -- Detects two-dimensional features in LC-MS data
- MapAlignerSpectrum -- Corrects retention time distortions between maps by spectrum alignment
- ProteinResolver -- protein inference
- SiriusAdapter -- Tool for metabolite identification using single and tandem mass spectrometry
- SpectraFilterBernNorm -- Applies thresholdfilter to peak spectra
- SpectraFilterScaler -- Applies thresholdfilter to peak spectra
- removed library code:
- HiddenMarkovModel
- PeakPickerMaxima
- DeNovo related, old marker code
- removed tutorials:
- Tutorial_PeakPickerCWT
- Tutorial_TOFCalibration
- removed tests:
- TOFCalibration_test
- ContinuousWaveletTransformNumIntegration_test
- ContinuousWaveletTransform_test
- FeatureFinderAlgorithmIsotopeWavelet_test
- IsotopeWaveletTransform_test
- IsotopeWavelet_test
- OptimizePeakDeconvolution_test
- OptimizePick_test
- PeakPickerCWT_test
- PeakShape_test
- Deprecated (and likely removed in the next release)
- XTandemAdapter
------------------------------------------------------------------------------------------
---- OpenMS 3.1 (released 10/2023) ----
------------------------------------------------------------------------------------------
We are excited to share an experimental update with our community, mainly targeted at platforms that depend on Conda packages.
Please note that this is a partial and unannounced release, focused on delivering novel features and major changes that we're actively testing and refining.
While these features are still in an experimental phase, we encourage adventurous users and platform integrators to explore and provide feedback.
Important Notes:
- Features are experimental and may undergo changes or be removed in future releases based on user feedback and stability.
- We welcome your feedback and suggestions to help us improve and refine these experimental features.
- For stability and production use, we recommend sticking with the latest stable release.
Please use this opportunity to test and provide feedback on these new features, as your input will play a vital role in shaping their development.
Thank you for being a part of our community and for helping us make OpenMS even better!
What's new:
- Major change: removed the distinction between TOPP tool and util and the TOPP and UTIL build targets were merged to a single TOPP target. All utils are considered tools now and categorized as "Utilities".
- Added SageAdapter. Support for standard identification tasks with sage (https://github.com/lazear/sage) (experimental).
- Require some advanced instruction sets for x64 CPUs: SSE3 (g++/clang) or AVX (MSVC); and NEON for ARM64 CPUs (#6978)
and report them via the OpenMSInfo tool (#7022)
- Base64 encoding/decoding using the SIMDe library (#6978)
- Filter features in ProteomicsLFQ according to feature p-value (additional parameters feature_with(out)_id_min_score, MBR is automatically active if targeted_only = false)
- TOPPAS: filter TOPP tools by name for faster access when building a pipeline (#7139)
Fixes:
- Fix a crash when loading mzML data with multiple threads which contains non-MS spectra, e.g. 'electromagnetic radiation spectrum' (#7011)
- InternalCalibration: improve visualization of calibration plots (#7064)
- Restore TOPPAS tutorial (#7076)
- various low impact UBSan fixes
- make mzData more robust against wrong 'length' attributes for binary data (#7113)
Misc:
- Report reading/writing throughput (MiB/sec) when loading/storing mzML (#7035)
- Add ability to create decoy features in FeatureFinderIdentification
- Restore developer quick guide in Doxygen docu - see https://openms.de/current_doxygen/html/index.html (#7109)
- Updated the changelog helper to set LD_LIBRARY_PATH automatically and other fixes
- Added "area" column to EICextractor output
Cleanup of old/unused tools and code:
- Removed old tools and associated code in the library for InclusionExclusionListCreator, SvmTheoreticalSpectrumGenerator, PrecursorIonSelector, and MSSimulator
Note: general SVC and SVR is still supported with the SimpleSVM class.
- Removed old RT and PT predict code and tools RTModel, RTPredict, PTModel, PTPredict, RTEvaluation and associated library code (SVMWrapper and LibSVMEncoder).
- Removed PepNovoAdapter
- Removed CompNovoAdapter and library code
- Removed simplistic evaluation tools FFEval, LabeledEval, TransformationEvaluation
- Removed EnzymaticDigestionLogModel
- Removed FidoAdapter (same functionality now in our own inference engines)
------------------------------------------------------------------------------------------
---- OpenMS 3.0 (released 7/2023) ----
------------------------------------------------------------------------------------------
New Tools:
FLASHDeconv -- Ultra-fast high-quality deconvolution enables online processing of top-down MS data (TOPP)
FLASHDeconvWizard -- A GUI assistant for FLASHDeconv execution.
New Features:
e.g.
TMT18plex support (#6390)
ProteinQuantifier supports iBAQ (#6107)
OpenSwath: Add support for diaPASEF data with overlapping m/z and IM windows, and add new outputs on ion mobility features (delta_im), IM calibration (#5911, #6234, #6268)
OpenSwathDecoyGenerator speed improvement and remove duplicates (#6054)
NucleicAcidSearchEngine (NASE): user defined ribonucleotides with phosphorothioate linkages (#6337), JSON based ribonucleotides and updated to latest Modomics database (#6482)
TargetedSpectraExtractor: more features (#6106)
TOPPView: TheoreticalSpectrumGenerationDialog now supports generation of isotope patterns for metabolites (#6023); faster loading of external drag'n'drop data (#6837)
colored commandline/console on all platforms (#6275)
support for 'no cleavage' for XTandemAdapter and CometAdapter (#6133).
Percolator pin file reader (#6824)
JSON export for OMS files(SQLite) (#6114)
ParamEditor with more convenient StringList editing (#5135)
load parameter values from a JSON formatted .json file. (Accessible via -ini. This will be
helpful for Common Workflow Language users and others)
FileFilter can remove convex hulls of features and consensusFeatures to reduce file size (#6140)
Faster compile time (#6618)
Improving code quality by fixing lots of linting warnings and leaks (e.g. #6839, #6831, #6829)
Documentation:
website redesign (visit openms.org)
OpenMS user documentation is moved to openms.readthedocs.io/en/latest.
OpenMS API reference and advanced developer documentation remains inside OpenMS doxygen
documentation (https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/)
pyopenms: pyopenms-extra is renamed to pyopenms-docs.
Bug fixes
e.g.
GaussFilter when using ppm as width (#6830)
NASE a-B ion masses (#6718), ID-Mapper for TMT data (#6758)
FeatureFinderMetaboliteIdentification speed improvements (#6619)
IDRipper speed improvements (#6584)
Honor MissedCleavages in SimpleSearchEngine (#6889)
TOPPView: fixed lots of display glitches, e.g. axis labels, goto dialog and easier re-use of components, etc (#6673, #6616, #6592, #6703, #6793)
mzTab fixes for empty IDs (#6445)
Fix GNPS error for empty scans in Bruker files (#6898)
PrecursorPurity: handle unknown charge (#6283)
OpenSwath: Fix duplicated transition error when multiple genes map to a single peptide (#5653)
Fixed race condition when logging messages.
Removed tools:
InspectAdapter
OMSSAAdapter
MyriMatchAdapter
CruxAdapter
Supported compilers (when building from source):
g++ (7.0 or later, tested up to v13.0)
clang (?, tested up to v16)
Visual Studio (2019(v16.8.4) or later)
Full changelog: [OpenMS 2.8 → 3.0](https://github.com/OpenMS/OpenMS/compare/Release2.8.0...Release3.0.0)
------------------------------------------------------------------------------------------
---- 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)
- SiriusExport -- 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