Recent Releases of openms
openms - release/3.4.1
Dear OpenMS-Users,
we are proud to announce the release of OpenMS 3.4.1. Grab it here
In the following you find all important changes to the previous version:
Minor updates to the Dockerfile.
Best regards, The OpenMS-Developers
- C++
Published by github-actions[bot] about 1 year ago
openms - release/3.4.0
Dear OpenMS-Users,
we are proud to announce the release of OpenMS 3.4. Grab it here
In the following you find all important changes to the previous version:
General: - OpenMS now expects a compiler that supports C++20 - OpenMSInfo now informs about custom CXX compile flags (#7846) - speed improvements: - TOPP tool FeatureFinderCentroided is 28-44% faster (internally GaussTraceFitter is 4-7x faster) (#7950) - mzML parsing is 6% faster (#7850)
Dependencies: - Switch to Qt 6 (>= 6.5) (#7525)
OpenSwath:
- Changes to -outfeatures (# 7793)
- Deprecate .tsv feature output
- Deprecate -outosw, -outtsv. -outfeatures 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 irtimextractionwindow not set and imwindow is set (#7813)
- Add auto add up spectra across the peak width in retention time for ion mobility extraction (#7742)
- Add peak-picking for extracted ion mobilogram (#7759)
- Add ion mobility scoring for identifying transitions for IPF (#7760)
- Bug fix, pass im_range to scoreIdentification_ instead of computing it in the function. Addresses issue #7883. (PR #7885)
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) - README.md: Added dedicated "Building OpenMS" section with direct links to platform-specific build instructions (#7912)
Fixes: - Add option to PeakFileOption to ignore loading of chromatograms or spectra from mzML (#7901) - fix Doxygen Docs contain stty warning for TOPP tool output (#7865)
Library: - IDScoreSwitcherAlgorithm: Added switchToScoreType and switchBackScoreType methods for score switching and reversion. (#7769) - Made FASTA file reader more robust in presence of whitespaces
- removed tools:
- XTandemAdapter
- MascotAdapter (note: MascotAdapterOnline still exists)
Best regards, The OpenMS-Developers
- C++
Published by github-actions[bot] about 1 year ago
openms - release/3.3.0
Dear OpenMS-Users,
we are proud to announce the release of OpenMS 3.3. Grab it here
In the following you find all important changes to the previous version:
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)
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) - FeatureFinderMetabo - added reportsmoothedintensities 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 - getfeaturedf() 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)
Best regards, The OpenMS-Developers
- C++
Published by github-actions[bot] over 1 year ago
openms - release/3.2.0
Dear OpenMS-Users,
we are proud to announce the release of OpenMS 3.2. The source code and precompiled installers (Windows, Linux, MacOSX) are available at the bottom of this page or here.
In the following you find all important changes to the previous version:
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)
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) - 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 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) - 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)
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
Best regards, The OpenMS-Developers
<!-- needed for jumping to the assets/downloads, which are just below here -->
- C++
Published by github-actions[bot] over 1 year ago
openms - OpenMS 3.1.0
Dear OpenMS-Users,
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 featurewith(out)idminscore, MBR is automatically active if targeted_only = false)
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/currentdoxygen/html/index.html (#7109) - Updated the changelog helper to set LDLIBRARY_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)
Full Changelog: https://github.com/OpenMS/OpenMS/compare/Release3.0.0...Release3.1.0
- C++
Published by timosachsenberg over 2 years ago
openms - OpenMS 3.0.0
Dear OpenMS-Users,
we are proud to announce the release of OpenMS 3.0.0 (June 2023).
The source code and precompiled installers (Windows, Linux, MacOSX) are available at the bottom of this page or here.
For detailed installation instructions and more options, please visit https://openms.readthedocs.io/en/release3.0.0/openms-applications-and-tools/installation.html.
This is a full release, i.e. a major version increase from 2.0 to 3.0. Highlights of these changes are listed at the end of this page.
Important changes to the previous version 2.8 from Feb 2022:
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
<!-- needed for jumping here -->
OpenMS 2.0 → 3.0 highlights
FLASHDeconv and FLASHDeconvWizard: Harness ultra-fast high-quality deconvolution of top-down MS data. These tools enable rapid and accurate deconvolution, ensuring efficient and precise data analysis.
NucleicAcidSearchEngine: Enter the world of RNA analysis with NucleicAcidSearchEngine, a tool that annotates nucleic acid identifications to MS/MS spectra.
OpenPepXL, OpenPepXLLF and related tools: Perform comprehensive protein-protein cross-link analysis covering a wide range of chemical cross-linkers.
Epifany: Take your protein inference to new heights with Epifany, a Bayesian protein inference tool that offers accurate and reliable results for complex proteomics analyses.
FeatureFinderMetaboIdent: Detect features in MS1 data based on metabolite identifications with FeatureFinderMetaboIdent. This tool enhances metabolomics analyses by accurately identifying features for further investigation. Check out our Umetaflow workflow or the pyopenms documentation for details.
GNPSExport: Export consensus features into MGF format with GNPSExport. This tool simplifies data sharing and collaboration, streamlining your data analysis workflow.
ProteomicsLFQ: Explore a standard proteomics LFQ pipeline in a single tool: ProteomicsLFQ. A tool designed for reliable quantification of proteins.
QualityControl: Compute various QC metrics from input files with QualityControl, providing essential quality assessments for your data. This versatile tool offers a comprehensive view of data quality.
Optimized RT alignment with MapAlignerTreeGuided, a new tool that aligns maps through hierarchical clustering based on shared IDs.
MetaProSIP, the tool for protein-SIP experiments gained support for Deuterium and heavy Oxygen labeling.
General Enhancements: Streamlining your developer experience The OpenMS 3.0 codebase has been updated to C++17. Additionally, the configuration storage path on Linux has changed to ~/.config/, making it easier to manage user-specific configurations.
Library and Performance Improvements: Enhancing Data Analysis The OpenMS library has undergone significant updates, resulting in improved mass calculations, peak integration, and isotope distributions. The library now supports more precise peak integration methods, ensuring the accuracy and reliability of your data analysis.
User Interface and Usability: Enhancing Your Workflow Several GUI tools have received notable improvements in OpenMS 3.0. TOPPView, TOPPAS, and ParamEditor have been enhanced for better usability and additional data visualization capabilities.
Module Removals and Deprecated Tools: Streamlined and Focused OpenMS 3.0 removes several deprecated modules and tools. This focused approach ensures a more efficient and effective user experience.
For an exhaustive list of changes between OpenMS 2.0 - OpenMS 3.0 please refer to the changelogs.
Best regards, The OpenMS-Developers
<!-- needed for jumping to the assets/downloads, which are just below here -->
- C++
Published by openms-jenkins-bot almost 3 years ago
openms - OpenMS 2.8.0
Dear OpenMS-Users,
we are proud to announce the release of OpenMS 2.8.0. Grab it here
In the following you find all important changes to the previous version:
- source + conda release only. This means installers, workflows and GUI are untested.
- 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 keepunidentifiedmasses to "true" (AccurateMassSearch/AccurateMassSearchEngine)
Best regards, The OpenMS-Developers
What's Changed
- Added wrap-doc methods #8 by @rahul799 in https://github.com/OpenMS/OpenMS/pull/5459
- Code Arrangement Changes #8 by @Arraxx in https://github.com/OpenMS/OpenMS/pull/5476
- code arrangement changes -10 by @Arraxx in https://github.com/OpenMS/OpenMS/pull/5492
- [Update] Allow more isotope errors in Comet by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5502
- [FIX] Better error message for nr runs in PLFQ IDs by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5503
- [FIX] Add origin for simulated IDs by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5504
[Feature] picked protein fdr by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5488
[Fix] picked protein fdr by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5509
Update Plot2DCanvas.cpp by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5480
code arrangement changes -14 by @Arraxx in https://github.com/OpenMS/OpenMS/pull/5510
Code Arrangement changes-15 by @Arraxx in https://github.com/OpenMS/OpenMS/pull/5519
adding-wrap-doc-method-17 by @rahul799 in https://github.com/OpenMS/OpenMS/pull/5520
fix bug if experimental design is not given by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5522
fix bug in Epifany introduced by new ParamValue class by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5527
adding-wrap-doc-method-19 by @rahul799 in https://github.com/OpenMS/OpenMS/pull/5532
[fix] add qc-cv legacy CVs by @poshul in https://github.com/OpenMS/OpenMS/pull/5529
adding-wrap-doc-method-20 by @rahul799 in https://github.com/OpenMS/OpenMS/pull/5537
PLFQ Write chromatograms for debugging by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5536
[Feature] Try to add descriptions to Param class repr in pyopenms by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5544
[Fix] Remaining memory leaks in tests by @dvdvgt in https://github.com/OpenMS/OpenMS/pull/5494
[cython] link to openmp by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5498
[FIX] AMS mztab by @oliveralka in https://github.com/OpenMS/OpenMS/pull/5549
[FIX] PyOpenMS macOS 11.5.1 (10.16) by @oliveralka in https://github.com/OpenMS/OpenMS/pull/5477
[fix] aaseq python ext. by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5555
overwrite design file names with input file names (as we know those e… by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5557
adding-wrap-doc-method-22 by @rahul799 in https://github.com/OpenMS/OpenMS/pull/5560
Do not overwrite OPENMSDATAPATH in PyOpenMS if it is already set by @radusuciu in https://github.com/OpenMS/OpenMS/pull/5562
[FIX] Consider fixed mods for terms, reading pepXML by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5548
[FIX] Forgot C-term fixed mod lookup in pepXML by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5564
[CMAKE] option to enable LTO by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5559
[FEATURE] Export isotope errors when reading pepXML by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5565
Added Unimod Modifications to parameters of MSFraggerAdapter by @tillenglert in https://github.com/OpenMS/OpenMS/pull/5512
[refactor] moved percolator in file functionality into library by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5570
[FIX] AssayGeneratorMetabo Test (wo SIRIUS) by @oliveralka in https://github.com/OpenMS/OpenMS/pull/5551
[Internal] Add ParamCTDFile to write Param to CTD File with only standard dependecies by @rubengruenberg in https://github.com/OpenMS/OpenMS/pull/5475
[Fix] missing cstddef for ptrdiff_t by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5576
[ADD] IDMerger annotatefileorigin default true by @oliveralka in https://github.com/OpenMS/OpenMS/pull/5578
[Feature] basicproteininference on cxml by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5561
[Pyopenms] Update help in init.py by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5583
make reindexing the default by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5581
[GH Actions] remove cmakefinddebug by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5586
[FIX] add missing include by @hroest in https://github.com/OpenMS/OpenMS/pull/5588
[Feature] make modifications better for pyopenms by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5584
fixed unused variable warnings by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5597
Feature/im calibration bugfix by @hroest in https://github.com/OpenMS/OpenMS/pull/5595
Spectra are not stored if only meta data is read. by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5600
Fix/comparator utils by @JangJang3 in https://github.com/OpenMS/OpenMS/pull/5601
[pyopenms] fix wrapping of idXML store by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5605
Feature/header cleanup inc by @hroest in https://github.com/OpenMS/OpenMS/pull/5608
[pyopenms] use np.empty instead of np.zeros by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5607
Fix doxygen warnings by @cbielow in https://github.com/OpenMS/OpenMS/pull/5609
Feature/header cleanup inc by @hroest in https://github.com/OpenMS/OpenMS/pull/5610
prep for quick MS1 peak accession for pyOpenMS / numpy by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5606
[FEATURE] speed improvement in OpenSwathAssayGenerator and OpenSwathDecoyGenerator by @hroest in https://github.com/OpenMS/OpenMS/pull/5611
[DOC] improved IM set/get documentation by @cbielow in https://github.com/OpenMS/OpenMS/pull/5614
Reduce OpenMS exposure to third-party headers by @hroest in https://github.com/OpenMS/OpenMS/pull/5603
[ADD] Spectrum Plotting and Spectrum Mirror Plotting Functions by @matteopilz in https://github.com/OpenMS/OpenMS/pull/5615
Fix msfragger file origin by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5620
[FIX] use static inline for namespace by @hroest in https://github.com/OpenMS/OpenMS/pull/5627
[FEATURE] New Deisotoping Algorithm by @emilpaulitz in https://github.com/OpenMS/OpenMS/pull/5306
[FIX] MetaboliteSpectralMatcher by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5630
fix ODR by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5632
[pyopenms] Fix pyopenms int size (on windows) by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5634
Fix tool scan in TOPPView by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5640
add pandas df conversion by @axelwalter in https://github.com/OpenMS/OpenMS/pull/5622
Isotopic distribution approximation by @emilpaulitz in https://github.com/OpenMS/OpenMS/pull/5633
Perf mini by @cbielow in https://github.com/OpenMS/OpenMS/pull/5644
Feature/separate interfaces by @hroest in https://github.com/OpenMS/OpenMS/pull/5626
[PYOPENMS] wrap checkspectrumtype parameter for pphires by @hroest in https://github.com/OpenMS/OpenMS/pull/5647
Swath by @vmusch in https://github.com/OpenMS/OpenMS/pull/5635
the amount of SN warnings in FFMid are just too much for jupyter note… by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5648
only detect features on MS1 (don't mix levels) by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5651
[fix] Elution peak detection: rare segfault if no features were detected (e.g., in blanks) by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5652
Emf test and ffmid move by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5654
Update PercolatorInfile.cpp by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5624
Feature/pep evidences df by @axelwalter in https://github.com/OpenMS/OpenMS/pull/5656
[FIX] Decoding ontology in PeptideIdentification df conversion by @axelwalter in https://github.com/OpenMS/OpenMS/pull/5659
[FIX] add parameter to disable output of warnings in GaussFilter by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5661
[gitpod] add python3-pip to use run-clang-tidy by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5664
add backlink to MS run in FFmetaboIdent by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5662
ffid annotate spectra file path already in algorithm by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5663
fix TOPPView checkbox state export by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5667
apply clang-tidy modernize by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5670
Fix race condition in TOPPView by @cbielow in https://github.com/OpenMS/OpenMS/pull/5674
[FEATURE] peptide export from feature map for pyOpenMS by @axelwalter in https://github.com/OpenMS/OpenMS/pull/5672
fix return to reference by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5679
clang-tidy performance-inefficient-vector/string-operation by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5676
workaround for rare segfault in elution peak detection by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5677
[SUBMODULE] add pyopenms-extra as submodule by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5665
move templates to cpp file to reduce Seqan exposure by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5516
add FileFilter option to overwrite precursor charge by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5684
[FIX] add move constructor and assignment operator by @hroest in https://github.com/OpenMS/OpenMS/pull/5686
clang-tidy add const to methods and replace size() == 0 with empty by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5673
GUI Layer refactoring -- preparations by @cbielow in https://github.com/OpenMS/OpenMS/pull/5682
Hide IsoSpec using pimpl and add some clang-tidy performance fixes on top by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5681
[fix] added 3' phosphate gain for unspecific cleavage of nucleotides.… by @poshul in https://github.com/OpenMS/OpenMS/pull/5694
Layer refactor #2 by @cbielow in https://github.com/OpenMS/OpenMS/pull/5696
Correct a-B fragment masses for DNA by @poshul in https://github.com/OpenMS/OpenMS/pull/5587
fix imputation bug on single peak mass traces by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5702
[ADD] GitHub Action Clang Format by @oliveralka in https://github.com/OpenMS/OpenMS/pull/5577
[FEATURE] add python compatible get precursor spectrum by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5704
adapt clang format by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5706
use on disc experiment by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5709
[FIX] clang format actions by @oliveralka in https://github.com/OpenMS/OpenMS/pull/5712
MapAlignerPoseClustering: print error message and fall back to identity if no data provided by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5711
[REFACTOR] New RangeManager by @cbielow in https://github.com/OpenMS/OpenMS/pull/5703
Layer refactor: StatisticsDialog by @cbielow in https://github.com/OpenMS/OpenMS/pull/5713
clang-format version 13 by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5715
Update rebase.yml by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5716
Only run clang-format if sth was changed by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5718
fix compile warnings by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5719
CVInspector: the mapping_file argument is mandatory by @bernt-matthias in https://github.com/OpenMS/OpenMS/pull/4425
add rvalue reference by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5685
Extend LayerStatistics by @cbielow in https://github.com/OpenMS/OpenMS/pull/5721
test of cppcheck action by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5727
[REFACTOR] function to copy spectrum meta data / settings by @hroest in https://github.com/OpenMS/OpenMS/pull/3913
[Feature] export MSExperiment to data frames for MassQL by @axelwalter in https://github.com/OpenMS/OpenMS/pull/5722
Fix/activation modes by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/4918
Layer refactor by @cbielow in https://github.com/OpenMS/OpenMS/pull/5729
Calculating a Corrected Database Suitability by @Waschi97 in https://github.com/OpenMS/OpenMS/pull/4905
Update GNPSExport.cpp by @eeko-kon in https://github.com/OpenMS/OpenMS/pull/5594
implementation of output prefix parameters by @bernt-matthias in https://github.com/OpenMS/OpenMS/pull/4527
[FIX] Resolve compatibility issues between IDRipper and IDMerger by @lkuchenb in https://github.com/OpenMS/OpenMS/pull/4957
TOPPView Preferences Dialog refactor by @cbielow in https://github.com/OpenMS/OpenMS/pull/5732
Layer refactor by @cbielow in https://github.com/OpenMS/OpenMS/pull/5733
Dhanmoni gsoc21 toppview by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5720
[FIX] Add MassTrace ctor in pyopenms by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5737
Allow overlapping elution profiles in elution peak detection by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5734
[FEATURE] Make pyopenms cmake better. And log output better. by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5730
add dll export by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5738
[FIX] Major error in pyopenms addon MSSpectrum by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5739
IdentificationData updates, integration with tools, and SQLite-based file format by @hendrikweisser in https://github.com/OpenMS/OpenMS/pull/5352
move GNPSExport to lib by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5638
use std::optional by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5723
reduce boost math usage by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5742
Bugfix MSFraggerAdapter by @tillenglert in https://github.com/OpenMS/OpenMS/pull/5749
Reduce warnings on unused functions by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5750
[FIX] pyopenms mac fix dependency order by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5751
[ADD] MzTabM support for AccurateMassSearch (based on IdentificationData) by @oliveralka in https://github.com/OpenMS/OpenMS/pull/5744
[PERFORMANCE] add index for peakannotations by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5753
Update install-linux.doxygen by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5759
typo fixes by @cbielow in https://github.com/OpenMS/OpenMS/pull/5763
forward declare all svm types by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5762
compile fixes by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5764
Revert "compile fixes" by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5766
move Wm5 dep to cpp by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5754
Require OPENMSTESTVERBOSE_SUCCESS env variable set if output of successful test executions should be printed by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5765
remove pxd for AhoCorasickAmbigous as it pulls in Seqan headers and is disfunctional by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5769
Disable successful test lines by default by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5767
replace boost with std variant by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5768
[Fix] MS3 TMT IdMapping by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5773
more reduction of test output by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5771
Rewrite of PeptideIndexer by @cbielow in https://github.com/OpenMS/OpenMS/pull/5776
Update GNPSExport.cpp by @eeko-kon in https://github.com/OpenMS/OpenMS/pull/5777
Remove seqan library from OpenMS by @cbielow in https://github.com/OpenMS/OpenMS/pull/5779
[FEATURE] add pyopenms option to not bundle dependencies. removes need for patch in conda by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5780
a few fixes by @cbielow in https://github.com/OpenMS/OpenMS/pull/5782
TV make sure that accessions are still exported by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5786
Rewrite MI and XCorr matrices calculation/storing of OpenSwathWorkflow by @khuenm in https://github.com/OpenMS/OpenMS/pull/5731
small cleanup by @cbielow in https://github.com/OpenMS/OpenMS/pull/5792
[FEATURE] Complete target-based find modules and CMake-based pyopenms builds by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5757
remove WM5 from headers by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5797
move WM5 to private libs by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5801
Fix/1983 by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5796
remove layout from splitter by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5806
don't show exception if unknown protein accession encountered by @timosachsenberg in https://github.com/OpenMS/OpenMS/pull/5807
[CMake] Move non-optional simulation models to non-examples share and improve installation granularity by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5808
put more cmake find stuff to the beginning by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5810
[FEATURE] Efficiently do "defaultdict" behaviour in Map by @jpfeuffer in https://github.com/OpenMS/OpenMS/pull/5816
Optimize PeptideIndexer by @cbielow in https://github.com/OpenMS/OpenMS/pull/5809
Mutual info test by @khuenm in https://github.com/OpenMS/OpenMS/pull/5823
A Painter1D class for Peaks by @cbielow in https://github.com/OpenMS/OpenMS/pull/5822
Update PULLREQUESTTEMPLATE.md by @cbielow in https://github.com/OpenMS/OpenMS/pull/5824
New Contributors
- @radusuciu made their first contribution in https://github.com/OpenMS/OpenMS/pull/5562
- @eeko-kon made their first contribution in https://github.com/OpenMS/OpenMS/pull/5594
- @khuenm made their first contribution in https://github.com/OpenMS/OpenMS/pull/5731
Full Changelog: https://github.com/OpenMS/OpenMS/compare/Release2.7.0...Release2.8.0
- C++
Published by openms-jenkins-bot over 4 years ago
openms - OpenMS 2.7.0
Dear OpenMS-Users,
we are proud to announce the release of OpenMS 2.7.0. Grab it here
In the following you find all important changes to the previous version:
General: - OpenMS now expects a compiler that supports C17 - Config storage path on linux changed to ~/.config/ - Some documentation improvements to pyOpenMS https://pyopenms.readthedocs.io/en/latest/
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
Best regards, The OpenMS-Developers
- C++
Published by openms-jenkins-bot over 4 years ago
openms - OpenMS 2.6.0
Dear OpenMS-Users,
we are proud to announce the release of OpenMS 2.6.0. Grab it here: https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/2.6.0
Our bioconda packages are available here https://anaconda.org/search?q=OpenMS
KNIME plugins are available soon via the KNIME update mechanism.
And our pyOpenMS 2.6.0 packages will be available soon here https://pypi.org/project/pyopenms/
In the following you find all important changes to the previous version:
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
Best regards, The OpenMS-Developers
- C++
Published by openms-jenkins-bot over 5 years ago
openms - OpenMS 2.5.0
Dear OpenMS-Users,
we are proud to announce the release of OpenMS 2.5.0. Grab it here
In the following you find all important changes to the previous version:
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)
Best regards, The OpenMS-Developers
- C++
Published by openms-jenkins-bot over 6 years ago
openms - OpenMS 2.4.0
Dear OpenMS-Users,
we are proud to announce the release of OpenMS 2.4.0. Grab it here
In the following you find all important changes to the previous version:
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 -- Adapter for the deNovo search engine novor (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.
Changed tool parameters:
Tool name Added/removed Parameter name Type Default value Restrictions Supported formats
AccurateMassSearch + out output-file .mzTab
AccurateMassSearch - out output-file *.tsv
CometAdapter + allowedmissedcleavages int 0 0:5
CometAdapter + enzyme string Trypsin glutamyl endopeptidase,Arg-C,Asp-N,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P,unspecific cleavage,Trypsin
CometAdapter + fragmentbinoffset double 0 0:1
CometAdapter + fragmentbintolerance double 0.02 0.01:
CometAdapter + isotopeerror string off off,0/1,0/1/2,-1/0/1/2/3,-8/-4/0/4/8
CometAdapter + massoffsets double
CometAdapter + maxfragmentcharge int 3 1:5
CometAdapter + maxprecursorcharge int 5 1:9
CometAdapter + minimumintensity double 0 0:
CometAdapter + overridecharge string keep known search unknown keep any known,ignore known,ignore outside range,keep known search unknown
CometAdapter + removeprecursorpeak string no no,yes,chargereduced,phosphateloss
CometAdapter + removeprecursortolerance double 1.5
CometAdapter + requirevariablemod string false true,false
CometAdapter + spectrumbatchsize int 20000 0:
CometAdapter - allowedmissedcleavages int 1
CometAdapter - enzyme string Trypsin unspecific cleavage,Lys-N,Lys-C,Chymotrypsin,CNBr,glutamyl endopeptidase,PepsinA,Arg-C,Trypsin/P,Trypsin,Asp-N
CometAdapter - fragmentbinoffset double 0.25
CometAdapter - fragmentbintolerance double 1.0005
CometAdapter - isotopeerror string off off,-1/0/1/2/3,-8/-4/0/4/8
CometAdapter - massoffsets double 0
CometAdapter - maxfragmentcharge int 3
CometAdapter - maxprecursorcharge string 0+
CometAdapter - minimumintensity int 0
CometAdapter - overridecharge string keep any known keep any known,ignore known,ignore outside range,keep known search unknown
CometAdapter - removeprecursorpeak string no no,yes,all
CometAdapter - removeprecursortolerance int 1
CometAdapter - spectrumbatchsize int 1000
DecoyDatabase + Decoy:keepPeptideCTerm string true true,false
DecoyDatabase + Decoy:keepPeptideNTerm string true true,false
DecoyDatabase + Decoy:nonshufflepattern string
DecoyDatabase + enzyme string Trypsin Trypsin,Arg-C,Asp-N/B,Asp-N,Asp-Nambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formicacid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C/P
DecoyDatabase + seed string 1
DecoyDatabase + shufflemaxattempts int 30
DecoyDatabase + shufflesequenceidentitythreshold double 0.5
Digestor + FASTA:ID string parent parent,number,both
Digestor + FASTA:description string remove remove,keep
Digestor + enzyme string Trypsin Asp-N,Trypsin,Arg-C/P,Chymotrypsin/P,CNBr,Arg-C,Formicacid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Asp-N/B,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Asp-Nambic,Chymotrypsin
Digestor - enzyme string Trypsin glutamyl endopeptidase,2-iodobenzoate,no cleavage,unspecific cleavage,Arg-C,Lys-C,Trypsin,Asp-N/B,Asp-N,Asp-Nambic,V8-DE,CNBr,leukocyte elastase,proline endopeptidase,Lys-N,Lys-C/P,Arg-C/P,Chymotrypsin,Formicacid,Chymotrypsin/P,V8-E,Alpha-lytic protease,PepsinA,TrypChymo,Trypsin/P
DigestorMotif + enzyme string Trypsin Trypsin,Arg-C/P,glutamyl endopeptidase,2-iodobenzoate,staphylococcal protease/D,Asp-N,Arg-C,CNBr,Formicacid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,iodosobenzoate,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Asp-Nambic,unspecific cleavage,Chymotrypsin,Asp-N/B,Chymotrypsin/P
DigestorMotif - enzyme string Trypsin Asp-Nambic,Trypsin,Asp-N/B,Chymotrypsin/P,Chymotrypsin,Trypsin/P,V8-DE,V8-E,PepsinA,TrypChymo,glutamyl endopeptidase,Lys-C/P,Formicacid,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,Lys-C,Lys-N,Arg-C,2-iodobenzoate,no cleavage,unspecific cleavage,Arg-C/P,Asp-N,CNBr
FalseDiscoveryRate + algorithm:adddecoyproteins string false true,false
FeatureFinderIdentification + debug int 0 0:
FeatureFinderIdentification - debug int 0
FeatureFinderMetabo + algorithm:ffm:removesingletraces string false false,true
FeatureFinderMultiplex + algorithm:averaginesimilarityscaling double 0.95 0:1
FeatureFinderMultiplex + algorithm:rtband double 0 0:
FeatureFinderMultiplex + out output-file *.featureXML
FeatureFinderMultiplex + outmultiplets output-file *.consensusXML
FeatureFinderMultiplex - algorithm:averaginesimilarityscaling double 0.75 0:1
FeatureFinderMultiplex - out output-file *.consensusXML
FeatureFinderMultiplex - outfeatures output-file *.featureXML
FeatureFinderMultiplex - outmzq output-file *.mzq
FeatureLinkerUnlabeled + algorithm:ignoreadduct string true true,false
FeatureLinkerUnlabeledKD + algorithm:ignoreadduct string true true,false
FeatureLinkerUnlabeledQT + algorithm:ignoreadduct string true true,false
FileConverter + converttochromatograms string false true,false
FileFilter + id:sequencecomparisonmethod string substring substring,exact
FileFilter + peakoptions:indexedfile string true true,false
FileFilter + peakoptions:numpress:floatda string none none,linear,pic,slof
FileFilter + peakoptions:numpress:lossymassaccuracy double -1
FileFilter + spectra:blackorwhitelist:blacklist string true false,true
FileFilter + spectra:blackorwhitelist:file input-file *.mzML
FileFilter + spectra:blackorwhitelist:mz double 0.01
FileFilter + spectra:blackorwhitelist:rt double 0.01
FileFilter + spectra:blackorwhitelist:similaritythreshold double -1 -1:1
FileFilter + spectra:blackorwhitelist:useppmtolerance string false
FileFilter - peakoptions:indexedfile string false true,false
FileFilter - peakoptions:numpress:intensityerror double 0.0001
FileFilter - peakoptions:numpress:masstimeerror double 0.0001
IDConflictResolver + resolvebetweenfeatures string off off,highest_intensity
IDFileConverter + in input-file *.pepXML,.protXML,.mascotXML,.omssaXML,.xml,.psms,.tsv,.idXML,.mzid,.xquest.xml
IDFileConverter + out output-file .idXML,.mzid,.pepXML,.FASTA,.xquest.xml
IDFileConverter + out_type string idXML,mzid,pepXML,FASTA,xquest.xml
IDFileConverter - in input-file *.pepXML,.protXML,.mascotXML,.omssaXML,.xml,.psms,.tsv,.idXML,.mzid
IDFileConverter - out output-file *.idXML,.mzid,.pepXML,.FASTA
IDFileConverter - outtype string idXML,mzid,pepXML,FASTA
IDFilter + insilicodigestion:enzyme string Trypsin Asp-N/B,Asp-N,Asp-Nambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formicacid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Trypsin,Arg-C,Arg-C/P,no cleavage,unspecific cleavage
IDFilter + insilicodigestion:fasta input-file *.fasta
IDFilter + insilicodigestion:methioninecleavage string false true,false
IDFilter + insilicodigestion:missedcleavages int -1 -1:
IDFilter + insilicodigestion:specificity string full full,semi,none
IDFilter + missedcleavages:enzyme string Trypsin Asp-N/B,Asp-N,Asp-Nambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formicacid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,Trypsin,Arg-C,Arg-C/P,no cleavage,unspecific cleavage
IDFilter + missedcleavages:numberofmissedcleavages string :
IDFilter - digest:enzyme string Trypsin Lys-C,V8-E,Trypsin/P,no cleavage,V8-DE,CNBr,Lys-C/P,Formicacid,unspecific cleavage,Alpha-lytic protease,2-iodobenzoate,Asp-N/B,Arg-C/P,proline endopeptidase,TrypChymo,Arg-C,leukocyte elastase,Chymotrypsin/P,Asp-N,Chymotrypsin,Trypsin,PepsinA,Asp-Nambic,glutamyl endopeptidase,Lys-N
IDFilter - digest:fasta input-file .fasta
IDFilter - digest:methioninecleavage string false true,false
IDFilter - digest:missedcleavages int -1 -1:
IDFilter - digest:specificity string full full,semi,none
IsobaricAnalyzer - idpool string
MRMMapper + algorithm:erroronunmapped string false true,false
MRMMapper + algorithm:mapmultipleassays string false true,false
MRMMapper + algorithm:precursortolerance double 0.1
MRMMapper + algorithm:producttolerance double 0.1
MRMMapper - allowmultiplemappings string false true,false
MRMMapper - no-strict string false true,false
MRMMapper - precursortolerance double 0.1
MRMMapper - producttolerance double 0.1
MRMTransitionGroupPicker + algorithm:PeakIntegrator:baselinetype string basetobase basetobase,verticaldivision,verticaldivisionmin,verticaldivisionmax
MRMTransitionGroupPicker + algorithm:PeakIntegrator:fitEMG string false false,true
MRMTransitionGroupPicker + algorithm:PeakIntegrator:integrationtype string intensitysum intensitysum,simpson,trapezoid
MRMTransitionGroupPicker + algorithm:backgroundsubtraction string none none,original,exact
MRMTransitionGroupPicker + algorithm:boundaryselectionmethod string largest largest,widest
MRMTransitionGroupPicker + algorithm:computepeakshapemetrics string false true,false
MRMTransitionGroupPicker + algorithm:computetotalmi string false true,false
MRMTransitionGroupPicker + algorithm:peakintegration string original original,smoothed
MRMTransitionGroupPicker + algorithm:useconsensus string true true,false
MRMTransitionGroupPicker - algorithm:backgroundsubtraction string none none,smoothed,original
MSGFPlusAdapter + addfeatures string true true,false
MSGFPlusAdapter + protocol string automatic automatic,phospho,iTRAQ,iTRAQphospho,TMT,none
MSGFPlusAdapter - addfeatures string false true,false
MSGFPlusAdapter - protocol string none none,phospho,iTRAQ,iTRAQphospho,TMT
MSSimulator + algorithm:MSSim:Digestion:enzyme string Trypsin Trypsin,Asp-N/B,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,CNBr,Formicacid,Lys-C,unspecific cleavage,Chymotrypsin,Asp-Nambic,Arg-C/P,Chymotrypsin/P,Asp-N,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Arg-C
MSSimulator - algorithm:MSSim:Digestion:enzyme string Trypsin PepsinA,2-iodobenzoate,no cleavage,Arg-C,Lys-C,Trypsin,Asp-N/B,Asp-N,Asp-Nambic,CNBr,Alpha-lytic protease,glutamyl endopeptidase,Lys-N,Lys-C/P,Chymotrypsin,Formicacid,Chymotrypsin/P,Arg-C/P,leukocyte elastase,proline endopeptidase,TrypChymo,Trypsin/P,V8-DE,V8-E,unspecific cleavage
MapAlignerIdentification + model:linear:xdatummax double 1e+15
MapAlignerIdentification + model:linear:xdatummin double 1e-15
MapAlignerIdentification + model:linear:xweight string 1/x,1/x2,ln(x),
MapAlignerIdentification + model:linear:ydatummax double 1e+15
MapAlignerIdentification + model:linear:ydatummin double 1e-15
MapAlignerIdentification + model:linear:yweight string 1/y,1/y2,ln(y),
MapAlignerPoseClustering + algorithm:pairfinder:ignore_adduct string true true,false
MapAlignerPoseClustering + in input-file *.featureXML,.mzML
MapAlignerPoseClustering + out output-file .featureXML,.mzML
MapAlignerPoseClustering + reference:file input-file .featureXML,.mzML
MapAlignerPoseClustering - in input-file .mzML,.featureXML
MapAlignerPoseClustering - out output-file .mzML,.featureXML
MapAlignerPoseClustering - reference:file input-file .mzML,.featureXML
MapAlignerSpectrum + model:linear:xdatummax double 1e+15
MapAlignerSpectrum + model:linear:xdatummin double 1e-15
MapAlignerSpectrum + model:linear:xweight string 1/x,1/x2,ln(x),
MapAlignerSpectrum + model:linear:ydatummax double 1e+15
MapAlignerSpectrum + model:linear:ydatummin double 1e-15
MapAlignerSpectrum + model:linear:yweight string 1/y,1/y2,ln(y),
MapRTTransformer + model:linear:xdatummax double 1e+15
MapRTTransformer + model:linear:xdatummin double 1e-15
MapRTTransformer + model:linear:xweight string 1/x,1/x2,ln(x),
MapRTTransformer + model:linear:ydatummax double 1e+15
MapRTTransformer + model:linear:ydatummin double 1e-15
MapRTTransformer + model:linear:yweight string 1/y,1/y2,ln(y),
MetaboliteAdductDecharger + algorithm:MetaboliteFeatureDeconvolution:maxminoritybound int 3 0:
MetaboliteAdductDecharger + algorithm:MetaboliteFeatureDeconvolution:maxneutrals int 1
MetaboliteAdductDecharger + algorithm:MetaboliteFeatureDeconvolution:useminoritybound string true
MetaboliteAdductDecharger - algorithm:MetaboliteFeatureDeconvolution:maxminoritybound int 2 0:
MetaboliteAdductDecharger - algorithm:MetaboliteFeatureDeconvolution:maxneutrals int 0
MetaboliteSpectralMatcher + out output-file .mzTab
MetaboliteSpectralMatcher - out output-file *.tsv
MzTabExporter + out output-file *.mzTab
MzTabExporter - out output-file *.tsv
OMSSAAdapter + enzyme string Trypsin glutamyl endopeptidase,no cleavage,unspecific cleavage,Asp-Nambic,Chymotrypsin,CNBr,Formicacid,Lys-C,Arg-C,Asp-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,Trypsin
OMSSAAdapter - enzyme string Trypsin Trypsin,Arg-C,PepsinA,TrypChymo,Trypsin/P,glutamyl endopeptidase,no cleavage,Asp-N,Lys-C,Lys-C/P,Chymotrypsin,CNBr,Formicacid,unspecific cleavage,Asp-Nambic
OpenPepXL + algorithm:deisotope string auto true,false,auto
OpenPepXL + ions:aions string false true,false
OpenPepXL + ions:bions string true true,false
OpenPepXL + ions:cions string false true,false
OpenPepXL + ions:neutrallosses string true true,false
OpenPepXL + ions:xions string false true,false
OpenPepXL + ions:yions string true true,false
OpenPepXL + ions:zions string false true,false
OpenPepXL + outxquest_specxml output-file *.xml,.spec.xml
OpenPepXL + outxquestxml output-file .xml,.xquest.xml
OpenPepXL + peptide:enzyme string Trypsin Asp-N,Asp-N/B,Asp-Nambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formicacid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Arg-C/P,Trypsin,Arg-C,unspecific cleavage
OpenPepXL + precursor:corrections int
OpenPepXL - outxquestspecxml output-file *.xml
OpenPepXL - outxquestxml output-file .xml
OpenPepXL - peptide:enzyme string Trypsin unspecific cleavage,no cleavage,TrypChymo,Lys-C,Lys-N,2-iodobenzoate,V8-E,PepsinA,proline endopeptidase,Trypsin/P,glutamyl endopeptidase,Alpha-lytic protease,V8-DE,Formicacid,leukocyte elastase,Lys-C/P,Chymotrypsin/P,CNBr,Asp-N,Asp-N/B,Asp-Nambic,Chymotrypsin,Arg-C/P,Trypsin,Arg-C
OpenPepXLLF + algorithm:deisotope string auto true,false,auto
OpenPepXLLF + algorithm:numberofscoredcandidates int 10000
OpenPepXLLF + algorithm:prescoring string false true,false
OpenPepXLLF + ions:aions string false true,false
OpenPepXLLF + ions:bions string true true,false
OpenPepXLLF + ions:cions string false true,false
OpenPepXLLF + ions:neutrallosses string true true,false
OpenPepXLLF + ions:xions string false true,false
OpenPepXLLF + ions:yions string true true,false
OpenPepXLLF + ions:zions string false true,false
OpenPepXLLF + outxquest_specxml output-file *.xml,.spec.xml
OpenPepXLLF + outxquestxml output-file .xml,.xquest.xml
OpenPepXLLF + peptide:enzyme string Trypsin Chymotrypsin/P,Asp-Nambic,Chymotrypsin,CNBr,Formicacid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Arg-C/P,Arg-C,unspecific cleavage,Trypsin,Asp-N/B,Asp-N
OpenPepXLLF + precursor:corrections int
OpenPepXLLF - outxquestspecxml output-file *.xml
OpenPepXLLF - outxquestxml output-file .xml
OpenPepXLLF - peptide:enzyme string Trypsin Arg-C/P,Asp-N,V8-DE,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,Lys-C,Lys-N,Asp-N/B,Asp-Nambic,Chymotrypsin/P,CNBr,Formicacid,Chymotrypsin,Arg-C,Trypsin,2-iodobenzoate,no cleavage,unspecific cleavage,leukocyte elastase,Alpha-lytic protease,glutamyl endopeptidase,V8-E,proline endopeptidase
OpenSwathAnalyzer + algorithm:DIAScoring:diaextractionunit string Th Th,ppm
OpenSwathAnalyzer + algorithm:Scores:usemiscore string false true,false
OpenSwathAnalyzer + algorithm:Scores:usems1mi string false true,false
OpenSwathAnalyzer + algorithm:Scores:usetotalmiscore string false true,false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakIntegrator:baselinetype string basetobase basetobase,verticaldivision,verticaldivisionmin,verticaldivisionmax
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakIntegrator:fitEMG string false false,true
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakIntegrator:integrationtype string intensitysum intensitysum,simpson,trapezoid
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:backgroundsubtraction string none none,original,exact
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:boundaryselectionmethod string largest largest,widest
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:computepeakshapemetrics string false true,false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:computetotalmi string false true,false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:peakintegration string original original,smoothed
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:useconsensus string true true,false
OpenSwathAnalyzer + algorithm:scoringmodel string default default,singletransition
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:backgroundsubtraction string none none,smoothed,original
OpenSwathAssayGenerator + disableidentificationms2precursors string false true,false
OpenSwathAssayGenerator + disableidentificationspecificlosses string false true,false
OpenSwathAssayGenerator + enableipf string false true,false
OpenSwathAssayGenerator + enableswath_specifity string false true,false
OpenSwathAssayGenerator + in input-file *.tsv,.mrm,.pqp,.TraML
OpenSwathAssayGenerator + intype string tsv,mrm,pqp,TraML
OpenSwathAssayGenerator + maxnumalternativelocalizations int 10000
OpenSwathAssayGenerator + out output-file .tsv,.pqp,.TraML
OpenSwathAssayGenerator + outtype string tsv,pqp,TraML
OpenSwathAssayGenerator + unimodfile input-file *.xml
OpenSwathAssayGenerator - enableidentificationms2precursors string false true,false
OpenSwathAssayGenerator - enableidentificationspecificlosses string false true,false
OpenSwathAssayGenerator - enablems1uisscoring string false true,false
OpenSwathAssayGenerator - enablems2uisscoring string false true,false
OpenSwathAssayGenerator - enablereannotation string false true,false
OpenSwathAssayGenerator - in input-file *.traML
OpenSwathAssayGenerator - maxnumalternativelocalizations int 20
OpenSwathAssayGenerator - out output-file *.traML
OpenSwathChromatogramExtractor + ionmobilitywindow double -1
OpenSwathDecoyGenerator + aimdecoyfraction double 1
OpenSwathDecoyGenerator + in input-file *.tsv,.mrm,.pqp,.TraML
OpenSwathDecoyGenerator + intype string tsv,mrm,pqp,TraML
OpenSwathDecoyGenerator + method string shuffle shuffle,pseudo-reverse,reverse,shift
OpenSwathDecoyGenerator + mindecoyfraction double 0.8
OpenSwathDecoyGenerator + out output-file .tsv,.pqp,*.TraML
OpenSwathDecoyGenerator + outtype string tsv,pqp,TraML
OpenSwathDecoyGenerator + productmzthreshold double 0.025
OpenSwathDecoyGenerator + separate string false true,false
OpenSwathDecoyGenerator + shiftprecursormzshift double 0
OpenSwathDecoyGenerator + shiftproductmzshift double 20
OpenSwathDecoyGenerator + shufflemaxattempts int 30
OpenSwathDecoyGenerator + shufflesequenceidentitythreshold double 0.5
OpenSwathDecoyGenerator + switchKR string true true,false
OpenSwathDecoyGenerator - append string false true,false
OpenSwathDecoyGenerator - excludesimilar string false true,false
OpenSwathDecoyGenerator - identitythreshold double 0.7
OpenSwathDecoyGenerator - in input-file *.traML
OpenSwathDecoyGenerator - maxattempts int 10
OpenSwathDecoyGenerator - method string shuffle
OpenSwathDecoyGenerator - mzshift double 20
OpenSwathDecoyGenerator - mzthreshold double 0.05
OpenSwathDecoyGenerator - out output-file .traML
OpenSwathDecoyGenerator - precursormassshift double 0
OpenSwathDecoyGenerator - removeCNtermmods string false true,false
OpenSwathDecoyGenerator - removeunannotated string false true,false
OpenSwathDecoyGenerator - similaritythreshold double -1
OpenSwathMzMLFileCacher + fullmeta string true true,false
OpenSwathMzMLFileCacher + lossycompression string true true,false
OpenSwathMzMLFileCacher + lossymassaccuracy double -1
OpenSwathMzMLFileCacher + lowmembatchsize int 500 0:
OpenSwathMzMLFileCacher + processlowmemory string false true,false
OpenSwathRTNormalizer + algorithm:DIAScoring:diaextractionunit string Th Th,ppm
OpenSwathRTNormalizer + algorithm:Scores:usemiscore string false true,false
OpenSwathRTNormalizer + algorithm:Scores:usems1mi string false true,false
OpenSwathRTNormalizer + algorithm:Scores:usetotalmiscore string false true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakIntegrator:baselinetype string basetobase basetobase,verticaldivision,verticaldivisionmin,verticaldivisionmax
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakIntegrator:fitEMG string false false,true
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakIntegrator:integrationtype string intensitysum intensitysum,simpson,trapezoid
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:backgroundsubtraction string none none,original,exact
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:boundaryselectionmethod string largest largest,widest
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:computepeakshapemetrics string false true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:computetotalmi string false true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:peakintegration string original original,smoothed
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:useconsensus string true true,false
OpenSwathRTNormalizer + algorithm:scoringmodel string default default,singletransition
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:backgroundsubtraction string none none,smoothed,original
OpenSwathWorkflow + Debugging:irtmzml string
OpenSwathWorkflow + Debugging:irttrafo string
OpenSwathWorkflow + Scoring:DIAScoring:diaextractionunit string Th Th,ppm
OpenSwathWorkflow + Scoring:Scores:usemiscore string false true,false
OpenSwathWorkflow + Scoring:Scores:usems1mi string false true,false
OpenSwathWorkflow + Scoring:Scores:usetotalmiscore string false true,false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakIntegrator:baselinetype string basetobase basetobase,verticaldivision,verticaldivisionmin,verticaldivisionmax
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakIntegrator:fitEMG string false false,true
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakIntegrator:integrationtype string intensitysum intensitysum,simpson,trapezoid
OpenSwathWorkflow + Scoring:TransitionGroupPicker:backgroundsubtraction string none none,original,exact
OpenSwathWorkflow + Scoring:TransitionGroupPicker:boundaryselectionmethod string largest largest,widest
OpenSwathWorkflow + Scoring:TransitionGroupPicker:computepeakshapemetrics string false true,false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:computetotalmi string false true,false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:peakintegration string original original,smoothed
OpenSwathWorkflow + Scoring:TransitionGroupPicker:useconsensus string true true,false
OpenSwathWorkflow + Scoring:scoringmodel string default default,singletransition
OpenSwathWorkflow + Scoring:uisthreshold_sn int 0
OpenSwathWorkflow + in input-file *.mzML,.mzXML,.sqMass
OpenSwathWorkflow + ionmobilitywindow double -1
OpenSwathWorkflow - Scoring:TransitionGroupPicker:backgroundsubtraction string none none,smoothed,original
OpenSwathWorkflow - Scoring:uisthreshold_sn int -1
OpenSwathWorkflow - in input-file *.mzML,.mzXML
PeptideIndexer + aaamax int 3 0:10
PeptideIndexer + decoystring string
PeptideIndexer + enzyme:name string Trypsin Chymotrypsin/P,CNBr,Formicacid,Arg-C/P,Asp-N/B,Asp-Nambic,Chymotrypsin,Arg-C,Asp-N,Trypsin,Lys-C,Lys-N,Lys-C/P,PepsinA,elastase-trypsin-chymotrypsin,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,no cleavage,unspecific cleavage
PeptideIndexer + mismatchesmax int 0 0:10
PeptideIndexer + missingdecoyaction string error error,warn,silent
PeptideIndexer - aaamax int 4 0:
PeptideIndexer - decoystring string DECOY
PeptideIndexer - enzyme:name string Trypsin Asp-N/B,Arg-C/P,Trypsin,V8-DE,CNBr,Arg-C,TrypChymo,Lys-N,leukocyte elastase,Alpha-lytic protease,Asp-Nambic,Chymotrypsin/P,Formicacid,PepsinA,V8-E,proline endopeptidase,Asp-N,Lys-C,Chymotrypsin,Trypsin/P,Lys-C/P,no cleavage,unspecific cleavage,glutamyl endopeptidase,2-iodobenzoate
PeptideIndexer - filteraaaproteins string false true,false
PeptideIndexer - fulltolerantsearch string false true,false
PeptideIndexer - mismatchesmax int 0 0:
PeptideIndexer - missingdecoyaction string error error,warn
PercolatorAdapter + inosw input-file .OSW
PercolatorAdapter + ipfmaxpeakgrouppep double 0.7
PercolatorAdapter + ipfmaxtransitionisotopeoverlap double 0.5
PercolatorAdapter + ipfmintransitionsn double 0
PercolatorAdapter + osw_level string ms2
PercolatorAdapter + out output-file *.mzid,.idXML,.osw
PercolatorAdapter + outpin output-file *.tab
PercolatorAdapter + outtype string mzid,idXML,osw
PercolatorAdapter + scoretype string q-value q-value,pep,svm
PercolatorAdapter + train-best-positive string false true,false
PercolatorAdapter - mzidout output-file *.mzid
PercolatorAdapter - out output-file *.idXML
PhosphoScoring + fragmentmasstolerance double 0.05 0:
PhosphoScoring + maxnumperm int 16384 0:
PhosphoScoring + maxpeptidelength int 40 0:
PhosphoScoring + out output-file
PhosphoScoring + unambiguousscore int 1000
PhosphoScoring - fragmentmasstolerance double 0.05
PhosphoScoring - maxnumperm int 16384 1:
PhosphoScoring - maxpeptidelength int 40 1:
PhosphoScoring - out output-file *.idXML
RNPxlSearch + RNPxl:cancrosslink string U
RNPxlSearch + RNPxl:decoys string false true,false
RNPxlSearch + RNPxl:scoring string fast fast,slow
RNPxlSearch + peptide:enzyme string Trypsin Arg-C/P,Trypsin,Arg-C,Asp-N/B,Asp-N,CNBr,Formicacid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,Asp-Nambic,Chymotrypsin/P,Chymotrypsin,glutamyl endopeptidase,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage
RNPxlSearch + peptide:maxsize int 1000000
RNPxlSearch - RNPxl:restrictions string
RNPxlSearch - peptide:enzyme string Trypsin glutamyl endopeptidase,Alpha-lytic protease,Asp-N,Lys-C,V8-DE,Lys-C/P,PepsinA,V8-E,Asp-N/B,CNBr,proline endopeptidase,unspecific cleavage,Lys-N,2-iodobenzoate,leukocyte elastase,Asp-Nambic,Formicacid,Arg-C/P,Arg-C,Chymotrypsin,TrypChymo,Trypsin/P,Trypsin,no cleavage,Chymotrypsin/P
SimpleSearchEngine + enzyme string Trypsin staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,iodosobenzoate,2-iodobenzoate,PepsinA + P,Clostripain/P,Arg-C/P,Trypsin,Arg-C,Asp-N,Asp-N/B,Asp-Nambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formicacid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,V8-DE,Trypsin/P,V8-E,leukocyte elastase,proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,cyanogen-bromide
SimpleSearchEngine + peptide:motif string
SimpleSearchEngine - enzyme string Trypsin Asp-N/B,V8-E,Chymotrypsin/P,Asp-Nambic,Lys-C,Alpha-lytic protease,leukocyte elastase,unspecific cleavage,Chymotrypsin,V8-DE,Trypsin,Arg-C,2-iodobenzoate,glutamyl endopeptidase,Lys-N,Lys-C/P,TrypChymo,proline endopeptidase,Asp-N,no cleavage,Formicacid,CNBr,Arg-C/P,PepsinA,Trypsin/P
SiriusAdapter + compoundtimeout int 10
SiriusAdapter + elements string CHNOP[5]S[8]Cl[1]
SiriusAdapter + featureonly string false true,false
SiriusAdapter + filterbynummasstraces int 1 1:
SiriusAdapter + infeatureinfo input-file *.featurexml
SiriusAdapter + iontree string false true,false
SiriusAdapter + isotopepatterniterations int 3
SiriusAdapter + mostintensems2 string false true,false
SiriusAdapter + nomasstraceinfoisotopepattern string false true,false
SiriusAdapter + outfingerid output-file *.mzTab
SiriusAdapter + outsirius output-file *.mzTab
SiriusAdapter + precursormztolerance double 0.005
SiriusAdapter + precursormztoleranceunit string Da Da,ppm
SiriusAdapter + precursorrttolerance double 5
SiriusAdapter + topnhits int 10
SiriusAdapter + treetimeout int 0
SiriusAdapter - elements string CHNOP[5]S
SiriusAdapter - iontree string false true,false
SiriusAdapter - number int 10
SiriusAdapter - outfingerid output-file *.tsv
SiriusAdapter - outsirius output-file *.tsv
SpecLibSearcher + fragment:masstolerance double 10
SpecLibSearcher + modifications:fixed string ...
SpecLibSearcher + modifications:variable string ...
SpecLibSearcher + modifications:variablemaxperpeptide int 2
SpecLibSearcher + precursor:isotopes int
SpecLibSearcher + precursor:masstolerance double 10
SpecLibSearcher + precursor:masstoleranceunit string ppm ppm,Da
SpecLibSearcher + precursor:maxcharge int 5
SpecLibSearcher + precursor:mincharge int 2
SpecLibSearcher + report:tophits int 10
SpecLibSearcher - fixedmodifications string ...
SpecLibSearcher - precursormasstolerance double 3
SpecLibSearcher - roundprecursortointeger int 10
SpecLibSearcher - tophits int 10
SpecLibSearcher - variablemodifications string ...
XFDR + decoystring string DECOY_
XFDR + in input-file *.xml,.idXML,.mzid,.xquest.xml
XFDR + intype string xml,idXML,mzid,xquest.xml
XFDR + outxquest output-file .xquest.xml
XFDR - in input-file *.xml,.idXML,*.mzid
XFDR - intype string xml,idXML,mzid
XTandemAdapter + enzyme string Trypsin Trypsin,Arg-C/P,Asp-Nambic,PepsinA,TrypChymo,Asp-N,Lys-N,Lys-C/P,unspecific cleavage,Lys-C,2-iodobenzoate,Asp-N/B,Arg-C,V8-DE,Chymotrypsin,Chymotrypsin/P,CNBr,Formicacid,Trypsin/P,V8-E,leukocyte elastase,Alpha-lytic protease,glutamyl endopeptidase
XTandemAdapter - enzyme string Trypsin glutamyl endopeptidase,Formicacid,TrypChymo,Arg-C/P,Lys-C,Alpha-lytic protease,2-iodobenzoate,CNBr,leukocyte elastase,unspecific cleavage,Lys-C/P,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Asp-N,V8-E,Lys-N,Asp-N/B,Trypsin,Arg-C,Trypsin/P,PepsinA,V8-DE
Best regards, The OpenMS-Developers
- C++
Published by openms-jenkins-bot over 7 years ago
openms - OpenMS 2.3.0
Dear OpenMS-Users,
we are proud to announce the release of OpenMS 2.3.0. Grab it here
In the following you find all important changes to the previous version:
OpenMS 2.3 introduces a considerable number of new features and bug fixes.
Notable changes since version 2.2 are:
TOPPView: - Deletion of selections of Peak Annotations is reflected in the Peptide Hit - Buttons for saving ID files were merged to one single button. Format is determined by file extension or selected filter - Clicking on a data point in 2D view, the search range for close fragment ion spectra is extended if no spectra are found initially
New tools: - CometAdapter -- Annotates MS/MS spectra using Comet (TOPP) - MetaboliteAdductDecharger -- Decharges and merges different feature charge variants of the same metabolite (UTIL) - OpenPepXL -- Tool for protein-protein cross-linking identification using labeled linkers (UTIL) - OpenPepXLLF -- Tool for protein-protein cross linking with label-free linkers (UTIL) - PSMFeatureExtractor -- Computes extra features for each input PSM (UTIL) - SiriusAdapter -- Tool for metabolite identification using single and tandem mass spectrometry (UTIL) - XFDR -- Calculates false discovery rate estimates on protein-protein-crosslink identifications (UTIL)
Deprecated and removed tools: - None
Renamed tool: - LowMemPeakPickerHiRes_RandomAccess was renamed to LowMemPeakPickerHiResRandomAccess
Major changes in functionality: - Experimental design - Add support for fractions - FeatureLinkerUnlabeledKD - m/z and retention time tolerances for warping and linking are now separate parameters - IsobaricAnalyzer - 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
Library: - TOPP tools report their peak memory usage when using -debug 1 (or higher) - idXML files can now be written faster (about 10%) - pyOpenMS bindings for DataArrayByName getters - Python build are now split in compilation units and can thus run in parallel - FASTA files can now be written - Allow String values to be passed to EnzymaticDigestion::isValidProduct
File formats: - consensusXML now supports both channels and MS runs. Information will also be exported in mzTab
Scripts: - None
Databases: - None
Third-party software: - New: Comet "2016.01 rev. 3" for Windows 32bit/64bit, Linux 64bit, and MacOS 64bit - New: Percolator 3.1.2 for Windows 32bit/64bit, Linux 64bit, and MacOS 64bit (still experimental) - New: Sirius 3.5.1 for Windows 64bit, Linux 64bit, and MacOS 64bit - New: SpectraST 5.0 for Windows 64bit, Linux 64bit, and MacOS 64bit - Update MS-GF+ to Release (v2017.07.21)
Best regards, The OpenMS-Developers
- C++
Published by openms-jenkins-bot over 8 years ago
openms - OpenMS 2.2.0
OpenMS 2.2 is a source-only release. It introduces a considerable number of new features and bug fixes. For using new versions of the dependencies we included a new source package below, called OpenMS-2.2.0-bugfixNewContrib.tar.gz.
Notable changes since version 2.1 are:
New tools: - RNPxlSearch -- Annotate RNA to peptide crosslinks in MS/MS spectra (UTIL) - SpectraSTSearchAdapter -- Interface to the SEARCH Mode of the SpectraST executable (UTIL) - FeatureLinkerUnlabeledKD -- Feature linking using a KD tree (TOPP) - DatabaseFilter -- Filters a protein database (FASTA format) based on identified proteins (UTIL) - TargetedFileConverter -- Conversion of multiple targeted file formats (CSV, TraML etc)
Deprecated and removed tools: - ITRAQAnalyzer -- superseded by IsobaricAnalyzer - TMTAnalyzer -- superseded by IsobaricAnalyzer - ConvertTSVToTraML - superseded by TargetedFileConverter - ConvertTraMLToTSV - superseded by TargetedFileConverter - MapAlignmentEvaluation -- removed as deprecated
Major changes in functionality: - OpenSWATH analysis - Support for metabolomics workflows - Support for scanning SWATH (SONAR) - Support for SQL-based file formats - XTandemAdapter - Simplified usage - Improved support for PTMs and newer X! Tandem versions ("Vengeance", "Alanine") - IsobaricAnalyzer - Support for TMT10plex - Support for quantification in MS3 data - IDMapper - Allows to map unidentified tandem mass spectra to features - FeatureFinderIdentification - Advanced multi-sample support using machine learning - FileFilter - Allows users to enable zlib and lossy compression (see "-lossy_compression") - Allows users to set desired mass accuracy - IDFilter - Added option to filter for valid digestion products - FalseDiscoveryRate - Allow filtering by q-value in the tool (no need for IDFilter with "score:pep" option)
Library: - Averagine approximation for fragment isotope distributions - Precursor mass correction supports correction to highest intensity peak in tolerance window - Functionality for resampling and adding of spectra - Protein-protein cross-link spectrum generator - Terminal modifications are now separated by "." in text output - SQLite support in OpenSWATH - TheoreticalSpectrumGenerator speed-up and removal of RichPeak code - Removal of template parameters from MSExperiment (reduced compile time and binary size) - Allow estimation of isotope distributions with predefined numbers of sulfur atoms - Improved handling of bracket notation for modified residues (e.g. N[2457.877]VSVK) - Improved handling of terminal and residue specificity of modifications - Improved annotation of peptide identifications with spectrum references - Improved handling of unknown amino acids ("X") in sequences
File formats: - Improved mzML support for SONAR data and mzML with drift time (experimental) - Improved support for cross-link data and unknown modifications in mzIdentML - mzXML writer able to write MaxQuant-compatible files - mzML files now routinely support substantial compression (up to 5x compression, see #2449, #2458) - Support for Percolator result files based on X! Tandem searches
Scripts: - New R script for visualizing RT transformations (trafoXML)
Databases: - By default, decoy sequences are now denoted by the prefix "DECOY_"
- C++
Published by jpfeuffer over 8 years ago
openms - OpenMS 2.1.0
---- OpenMS 2.1 ----
OpenMS 2.1 introduces a considerable number of new features and bug fixes.
Notable changes since version 2.0.1 are:
New tools: - ExternalCalibration -- Applies an external mass recalibration (TOPP) - OpenSwathFileSplitter -- Splits SWATH files into n files, each containing one window (TOPP) - MultiplexResolver -- Completes peptide multiplets and resolves conflicts within them (UTIL) - TICCalculator -- Calculates the TIC from a mass spectrometric raw file (useful for benchmarking) (UTIL)
Deprecated and removed tools: - PILISIdentification -- performs a peptide/protein identification with the PILIS engine (TOPP) - PILISModelCV -- Perform a cross validation of the PILIS model parameters (TOPP) - PILISModelTrainer -- Train the PILIS model with a given set of spectra and identifications (TOPP) - PILISSpectraGenerator -- Generate spectra given a list of peptides and a PILIS model (TOPP)
Major changes in functionality: - Update notification: starting with OpenMS 2.1 all TOPP tools will check for updated versions of the tools online and will print an information message if a newer version is available. This version check occurs only once per day and tool. Information on which tools are executed will be collected anonymously to identify which tools are no longer used and to optimally distribute development resources. If the feature causes problems or concerns, it can be disabled through a command line switch or environment variable (see the documentation). - InternalCalibration: - supports calibration using a table of lock masses and peptide ids. - global or RT-chunked calibration - linear & quadratic models (with intensity weighting) - outlier removal via RANSAC - reoccurring calibrations can be quickly applied to other files using the novel ExternalCalibration tool - OpenSwathWorkflow - support for metabolites / small molecules - MapAlignerIdentification - support for "lowess" transformation model - AccurateMassSearch: - support for multiple databases - FeatureFinderMetabo - isotope spacing model for carbon rich molecules (e.g. lipids) - PeakPickerHiRes and MassTraceExtractor: - support for FWHM annotation
File formats: - Improved mzIdentML support (experimental) - Improved pepXML support - Improved support for indexed mzML files - Improved TraML support
Databases: - By default, decoy sequences are now denoted by a prefix 'DECOY_'.
Third-party software: - update for X!Tandem VENGEANCE (2015.12.15) - update for MS-GF+ Release v2016.10.14, released October 14, 2016 - update for pwiz 3.0.9935
- C++
Published by timosachsenberg over 9 years ago
openms - Source-only release of the OpenMS library
---- OpenMS 2.0.1 ----
OpenMS 2.0.1 is a source only release of the core libraries and tools. This means that although we release the automatically generated installers, we denote that these are not fully supported/tested. The same holds for the use of the provided tools in the third-party workflow systems for which we established integration (e.g. KNIME). With over 300 merged pull requests, it introduces a considerable number of new features, bug fixes and speed improvements.
Notable changes are:
File formats: - Improved mzIdentML support (experimental) - Improved mzTab support (experimental) - Comet pepXML file reading support (experimental) - Search parameter units are retained through id files - Faster base64 decoding in XML files
Databases: - HMDB has been updated to version 3.6
TOPPView: - Added slight margin around data range (%2) for improved visualization - Added FeatureFinderMultiplex to the tools accessible from TOPPView - Some fixes to the scrollbar behaviour
Added tools: - IDScoreSwitcher -- Switches between different scores of peptide or protein hits in identification data (UTIL) - LuciphorAdapter -- Modification site localisation using LuciPHOr2 (TOPP) - MetaProSIP -- Performs proteinSIP on peptide features for elemental flux analysis (UTIL) - MzMLSplitter -- Splits an mzML file into multiple parts (UTIL) - OpenSwathAssayGenerator -- Generates assays according to different models for a specific TraML (TOPP)
Removed tools: - RTAnnotator -- Annotates identification files that are missing the RT field (UTIL)
Tools with major changes: - OpenSWATH now outputs peak apices - Improved iRT correction - Assay generator - UIS scoring - Deuterium labeling in MetaProSIP (experimental) - XTandemAdapter allows for external config file - TextExporter can optionally export PeptideIdentification and PeptideHits meta-values - FeatureLinkerUnlabeledQT speed improvements - FileMerger allows to concatenate files in RT - MzTabExporter supports protein IDs - PeakPickerWavelet speedup - HiResPrecursorMassCorrector supports correction of precursors to detected features - FeatureFinderMultiplex speed improvements
Library: - Support for user definable enzymes available in EnzymesDB.xml - PeptideIndexing is now available as internal algorithm - EnzymaticDigestion allows for minimum / maximum length constraints - HyperScore and PScore implementations - Fits allow extrapolation of data values - QT clustering is now order independent - Additional convinience functions to access the nearest spectrum peak in a mass tolerance window - User defined averagine compositions - A fast linear lowess implementation has been added - MetaInfoInterface has been added to FeatureMap to store additional meta-values - Calculation of Median Absolute Deviation
General: - OpenMS writes indexed mzML by default - OpenMS home directory can be configured through OPENMSHOMEDIR 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/)
- C++
Published by timosachsenberg about 10 years ago