OpenMS Versions Save

The codebase of the OpenMS project

Release3.1.0

6 months ago

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.

The source code and precompiled installers (Windows, Linux, MacOSX) are available at the bottom of this page or here.

Note: the Windows installer has been updated (Nov 16th 2023) to re-establish functionality of the OpenMS GUI tools (like TOPPView, TOPPAS etc) - which were misconfigured in the first release.

Important Notes:

  • Features are experimental and may undergo changes or be removed in future releases based on user feedback and stability.
  • We welcome your feedback and suggestions to help us improve and refine these experimental features.
  • For stability and production use, we recommend sticking with the latest stable release.

Please use this opportunity to test and provide feedback on these new features, as your input will play a vital role in shaping their development.

Thank you for being a part of our community and for helping us make OpenMS even better!

What's new:

  • Major change: removed the distinction between TOPP tool and util and the TOPP and UTIL build targets were merged to a single TOPP target. All utils are considered tools now and categorized as "Utilities".
  • Added SageAdapter. Support for standard identification tasks with sage (https://github.com/lazear/sage) (experimental).
  • Require some advanced instruction sets for x64 CPUs: SSE3 (g++/clang) or AVX (MSVC); and NEON for ARM64 CPUs (#6978) and report them via the OpenMSInfo tool (#7022)
  • Base64 encoding/decoding using the SIMDe library (#6978)
  • Filter features in ProteomicsLFQ according to feature p-value (additional parameters feature_with(out)_id_min_score, MBR is automatically active if targeted_only = false)

Fixes:

  • Fix a crash when loading mzML data with multiple threads which contains non-MS spectra, e.g. 'electromagnetic radiation spectrum' (#7011)
  • InternalCalibration: improve visualization of calibration plots (#7064)
  • Restore TOPPAS tutorial (#7076)
  • various low impact UBSan fixes
  • make mzData more robust against wrong 'length' attributes for binary data (#7113)

Misc:

  • Report reading/writing throughput (MiB/sec) when loading/storing mzML (#7035)
  • Add ability to create decoy features in FeatureFinderIdentification
  • Restore developer quick guide in Doxygen docu - see https://openms.de/current_doxygen/html/index.html (#7109)
  • Updated the changelog helper to set LD_LIBRARY_PATH automatically and other fixes
  • Added "area" column to EICextractor output

Cleanup of old/unused tools and code:

  • Removed old tools and associated code in the library for InclusionExclusionListCreator, SvmTheoreticalSpectrumGenerator, PrecursorIonSelector, and MSSimulator Note: general SVC and SVR is still supported with the SimpleSVM class.
  • Removed old RT and PT predict code and tools RTModel, RTPredict, PTModel, PTPredict, RTEvaluation and associated library code (SVMWrapper and LibSVMEncoder).
  • Removed PepNovoAdapter
  • Removed CompNovoAdapter and library code
  • Removed simplistic evaluation tools FFEval, LabeledEval, TransformationEvaluation
  • Removed EnzymaticDigestionLogModel
  • Removed FidoAdapter (same functionality now in our own inference engines)

Full Changelog: https://github.com/OpenMS/OpenMS/compare/Release3.0.0...Release3.1.0

Release3.0.0

9 months ago

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.

Note: The Windows-Installer has been updated on Nov 16th 2023 to allow installation on systems with a lot of other software preinstalled (potentially leading to errors during installation of OpenMS).

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

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

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

Release2.8.0

2 years ago

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 keep_unidentified_masses to "true" (AccurateMassSearch/AccurateMassSearchEngine)

Best regards, The OpenMS-Developers

What's Changed

New Contributors

Full Changelog: https://github.com/OpenMS/OpenMS/compare/Release2.7.0...Release2.8.0

Release2.7.0

2 years ago

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:

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

Release2.6.0

3 years ago

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

Release2.5.0

4 years ago

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

Release2.4.0

5 years ago

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 + allowed_missed_cleavages 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 + fragment_bin_offset double 0 0:1 CometAdapter + fragment_bin_tolerance double 0.02 0.01: CometAdapter + isotope_error string off off,0/1,0/1/2,-1/0/1/2/3,-8/-4/0/4/8 CometAdapter + mass_offsets double CometAdapter + max_fragment_charge int 3 1:5 CometAdapter + max_precursor_charge int 5 1:9 CometAdapter + minimum_intensity double 0 0: CometAdapter + override_charge string keep known search unknown keep any known,ignore known,ignore outside range,keep known search unknown CometAdapter + remove_precursor_peak string no no,yes,charge_reduced,phosphate_loss CometAdapter + remove_precursor_tolerance double 1.5 CometAdapter + require_variable_mod string false true,false CometAdapter + spectrum_batch_size int 20000 0: CometAdapter - allowed_missed_cleavages 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 - fragment_bin_offset double 0.25 CometAdapter - fragment_bin_tolerance double 1.0005 CometAdapter - isotope_error string off off,-1/0/1/2/3,-8/-4/0/4/8 CometAdapter - mass_offsets double 0 CometAdapter - max_fragment_charge int 3 CometAdapter - max_precursor_charge string 0+ CometAdapter - minimum_intensity int 0 CometAdapter - override_charge string keep any known keep any known,ignore known,ignore outside range,keep known search unknown CometAdapter - remove_precursor_peak string no no,yes,all CometAdapter - remove_precursor_tolerance int 1 CometAdapter - spectrum_batch_size int 1000 DecoyDatabase + Decoy:keepPeptideCTerm string true true,false DecoyDatabase + Decoy:keepPeptideNTerm string true true,false DecoyDatabase + Decoy:non_shuffle_pattern string DecoyDatabase + enzyme string Trypsin Trypsin,Arg-C,Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formic_acid,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 + shuffle_max_attempts int 30 DecoyDatabase + shuffle_sequence_identity_threshold 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,Formic_acid,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-N_ambic,Chymotrypsin Digestor - enzyme string Trypsin glutamyl endopeptidase,2-iodobenzoate,no cleavage,unspecific cleavage,Arg-C,Lys-C,Trypsin,Asp-N/B,Asp-N,Asp-N_ambic,V8-DE,CNBr,leukocyte elastase,proline endopeptidase,Lys-N,Lys-C/P,Arg-C/P,Chymotrypsin,Formic_acid,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,Formic_acid,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-N_ambic,unspecific cleavage,Chymotrypsin,Asp-N/B,Chymotrypsin/P DigestorMotif - enzyme string Trypsin Asp-N_ambic,Trypsin,Asp-N/B,Chymotrypsin/P,Chymotrypsin,Trypsin/P,V8-DE,V8-E,PepsinA,TrypChymo,glutamyl endopeptidase,Lys-C/P,Formic_acid,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:add_decoy_proteins string false true,false FeatureFinderIdentification + debug int 0 0: FeatureFinderIdentification - debug int 0 FeatureFinderMetabo + algorithm:ffm:remove_single_traces string false false,true FeatureFinderMultiplex + algorithm:averagine_similarity_scaling double 0.95 0:1 FeatureFinderMultiplex + algorithm:rt_band double 0 0: FeatureFinderMultiplex + out output-file .featureXML FeatureFinderMultiplex + out_multiplets output-file .consensusXML FeatureFinderMultiplex - algorithm:averagine_similarity_scaling double 0.75 0:1 FeatureFinderMultiplex - out output-file .consensusXML FeatureFinderMultiplex - out_features output-file .featureXML FeatureFinderMultiplex - out_mzq output-file .mzq FeatureLinkerUnlabeled + algorithm:ignore_adduct string true true,false FeatureLinkerUnlabeledKD + algorithm:ignore_adduct string true true,false FeatureLinkerUnlabeledQT + algorithm:ignore_adduct string true true,false FileConverter + convert_to_chromatograms string false true,false FileFilter + id:sequence_comparison_method string substring substring,exact FileFilter + peak_options:indexed_file string true true,false FileFilter + peak_options:numpress:float_da string none none,linear,pic,slof FileFilter + peak_options:numpress:lossy_mass_accuracy 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:similarity_threshold double -1 -1:1 FileFilter + spectra:blackorwhitelist:use_ppm_tolerance string false FileFilter - peak_options:indexed_file string false true,false FileFilter - peak_options:numpress:intensity_error double 0.0001 FileFilter - peak_options:numpress:masstime_error double 0.0001 IDConflictResolver + resolve_between_features 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 - out_type string idXML,mzid,pepXML,FASTA IDFilter + in_silico_digestion:enzyme string Trypsin Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formic_acid,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 + in_silico_digestion:fasta input-file *.fasta IDFilter + in_silico_digestion:methionine_cleavage string false true,false IDFilter + in_silico_digestion:missed_cleavages int -1 -1: IDFilter + in_silico_digestion:specificity string full full,semi,none IDFilter + missed_cleavages:enzyme string Trypsin Asp-N/B,Asp-N,Asp-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formic_acid,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 + missed_cleavages:number_of_missed_cleavages string : IDFilter - digest:enzyme string Trypsin Lys-C,V8-E,Trypsin/P,no cleavage,V8-DE,CNBr,Lys-C/P,Formic_acid,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-N_ambic,glutamyl endopeptidase,Lys-N IDFilter - digest:fasta input-file *.fasta IDFilter - digest:methionine_cleavage string false true,false IDFilter - digest:missed_cleavages int -1 -1: IDFilter - digest:specificity string full full,semi,none IsobaricAnalyzer - id_pool string MRMMapper + algorithm:error_on_unmapped string false true,false MRMMapper + algorithm:map_multiple_assays string false true,false MRMMapper + algorithm:precursor_tolerance double 0.1 MRMMapper + algorithm:product_tolerance double 0.1 MRMMapper - allow_multiple_mappings string false true,false MRMMapper - no-strict string false true,false MRMMapper - precursor_tolerance double 0.1 MRMMapper - product_tolerance double 0.1 MRMTransitionGroupPicker + algorithm:PeakIntegrator:baseline_type string base_to_base base_to_base,vertical_division,vertical_division_min,vertical_division_max MRMTransitionGroupPicker + algorithm:PeakIntegrator:fit_EMG string false false,true MRMTransitionGroupPicker + algorithm:PeakIntegrator:integration_type string intensity_sum intensity_sum,simpson,trapezoid MRMTransitionGroupPicker + algorithm:background_subtraction string none none,original,exact MRMTransitionGroupPicker + algorithm:boundary_selection_method string largest largest,widest MRMTransitionGroupPicker + algorithm:compute_peak_shape_metrics string false true,false MRMTransitionGroupPicker + algorithm:compute_total_mi string false true,false MRMTransitionGroupPicker + algorithm:peak_integration string original original,smoothed MRMTransitionGroupPicker + algorithm:use_consensus string true true,false MRMTransitionGroupPicker - algorithm:background_subtraction string none none,smoothed,original MSGFPlusAdapter + add_features string true true,false MSGFPlusAdapter + protocol string automatic automatic,phospho,iTRAQ,iTRAQ_phospho,TMT,none MSGFPlusAdapter - add_features string false true,false MSGFPlusAdapter - protocol string none none,phospho,iTRAQ,iTRAQ_phospho,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,Formic_acid,Lys-C,unspecific cleavage,Chymotrypsin,Asp-N_ambic,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-N_ambic,CNBr,Alpha-lytic protease,glutamyl endopeptidase,Lys-N,Lys-C/P,Chymotrypsin,Formic_acid,Chymotrypsin/P,Arg-C/P,leukocyte elastase,proline endopeptidase,TrypChymo,Trypsin/P,V8-DE,V8-E,unspecific cleavage MapAlignerIdentification + model:linear:x_datum_max double 1e+15 MapAlignerIdentification + model:linear:x_datum_min double 1e-15 MapAlignerIdentification + model:linear:x_weight string 1/x,1/x2,ln(x), MapAlignerIdentification + model:linear:y_datum_max double 1e+15 MapAlignerIdentification + model:linear:y_datum_min double 1e-15 MapAlignerIdentification + model:linear:y_weight 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:x_datum_max double 1e+15 MapAlignerSpectrum + model:linear:x_datum_min double 1e-15 MapAlignerSpectrum + model:linear:x_weight string 1/x,1/x2,ln(x), MapAlignerSpectrum + model:linear:y_datum_max double 1e+15 MapAlignerSpectrum + model:linear:y_datum_min double 1e-15 MapAlignerSpectrum + model:linear:y_weight string 1/y,1/y2,ln(y), MapRTTransformer + model:linear:x_datum_max double 1e+15 MapRTTransformer + model:linear:x_datum_min double 1e-15 MapRTTransformer + model:linear:x_weight string 1/x,1/x2,ln(x), MapRTTransformer + model:linear:y_datum_max double 1e+15 MapRTTransformer + model:linear:y_datum_min double 1e-15 MapRTTransformer + model:linear:y_weight string 1/y,1/y2,ln(y), MetaboliteAdductDecharger + algorithm:MetaboliteFeatureDeconvolution:max_minority_bound int 3 0: MetaboliteAdductDecharger + algorithm:MetaboliteFeatureDeconvolution:max_neutrals int 1 MetaboliteAdductDecharger + algorithm:MetaboliteFeatureDeconvolution:use_minority_bound string true MetaboliteAdductDecharger - algorithm:MetaboliteFeatureDeconvolution:max_minority_bound int 2 0: MetaboliteAdductDecharger - algorithm:MetaboliteFeatureDeconvolution:max_neutrals 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-N_ambic,Chymotrypsin,CNBr,Formic_acid,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,Formic_acid,unspecific cleavage,Asp-N_ambic OpenPepXL + algorithm:deisotope string auto true,false,auto OpenPepXL + ions:a_ions string false true,false OpenPepXL + ions:b_ions string true true,false OpenPepXL + ions:c_ions string false true,false OpenPepXL + ions:neutral_losses string true true,false OpenPepXL + ions:x_ions string false true,false OpenPepXL + ions:y_ions string true true,false OpenPepXL + ions:z_ions string false true,false OpenPepXL + out_xquest_specxml output-file .xml,.spec.xml OpenPepXL + out_xquestxml output-file .xml,.xquest.xml OpenPepXL + peptide:enzyme string Trypsin Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,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 - out_xquest_specxml output-file *.xml OpenPepXL - out_xquestxml 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,Formic_acid,leukocyte elastase,Lys-C/P,Chymotrypsin/P,CNBr,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Arg-C/P,Trypsin,Arg-C OpenPepXLLF + algorithm:deisotope string auto true,false,auto OpenPepXLLF + algorithm:number_of_scored_candidates int 10000 OpenPepXLLF + algorithm:pre_scoring string false true,false OpenPepXLLF + ions:a_ions string false true,false OpenPepXLLF + ions:b_ions string true true,false OpenPepXLLF + ions:c_ions string false true,false OpenPepXLLF + ions:neutral_losses string true true,false OpenPepXLLF + ions:x_ions string false true,false OpenPepXLLF + ions:y_ions string true true,false OpenPepXLLF + ions:z_ions string false true,false OpenPepXLLF + out_xquest_specxml output-file .xml,.spec.xml OpenPepXLLF + out_xquestxml output-file .xml,.xquest.xml OpenPepXLLF + peptide:enzyme string Trypsin Chymotrypsin/P,Asp-N_ambic,Chymotrypsin,CNBr,Formic_acid,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 - out_xquest_specxml output-file .xml OpenPepXLLF - out_xquestxml 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-N_ambic,Chymotrypsin/P,CNBr,Formic_acid,Chymotrypsin,Arg-C,Trypsin,2-iodobenzoate,no cleavage,unspecific cleavage,leukocyte elastase,Alpha-lytic protease,glutamyl endopeptidase,V8-E,proline endopeptidase OpenSwathAnalyzer + algorithm:DIAScoring:dia_extraction_unit string Th Th,ppm OpenSwathAnalyzer + algorithm:Scores:use_mi_score string false true,false OpenSwathAnalyzer + algorithm:Scores:use_ms1_mi string false true,false OpenSwathAnalyzer + algorithm:Scores:use_total_mi_score string false true,false OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type string base_to_base base_to_base,vertical_division,vertical_division_min,vertical_division_max OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakIntegrator:fit_EMG string false false,true OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakIntegrator:integration_type string intensity_sum intensity_sum,simpson,trapezoid OpenSwathAnalyzer + algorithm:TransitionGroupPicker:background_subtraction string none none,original,exact OpenSwathAnalyzer + algorithm:TransitionGroupPicker:boundary_selection_method string largest largest,widest OpenSwathAnalyzer + algorithm:TransitionGroupPicker:compute_peak_shape_metrics string false true,false OpenSwathAnalyzer + algorithm:TransitionGroupPicker:compute_total_mi string false true,false OpenSwathAnalyzer + algorithm:TransitionGroupPicker:peak_integration string original original,smoothed OpenSwathAnalyzer + algorithm:TransitionGroupPicker:use_consensus string true true,false OpenSwathAnalyzer + algorithm:scoring_model string default default,single_transition OpenSwathAnalyzer - algorithm:TransitionGroupPicker:background_subtraction string none none,smoothed,original OpenSwathAssayGenerator + disable_identification_ms2_precursors string false true,false OpenSwathAssayGenerator + disable_identification_specific_losses string false true,false OpenSwathAssayGenerator + enable_ipf string false true,false OpenSwathAssayGenerator + enable_swath_specifity string false true,false OpenSwathAssayGenerator + in input-file .tsv,.mrm,.pqp,.TraML OpenSwathAssayGenerator + in_type string tsv,mrm,pqp,TraML OpenSwathAssayGenerator + max_num_alternative_localizations int 10000 OpenSwathAssayGenerator + out output-file .tsv,.pqp,.TraML OpenSwathAssayGenerator + out_type string tsv,pqp,TraML OpenSwathAssayGenerator + unimod_file input-file .xml OpenSwathAssayGenerator - enable_identification_ms2_precursors string false true,false OpenSwathAssayGenerator - enable_identification_specific_losses string false true,false OpenSwathAssayGenerator - enable_ms1_uis_scoring string false true,false OpenSwathAssayGenerator - enable_ms2_uis_scoring string false true,false OpenSwathAssayGenerator - enable_reannotation string false true,false OpenSwathAssayGenerator - in input-file .traML OpenSwathAssayGenerator - max_num_alternative_localizations int 20 OpenSwathAssayGenerator - out output-file .traML OpenSwathChromatogramExtractor + ion_mobility_window double -1 OpenSwathDecoyGenerator + aim_decoy_fraction double 1 OpenSwathDecoyGenerator + in input-file .tsv,.mrm,.pqp,.TraML OpenSwathDecoyGenerator + in_type string tsv,mrm,pqp,TraML OpenSwathDecoyGenerator + method string shuffle shuffle,pseudo-reverse,reverse,shift OpenSwathDecoyGenerator + min_decoy_fraction double 0.8 OpenSwathDecoyGenerator + out output-file .tsv,.pqp,.TraML OpenSwathDecoyGenerator + out_type string tsv,pqp,TraML OpenSwathDecoyGenerator + product_mz_threshold double 0.025 OpenSwathDecoyGenerator + separate string false true,false OpenSwathDecoyGenerator + shift_precursor_mz_shift double 0 OpenSwathDecoyGenerator + shift_product_mz_shift double 20 OpenSwathDecoyGenerator + shuffle_max_attempts int 30 OpenSwathDecoyGenerator + shuffle_sequence_identity_threshold double 0.5 OpenSwathDecoyGenerator + switchKR string true true,false OpenSwathDecoyGenerator - append string false true,false OpenSwathDecoyGenerator - exclude_similar string false true,false OpenSwathDecoyGenerator - identity_threshold double 0.7 OpenSwathDecoyGenerator - in input-file *.traML OpenSwathDecoyGenerator - max_attempts int 10 OpenSwathDecoyGenerator - method string shuffle OpenSwathDecoyGenerator - mz_shift double 20 OpenSwathDecoyGenerator - mz_threshold double 0.05 OpenSwathDecoyGenerator - out output-file .traML OpenSwathDecoyGenerator - precursor_mass_shift double 0 OpenSwathDecoyGenerator - remove_CNterm_mods string false true,false OpenSwathDecoyGenerator - remove_unannotated string false true,false OpenSwathDecoyGenerator - similarity_threshold double -1 OpenSwathMzMLFileCacher + full_meta string true true,false OpenSwathMzMLFileCacher + lossy_compression string true true,false OpenSwathMzMLFileCacher + lossy_mass_accuracy double -1 OpenSwathMzMLFileCacher + lowmem_batchsize int 500 0: OpenSwathMzMLFileCacher + process_lowmemory string false true,false OpenSwathRTNormalizer + algorithm:DIAScoring:dia_extraction_unit string Th Th,ppm OpenSwathRTNormalizer + algorithm:Scores:use_mi_score string false true,false OpenSwathRTNormalizer + algorithm:Scores:use_ms1_mi string false true,false OpenSwathRTNormalizer + algorithm:Scores:use_total_mi_score string false true,false OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakIntegrator:baseline_type string base_to_base base_to_base,vertical_division,vertical_division_min,vertical_division_max OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakIntegrator:fit_EMG string false false,true OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakIntegrator:integration_type string intensity_sum intensity_sum,simpson,trapezoid OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:background_subtraction string none none,original,exact OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:boundary_selection_method string largest largest,widest OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:compute_peak_shape_metrics string false true,false OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:compute_total_mi string false true,false OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:peak_integration string original original,smoothed OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:use_consensus string true true,false OpenSwathRTNormalizer + algorithm:scoring_model string default default,single_transition OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:background_subtraction string none none,smoothed,original OpenSwathWorkflow + Debugging:irt_mzml string OpenSwathWorkflow + Debugging:irt_trafo string OpenSwathWorkflow + Scoring:DIAScoring:dia_extraction_unit string Th Th,ppm OpenSwathWorkflow + Scoring:Scores:use_mi_score string false true,false OpenSwathWorkflow + Scoring:Scores:use_ms1_mi string false true,false OpenSwathWorkflow + Scoring:Scores:use_total_mi_score string false true,false OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakIntegrator:baseline_type string base_to_base base_to_base,vertical_division,vertical_division_min,vertical_division_max OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakIntegrator:fit_EMG string false false,true OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakIntegrator:integration_type string intensity_sum intensity_sum,simpson,trapezoid OpenSwathWorkflow + Scoring:TransitionGroupPicker:background_subtraction string none none,original,exact OpenSwathWorkflow + Scoring:TransitionGroupPicker:boundary_selection_method string largest largest,widest OpenSwathWorkflow + Scoring:TransitionGroupPicker:compute_peak_shape_metrics string false true,false OpenSwathWorkflow + Scoring:TransitionGroupPicker:compute_total_mi string false true,false OpenSwathWorkflow + Scoring:TransitionGroupPicker:peak_integration string original original,smoothed OpenSwathWorkflow + Scoring:TransitionGroupPicker:use_consensus string true true,false OpenSwathWorkflow + Scoring:scoring_model string default default,single_transition OpenSwathWorkflow + Scoring:uis_threshold_sn int 0 OpenSwathWorkflow + in input-file .mzML,.mzXML,.sqMass OpenSwathWorkflow + ion_mobility_window double -1 OpenSwathWorkflow - Scoring:TransitionGroupPicker:background_subtraction string none none,smoothed,original OpenSwathWorkflow - Scoring:uis_threshold_sn int -1 OpenSwathWorkflow - in input-file .mzML,.mzXML PeptideIndexer + aaa_max int 3 0:10 PeptideIndexer + decoy_string string PeptideIndexer + enzyme:name string Trypsin Chymotrypsin/P,CNBr,Formic_acid,Arg-C/P,Asp-N/B,Asp-N_ambic,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 + mismatches_max int 0 0:10 PeptideIndexer + missing_decoy_action string error error,warn,silent PeptideIndexer - aaa_max int 4 0: PeptideIndexer - decoy_string 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-N_ambic,Chymotrypsin/P,Formic_acid,PepsinA,V8-E,proline endopeptidase,Asp-N,Lys-C,Chymotrypsin,Trypsin/P,Lys-C/P,no cleavage,unspecific cleavage,glutamyl endopeptidase,2-iodobenzoate PeptideIndexer - filter_aaa_proteins string false true,false PeptideIndexer - full_tolerant_search string false true,false PeptideIndexer - mismatches_max int 0 0: PeptideIndexer - missing_decoy_action string error error,warn PercolatorAdapter + in_osw input-file .OSW PercolatorAdapter + ipf_max_peakgroup_pep double 0.7 PercolatorAdapter + ipf_max_transition_isotope_overlap double 0.5 PercolatorAdapter + ipf_min_transition_sn double 0 PercolatorAdapter + osw_level string ms2 PercolatorAdapter + out output-file .mzid,.idXML,.osw PercolatorAdapter + out_pin output-file *.tab PercolatorAdapter + out_type string mzid,idXML,osw PercolatorAdapter + score_type string q-value q-value,pep,svm PercolatorAdapter + train-best-positive string false true,false PercolatorAdapter - mzid_out output-file *.mzid PercolatorAdapter - out output-file *.idXML PhosphoScoring + fragment_mass_tolerance double 0.05 0: PhosphoScoring + max_num_perm int 16384 0: PhosphoScoring + max_peptide_length int 40 0: PhosphoScoring + out output-file PhosphoScoring + unambiguous_score int 1000 PhosphoScoring - fragment_mass_tolerance double 0.05 PhosphoScoring - max_num_perm int 16384 1: PhosphoScoring - max_peptide_length int 40 1: PhosphoScoring - out output-file *.idXML RNPxlSearch + RNPxl:can_cross_link 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,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,Alpha-lytic protease,leukocyte elastase,proline endopeptidase,Asp-N_ambic,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:max_size 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-N_ambic,Formic_acid,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-N_ambic,Chymotrypsin/P,Chymotrypsin,CNBr,Formic_acid,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-N_ambic,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,Formic_acid,CNBr,Arg-C/P,PepsinA,Trypsin/P SiriusAdapter + compound_timeout int 10 SiriusAdapter + elements string CHNOP[5]S[8]Cl[1] SiriusAdapter + feature_only string false true,false SiriusAdapter + filter_by_num_masstraces int 1 1: SiriusAdapter + in_featureinfo input-file *.featurexml SiriusAdapter + ion_tree string false true,false SiriusAdapter + isotope_pattern_iterations int 3 SiriusAdapter + most_intense_ms2 string false true,false SiriusAdapter + no_masstrace_info_isotope_pattern string false true,false SiriusAdapter + out_fingerid output-file *.mzTab SiriusAdapter + out_sirius output-file *.mzTab SiriusAdapter + precursor_mz_tolerance double 0.005 SiriusAdapter + precursor_mz_tolerance_unit string Da Da,ppm SiriusAdapter + precursor_rt_tolerance double 5 SiriusAdapter + top_n_hits int 10 SiriusAdapter + tree_timeout int 0 SiriusAdapter - elements string CHNOP[5]S SiriusAdapter - iontree string false true,false SiriusAdapter - number int 10 SiriusAdapter - out_fingerid output-file .tsv SiriusAdapter - out_sirius output-file .tsv SpecLibSearcher + fragment:mass_tolerance double 10 SpecLibSearcher + modifications:fixed string ... SpecLibSearcher + modifications:variable string ... SpecLibSearcher + modifications:variable_max_per_peptide int 2 SpecLibSearcher + precursor:isotopes int SpecLibSearcher + precursor:mass_tolerance double 10 SpecLibSearcher + precursor:mass_tolerance_unit string ppm ppm,Da SpecLibSearcher + precursor:max_charge int 5 SpecLibSearcher + precursor:min_charge int 2 SpecLibSearcher + report:top_hits int 10 SpecLibSearcher - fixed_modifications string ... SpecLibSearcher - precursor_mass_tolerance double 3 SpecLibSearcher - round_precursor_to_integer int 10 SpecLibSearcher - top_hits int 10 SpecLibSearcher - variable_modifications string ... XFDR + decoy_string string DECOY_ XFDR + in input-file .xml,.idXML,.mzid,.xquest.xml XFDR + in_type string xml,idXML,mzid,xquest.xml XFDR + out_xquest output-file .xquest.xml XFDR - in input-file .xml,.idXML,.mzid XFDR - in_type string xml,idXML,mzid XTandemAdapter + enzyme string Trypsin Trypsin,Arg-C/P,Asp-N_ambic,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,Formic_acid,Trypsin/P,V8-E,leukocyte elastase,Alpha-lytic protease,glutamyl endopeptidase XTandemAdapter - enzyme string Trypsin glutamyl endopeptidase,Formic_acid,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

Release2.3.0

6 years ago

Dear OpenMS-Users,

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

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

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

Notable changes since version 2.2 are:

TOPPView:

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

New tools:

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

Deprecated and removed tools:

  • None

Renamed tool:

  • LowMemPeakPickerHiRes_RandomAccess was renamed to LowMemPeakPickerHiResRandomAccess

Major changes in functionality:

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

Library:

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

File formats:

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

Scripts:

  • None

Databases:

  • None

Third-party software:

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

Best regards, The OpenMS-Developers

Release2.2.0

6 years ago

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_"

Release2.1.0

7 years ago

---- 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