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@openms-jenkins-bot openms-jenkins-bot released this Oct 2, 2020 · 160 commits to develop since this release

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

Assets 6

@openms-jenkins-bot openms-jenkins-bot released this Feb 24, 2020 · 3 commits to release/2.5.0 since this release

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

Assets 6

@openms-jenkins-bot openms-jenkins-bot released this Oct 30, 2018 · 4979 commits to develop since this release

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

Assets 7

@openms-jenkins-bot openms-jenkins-bot released this Jan 3, 2018 · 8757 commits to develop since this release

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

Assets 6

@jpfeuffer jpfeuffer released this Nov 13, 2017 · 10113 commits to master since this release

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_"
Assets 5

@timosachsenberg timosachsenberg released this Nov 21, 2016 · 11868 commits to master since this release


---- OpenMS 2.1 ----

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

Notable changes since version 2.0.1 are:

New tools:

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

Deprecated and removed tools:

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

Major changes in functionality:

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

File formats:

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

Databases:

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

Third-party software:

  • update for X!Tandem VENGEANCE (2015.12.15)
  • update for MS-GF+ Release v2016.10.14, released October 14, 2016
  • update for pwiz 3.0.9935
Assets 5

@timosachsenberg timosachsenberg released this Apr 22, 2016 · 12715 commits to master since this release


---- OpenMS 2.0.1 ----

OpenMS 2.0.1 is a source only release of the core libraries and tools.
This means that although we release the automatically generated installers,
we denote that these are not fully supported/tested. The same holds for
the use of the provided tools in the third-party workflow systems
for which we established integration (e.g. KNIME).
With over 300 merged pull requests, it introduces a considerable number of new features,
bug fixes and speed improvements.

Notable changes are:

File formats:

  • Improved mzIdentML support (experimental)
  • Improved mzTab support (experimental)
  • Comet pepXML file reading support (experimental)
  • Search parameter units are retained through id files
  • Faster base64 decoding in XML files

Databases:

  • HMDB has been updated to version 3.6

TOPPView:

  • Added slight margin around data range (%2) for improved visualization
  • Added FeatureFinderMultiplex to the tools accessible from TOPPView
  • Some fixes to the scrollbar behaviour

Added tools:

  • IDScoreSwitcher -- Switches between different scores of peptide or protein hits in identification data (UTIL)
  • LuciphorAdapter -- Modification site localisation using LuciPHOr2 (TOPP)
  • MetaProSIP -- Performs proteinSIP on peptide features for elemental flux analysis (UTIL)
  • MzMLSplitter -- Splits an mzML file into multiple parts (UTIL)
  • OpenSwathAssayGenerator -- Generates assays according to different models for a specific TraML (TOPP)

Removed tools:

  • RTAnnotator -- Annotates identification files that are missing the RT field (UTIL)

Tools with major changes:

  • OpenSWATH now outputs peak apices
    • Improved iRT correction
    • Assay generator
    • UIS scoring
  • Deuterium labeling in MetaProSIP (experimental)
  • XTandemAdapter allows for external config file
  • TextExporter can optionally export PeptideIdentification and PeptideHits meta-values
  • FeatureLinkerUnlabeledQT speed improvements
  • FileMerger allows to concatenate files in RT
  • MzTabExporter supports protein IDs
  • PeakPickerWavelet speedup
  • HiResPrecursorMassCorrector supports correction of precursors to detected features
  • FeatureFinderMultiplex speed improvements

Library:

  • Support for user definable enzymes available in EnzymesDB.xml
  • PeptideIndexing is now available as internal algorithm
  • EnzymaticDigestion allows for minimum / maximum length constraints
  • HyperScore and PScore implementations
  • Fits allow extrapolation of data values
  • QT clustering is now order independent
  • Additional convinience functions to access the nearest spectrum peak in a mass tolerance window
  • User defined averagine compositions
  • A fast linear lowess implementation has been added
  • MetaInfoInterface has been added to FeatureMap to store additional meta-values
  • Calculation of Median Absolute Deviation

General:

  • OpenMS writes indexed mzML by default
  • OpenMS home directory can be configured through OPENMS_HOME_DIR environment variable
  • Updated GenericWrapper definitions for MS-GF+ and Mascot

Third party software:

Assets 6
Apr 9, 2015
Merge pull request #1340 from OpenMS/master_mac10.8_10.9_legacy_support
Master mac10.8 10.9 legacy support
Nov 13, 2013
[FIX-#633] ConsoleUtils::breakStrings_ checks for ' ' before calling …
…String::suffix()

 * updated changelog accordingly



git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11.1@11976 6adb6e08-d915-0410-941f-83917bcadc18
Aug 22, 2013
[DOC] added #603 to list of fixed bugs (addendum to r11699)
git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11700 6adb6e08-d915-0410-941f-83917bcadc18
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