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CHANGELOG
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Glossary:
OpenMS - Name of the project and our C++ library
TOPP - "The OpenMS Proteomics Pipeline", collection of chainable tools for flexible HPLC/MS workflows
TOPPAS - "The OpenMS Proteomics Pipeline Assistant", graphical tool to interactively build and run HPLC/MS workflows
TOPPView - Versatile viewer for HPLC/MS data
INI file - parameter configuration file, holding custom parameter settings for TOPP tools
INIFileEditor - graphical parameter editor for INI files
Parameters - list of algorithm or TOPP tool parameters that changed in this release
------------------------------------------------------------------------------------------
---- OpenMS 2.2 ----
------------------------------------------------------------------------------------------
OpenMS 2.2 introduces a considerable number of new features and bug fixes.
Notable changes since version 2.1 are:
New tools:
- RNPxlSearch -- Annotate RNA to peptide crosslinks in MS/MS spectra (UTIL)
- SpectraSTSearchAdapter -- Interface to the SEARCH Mode of the SpectraST executable (UTIL)
- FeatureLinkerUnlabeledKD -- Feature linking using a KD tree (TOPP)
- DatabaseFilter -- Filters a protein database (FASTA format) based on identified proteins (UTIL)
- TargetedFileConverter -- Conversion of multiple targeted file formats (CSV, TraML etc)
Deprecated and removed tools:
- ITRAQAnalyzer -- superseded by IsobaricAanalyzer
- TMTAnalyzer -- superseded by IsobaricAanalyzer
- ConvertTSVToTraML - superseded by TargetedFileConverter
- ConvertTraMLToTSV - superseded by TargetedFileConverter
- MapAlignmentEvaluation -- removed as deprecated
Major changes in functionality:
- OpenSWATH analysis
- Support for metabolomics workflows
- Support for scanning SWATH (SONAR)
- Support for SQL-based file formats
- XTandemAdapter
- Simplified usage
- Improved support for PTMs and newer X! Tandem versions ("Vengeance", "Alanine")
- IsobaricAnalyzer
- Support for TMT10plex
- Support for quantification in MS3 data
- IDMapper
- Allows to map unidentified tandem mass spectra to features
- FeatureFinderIdentification
- Advanced multi-sample support using machine learning
- FileFilter
- Allows users to enable zlib and lossy compression (see "-lossy_compression")
- Allows users to set desired mass accuracy
- IDFilter
- Added option to filter for valid digestion products
- FalseDiscoveryRate
- Allow filtering by q-value in the tool (no need for IDFilter with "score:pep" option)
Library:
- Averagine approximation for fragment isotope distributions
- Precursor mass correction supports correction to highest intensity peak in tolerance window
- Functionality for resampling and adding of spectra
- Protein-protein cross-link spectrum generator
- Terminal modifications are now separated by "." in text output
- SQLite support in OpenSWATH
- TheoreticalSpectrumGenerator speed-up and removal of RichPeak code
- Removal of template parameters from MSExperiment (reduced compile time and binary size)
- Allow estimation of isotope distributions with predefined numbers of sulfur atoms
- Improved handling of bracket notation for modified residues (e.g. N[2457.877]VSVK)
- Improved handling of terminal and residue specificity of modifications
- Improved annotation of peptide identifications with spectrum references
- Improved handling of unknown amino acids ("X") in sequences
File formats:
- Improved mzML support for SONAR data and mzML with drift time (experimental)
- Improved support for cross-link data and unknown modifications in mzIdentML
- mzXML writer able to write MaxQuant-compatible files
- mzML files now routinely support substantial compression (up to 5x compression, see #2449, #2458)
- Support for Percolator result files based on X! Tandem searches
Scripts:
- New R script for visualizing RT transformations (trafoXML)
Databases:
- By default, decoy sequences are now denoted by the prefix "DECOY_"
Third-party software:
Changed tool parameters:
Tool name Added/removed Parameter name Type Default value Restrictions Supported formats
DecoyDatabase + only_decoy string false true,false
DecoyDatabase - append string true true,false
Digestor + enzyme string Trypsin CNBr,proline endopeptidase,TrypChymo,no cleavage,V8-E,leukocyte elastase,Trypsin/P,Lys-C,Formic_acid,glutamyl endopeptidase,Lys-C/P,2-iodobenzoate,Trypsin,V8-DE,Chymotrypsin,PepsinA,Asp-N_ambic,unspecific cleavage,Asp-N,Arg-C
Digestor - enzyme string Trypsin Trypsin,V8-E,leukocyte elastase,Lys-C,Asp-N_ambic,no cleavage,unspecific cleavage,Chymotrypsin,Arg-C,V8-DE,Lys-C/P,2-iodobenzoate,proline endopeptidase,glutamyl endopeptidase,CNBr,TrypChymo,Trypsin/P,Asp-N,PepsinA,Formic_acid
DigestorMotif + enzyme string Trypsin Lys-C,leukocyte elastase,Formic_acid,CNBr,2-iodobenzoate,V8-DE,Trypsin,Lys-C/P,PepsinA,unspecific cleavage,TrypChymo,glutamyl endopeptidase,Arg-C,Asp-N,Chymotrypsin,V8-E,no cleavage,proline endopeptidase,Trypsin/P,Asp-N_ambic
DigestorMotif - enzyme string Trypsin PepsinA,glutamyl endopeptidase,Lys-C,Chymotrypsin,unspecific cleavage,CNBr,Lys-C/P,V8-DE,leukocyte elastase,no cleavage,Asp-N_ambic,Trypsin,proline endopeptidase,2-iodobenzoate,TrypChymo,Trypsin/P,V8-E,Asp-N,Arg-C,Formic_acid
FalseDiscoveryRate + FDR:PSM double 1 0:1
FalseDiscoveryRate + FDR:protein double 1 0:1
FalseDiscoveryRate + PSM string true true,false
FalseDiscoveryRate + protein string true true,false
FalseDiscoveryRate - in_decoy input-file *.idXML
FalseDiscoveryRate - in_target input-file *.idXML
FalseDiscoveryRate - peptides_only string false true,false
FalseDiscoveryRate - proteins_only string false true,false
FeatureFinderIdentification + candidates_in input-file *.featureXML
FeatureFinderIdentification + candidates_out output-file *.featureXML
FeatureFinderIdentification + detect:mapping_tolerance double 0 0:
FeatureFinderIdentification + detect:min_peak_width double 0.2 0:
FeatureFinderIdentification + detect:peak_width double 60 0:
FeatureFinderIdentification + detect:signal_to_noise double 0.8 0.1:
FeatureFinderIdentification + extract:isotope_pmin double 0 0:1
FeatureFinderIdentification + extract:n_isotopes int 2 2:
FeatureFinderIdentification + extract:rt_quantile double 0.95 0:1
FeatureFinderIdentification + extract:rt_window double 0 0:
FeatureFinderIdentification + id_ext input-file *.idXML
FeatureFinderIdentification + model:check:min_area double 1 0:
FeatureFinderIdentification + svm:cache_size double 100 1:
FeatureFinderIdentification + svm:epsilon double 0.001 0:
FeatureFinderIdentification + svm:kernel string RBF RBF,linear
FeatureFinderIdentification + svm:log2_C double
FeatureFinderIdentification + svm:log2_gamma double
FeatureFinderIdentification + svm:min_prob double 0 0:1
FeatureFinderIdentification + svm:no_selection string false true,false
FeatureFinderIdentification + svm:no_shrinking string false true,false
FeatureFinderIdentification + svm:predictors string peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score
FeatureFinderIdentification + svm:samples int 0 0:
FeatureFinderIdentification + svm:xval int 5 1:
FeatureFinderIdentification + svm:xval_out output-file *.csv
FeatureFinderIdentification - detect:all_features string false true,false
FeatureFinderIdentification - detect:peak_width double 30 0:
FeatureFinderIdentification - extract:isotope_pmin double 0.03 0:1
FeatureFinderIdentification - extract:reference_rt string adapt adapt,score,intensity,median,all
FeatureFinderIdentification - extract:rt_window double 60 0:
FeatureFinderIdentification - trafo_out output-file *.trafoXML
FeatureFinderMultiplex + algorithm:spectrum_type string automatic profile,centroid,automatic
FeatureLinkerUnlabeled + algorithm:distance_intensity:log_transform string disabled enabled,disabled
FeatureLinkerUnlabeledQT + algorithm:distance_intensity:log_transform string disabled enabled,disabled
FeatureLinkerUnlabeledQT + algorithm:nr_partitions int 100 1:
FeatureLinkerUnlabeledQT - algorithm:nr_partitions int 1 1:
FileConverter + force_MaxQuant_compatibility string false true,false
FileConverter + lossy_compression string false true,false
FileConverter + lossy_mass_accuracy double -1
FileConverter + write_scan_index string true true,false
FileConverter - write_mzML_index string false true,false
FileFilter + peak_options:zlib_compression string false true,false
FileInfo + in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML
FileInfo + in_type string mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid,trafoXML
FileInfo - in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid
FileInfo - in_type string mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid
HighResPrecursorMassCorrector + highest_intensity_peak:mz_tolerance double 0
IDFileConverter + no_spectra_data_override string false true,false
IDFilter + digest:enzyme string Trypsin unspecific cleavage,Arg-C,Trypsin,Formic_acid,proline endopeptidase,TrypChymo,V8-E,Asp-N_ambic,glutamyl endopeptidase,CNBr,PepsinA,2-iodobenzoate,Chymotrypsin,Lys-C/P,Asp-N,Lys-C,Trypsin/P,leukocyte elastase,no cleavage,V8-DE
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
IDMapper + spectra:in input-file *.mzML
IsobaricAnalyzer + extraction:reporter_mass_shift double 0.002 0.0001:0.5
IsobaricAnalyzer - extraction:reporter_mass_shift double 0.1 1e-08:0.5
LowMemPeakPickerHiRes + algorithm:report_FWHM_unit string relative relative,absolute
LowMemPeakPickerHiRes + algorithm:signal_to_noise double 0 0:
LowMemPeakPickerHiRes - algorithm:report_FWHM_unit string relative(ppm) absolute,relative(ppm)
LowMemPeakPickerHiRes - algorithm:signal_to_noise double 1 0:
LowMemPeakPickerHiRes_RandomAccess + algorithm:report_FWHM_unit string relative relative,absolute
LowMemPeakPickerHiRes_RandomAccess + algorithm:signal_to_noise double 0 0:
LowMemPeakPickerHiRes_RandomAccess - algorithm:report_FWHM_unit string relative(ppm) absolute,relative(ppm)
LowMemPeakPickerHiRes_RandomAccess - algorithm:signal_to_noise double 1 0:
LuciphorAdapter + java_memory int 3500
LuciphorAdapter + java_permgen int 0
MRMTransitionGroupPicker + algorithm:compute_peak_quality string false true,false
MRMTransitionGroupPicker + algorithm:recalculate_peaks string false true,false
MRMTransitionGroupPicker + algorithm:use_precursors string false true,false
MRMTransitionGroupPicker - algorithm:compute_peak_quality string false
MRMTransitionGroupPicker - algorithm:recalculate_peaks string false
MSSimulator + algorithm:MSSim:Digestion:enzyme string Trypsin unspecific cleavage,Lys-C,Formic_acid,no cleavage,Chymotrypsin,V8-DE,glutamyl endopeptidase,V8-E,Trypsin,Asp-N,CNBr,Trypsin/P,TrypChymo,PepsinA,Arg-C,leukocyte elastase,Lys-C/P,proline endopeptidase,Asp-N_ambic,2-iodobenzoate
MSSimulator + algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges string false true,false
MSSimulator - algorithm:MSSim:Digestion:enzyme string Trypsin Asp-N,leukocyte elastase,proline endopeptidase,Lys-C,Lys-C/P,V8-DE,Asp-N_ambic,Formic_acid,no cleavage,Chymotrypsin,glutamyl endopeptidase,2-iodobenzoate,CNBr,unspecific cleavage,V8-E,TrypChymo,Arg-C,Trypsin,Trypsin/P,PepsinA
MapAlignerPoseClustering + algorithm:pairfinder:distance_intensity:log_transform string disabled enabled,disabled
MetaboliteSpectralMatcher + database input-file CHEMISTRY/MetaboliteSpectralDB.mzML *.mzML
MetaboliteSpectralMatcher + out output-file *.tsv
MetaboliteSpectralMatcher - out output-file *.csv
OMSSAAdapter + enzyme string Trypsin Trypsin,TrypChymo,Lys-C/P,PepsinA,glutamyl endopeptidase,Asp-N,Lys-C,CNBr,Trypsin/P,Asp-N_ambic,Chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Formic_acid
OMSSAAdapter - enzyme string Trypsin Trypsin,Lys-C/P,CNBr,Lys-C,Chymotrypsin,unspecific cleavage,no cleavage,Trypsin/P,Formic_acid,Asp-N_ambic,TrypChymo,PepsinA,glutamyl endopeptidase,Asp-N,Arg-C
OpenSwathAnalyzer + algorithm:Scores:use_sonar_scores string false true,false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:compute_peak_quality string false true,false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:recalculate_peaks string false true,false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:use_precursors string false true,false
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:compute_peak_quality string false
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:recalculate_peaks string false
OpenSwathMzMLFileCacher + in input-file *.mzML,*.sqMass
OpenSwathMzMLFileCacher + in_type string mzML,sqMass
OpenSwathMzMLFileCacher + out output-file *.mzML,*.sqMass
OpenSwathMzMLFileCacher + out_type string mzML,sqMass
OpenSwathMzMLFileCacher - in input-file *.mzML
OpenSwathMzMLFileCacher - out output-file
OpenSwathRTNormalizer + algorithm:Scores:use_sonar_scores string false true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:compute_peak_quality string false true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:recalculate_peaks string false true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:use_precursors string false true,false
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:compute_peak_quality string false
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:recalculate_peaks string false
OpenSwathWorkflow + Library:force_invalid_mods string false true,false
OpenSwathWorkflow + Library:override_group_label_check string false true,false
OpenSwathWorkflow + Library:retentionTimeInterpretation string iRT iRT,seconds,minutes
OpenSwathWorkflow + Scoring:Scores:use_sonar_scores string false true,false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:compute_peak_quality string true true,false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:recalculate_peaks string true true,false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:use_precursors string false true,false
OpenSwathWorkflow + irt_mz_extraction_window double 0.05
OpenSwathWorkflow + out_chrom output-file *.mzML,*.sqMass
OpenSwathWorkflow + out_osw output-file *.osw
OpenSwathWorkflow + out_tsv output-file *.tsv
OpenSwathWorkflow + ppm_irtwindow string false true,false
OpenSwathWorkflow + readOptions string normal normal,cache,cacheWorkingInMemory,workingInMemory
OpenSwathWorkflow + sonar string false true,false
OpenSwathWorkflow + tr input-file *.traML,*.tsv,*.pqp
OpenSwathWorkflow + tr_type string traML,tsv,pqp
OpenSwathWorkflow - Scoring:TransitionGroupPicker:compute_peak_quality string true
OpenSwathWorkflow - Scoring:TransitionGroupPicker:recalculate_peaks string true
OpenSwathWorkflow - out_chrom output-file *.mzML
OpenSwathWorkflow - out_tsv string
OpenSwathWorkflow - readOptions string normal normal,cache,cacheWorkingInMemory
OpenSwathWorkflow - tr input-file *.traML,*.tsv,*.csv
OpenSwathWorkflow - tr_type string traML,tsv,csv
PeakPickerHiRes + algorithm:report_FWHM_unit string relative relative,absolute
PeakPickerHiRes + algorithm:signal_to_noise double 0 0:
PeakPickerHiRes - algorithm:report_FWHM_unit string relative(ppm) absolute,relative(ppm)
PeakPickerHiRes - algorithm:signal_to_noise double 1 0:
PeptideIndexer + enzyme:name string Trypsin V8-E,Chymotrypsin,glutamyl endopeptidase,Formic_acid,proline endopeptidase,Trypsin/P,CNBr,Asp-N_ambic,Asp-N,Arg-C,Lys-C/P,PepsinA,Trypsin,2-iodobenzoate,V8-DE,TrypChymo,unspecific cleavage,no cleavage,leukocyte elastase,Lys-C
PeptideIndexer - enzyme:name string Trypsin Asp-N_ambic,V8-E,Arg-C,CNBr,Formic_acid,Asp-N,no cleavage,leukocyte elastase,proline endopeptidase,Trypsin/P,Trypsin,glutamyl endopeptidase,2-iodobenzoate,V8-DE,PepsinA,Lys-C,unspecific cleavage,Chymotrypsin,Lys-C/P,TrypChymo
RTModel + out_oligo_params output-file *.paramXML
RTModel + out_oligo_trainset output-file *.txt
RTPredict + in_oligo_params input-file *.paramXML
RTPredict + in_oligo_trainset input-file *.txt
SimpleSearchEngine + enzyme string Trypsin TrypChymo,V8-E,2-iodobenzoate,proline endopeptidase,PepsinA,Lys-C,no cleavage,CNBr,leukocyte elastase,Formic_acid,Chymotrypsin,glutamyl endopeptidase,Trypsin/P,Trypsin,unspecific cleavage,Arg-C,Lys-C/P,Asp-N,V8-DE,Asp-N_ambic
SimpleSearchEngine - enzyme string Trypsin Trypsin/P,no cleavage,leukocyte elastase,PepsinA,2-iodobenzoate,Lys-C/P,Lys-C,V8-E,Formic_acid,Chymotrypsin,V8-DE,TrypChymo,unspecific cleavage,Asp-N,proline endopeptidase,Arg-C,Trypsin,CNBr,Asp-N_ambic,glutamyl endopeptidase
XTandemAdapter + default_config_file input-file *.xml
XTandemAdapter + enzyme string Trypsin Asp-N_ambic,V8-E,unspecific cleavage,V8-DE,PepsinA,Trypsin/P,Lys-C,glutamyl endopeptidase,2-iodobenzoate,Lys-C/P,Arg-C,Formic_acid,CNBr,TrypChymo,Chymotrypsin,Asp-N,Trypsin,leukocyte elastase
XTandemAdapter + max_precursor_charge int 4 0:
XTandemAdapter + no_isotope_error string false true,false
XTandemAdapter + xml_out output-file *.xml
XTandemAdapter - allow_isotope_error string yes yes,no
XTandemAdapter - cleavage_site string Trypsin Lys-C/P,CNBr,Arg-C,Chymotrypsin,PepsinA,2-iodobenzoate,Trypsin/P,TrypChymo,V8-DE,Asp-N,Asp-N_ambic,Lys-C,unspecific cleavage,Formic_acid,Trypsin,V8-E,leukocyte elastase,glutamyl endopeptidase
XTandemAdapter - default_config_file input-file CHEMISTRY/XTandem_default_input.xml *.xml
XTandemAdapter - max_precursor_charge int 4
XTandemAdapter - min_precursor_charge int 2
XTandemAdapter - refinement string false true,false
XTandemAdapter - use_noise_suppression string false true,false
------------------------------------------------------------------------------------------
---- 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 64-bit X!Tandem VENGEANCE (2015.12.15) NOTE: 32-bit version kept at SLEDGEHAMMER (2013.09.01)
- update for MS-GF+ Release v2016.10.14, released October 14, 2016
- update for pwiz 3.0.9935
Changed tool parameters:
Tool name Added/removed Parameter name Type Default value Restrictions Supported formats
AccurateMassSearch + db:mapping input-file *.tsv
AccurateMassSearch + db:struct input-file *.tsv
AccurateMassSearch - db:mapping input-file CHEMISTRY/HMDBMappingFile.tsv *.tsv
AccurateMassSearch - db:struct input-file CHEMISTRY/HMDB2StructMapping.tsv *.tsv
DecoyDatabase + append string true true,false
DecoyDatabase + decoy_string string DECOY_
DecoyDatabase + decoy_string_position string prefix prefix,suffix
DecoyDatabase + method string reverse reverse,shuffle
DecoyDatabase - append string false true,false
DecoyDatabase - decoy_string string _rev
DecoyDatabase - decoy_string_position string suffix prefix,suffix
DecoyDatabase - shuffle string false true,false
FeatureFinderMetabo + algorithm:ffm:isotope_filtering_model string metabolites (5% RMS) metabolites (2% RMS),metabolites (5% RMS),peptides,none
FeatureFinderMetabo + algorithm:ffm:mz_scoring_13C string false false,true
FeatureFinderMetabo + algorithm:ffm:report_convex_hulls string false false,true
FeatureFinderMetabo + algorithm:mtd:quant_method string area area,median
FeatureFinderMetabo - algorithm:ffm:disable_isotope_filtering string false false,true
FeatureFinderMetabo - algorithm:ffm:isotope_model string metabolites metabolites,peptides
FeatureFinderMetabo - algorithm:ffm:isotope_noisemodel string 5%RMS 5%RMS,2%RMS
FeatureFinderMetabo - algorithm:ffm:quant_method string area area,median
FeatureFinderMultiplex + labels:Leu3 double 3.01883 0:
FileConverter + in input-file *.mzData,*.mzXML,*.mzML,*.cachedMzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.ms2,*.fid,*.tsv,*.peplist,*.kroenik,*.edta
FileConverter + in_type string mzData,mzXML,mzML,cachedMzML,dta,dta2d,mgf,featureXML,consensusXML,ms2,fid,tsv,peplist,kroenik,edta
FileConverter + out output-file *.mzData,*.mzXML,*.mzML,*.cachedMzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta,*.csv
FileConverter + out_type string mzData,mzXML,mzML,cachedMzML,dta2d,mgf,featureXML,consensusXML,edta,csv
FileConverter - in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.ms2,*.fid,*.tsv,*.peplist,*.kroenik,*.edta
FileConverter - in_type string mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,ms2,fid,tsv,peplist,kroenik,edta
FileConverter - out output-file *.mzData,*.mzXML,*.mzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta,*.csv
FileConverter - out_type string mzData,mzXML,mzML,dta2d,mgf,featureXML,consensusXML,edta,csv
InternalCalibration + RANSAC:enabled string false true,false
InternalCalibration + RANSAC:iter int 70
InternalCalibration + RANSAC:pc_inliers int 30 1:99
InternalCalibration + RANSAC:threshold double 10
InternalCalibration + RT_chunking double 300
InternalCalibration + cal:id_in input-file *.idXML,*.featureXML
InternalCalibration + cal:lock_fail_out output-file *.mzML
InternalCalibration + cal:lock_in input-file *.csv
InternalCalibration + cal:lock_out output-file *.mzML
InternalCalibration + cal:lock_require_iso string false true,false
InternalCalibration + cal:lock_require_mono string false true,false
InternalCalibration + cal:model_type string linear_weighted linear,linear_weighted,quadratic,quadratic_weighted
InternalCalibration + goodness:MAD double 1
InternalCalibration + goodness:median double 4
InternalCalibration + in input-file *.mzML
InternalCalibration + ms_level int
InternalCalibration + out output-file *.mzML
InternalCalibration + ppm_match_tolerance double 25
InternalCalibration + quality_control:models output-file *.csv
InternalCalibration + quality_control:models_plot output-file *.png
InternalCalibration + quality_control:residuals output-file *.csv
InternalCalibration + quality_control:residuals_plot output-file *.png
InternalCalibration - algorithm:mz_tolerance double 1 0:
InternalCalibration - algorithm:mz_tolerance_unit string Da Da,ppm
InternalCalibration - algorithm:rt_tolerance int 10
InternalCalibration - in input-file *.mzML,*.featureXML
InternalCalibration - out output-file *.mzML,*.featureXML
InternalCalibration - ref_peaks input-file *.csv,*.idXML
InternalCalibration - trafo output-file *.trafoXML
InternalCalibration - type string spectrumwise spectrumwise,global
LowMemPeakPickerHiRes + algorithm:report_FWHM string false true,false
LowMemPeakPickerHiRes + algorithm:report_FWHM_unit string relative(ppm) absolute,relative(ppm)
LowMemPeakPickerHiRes_RandomAccess + algorithm:report_FWHM string false true,false
LowMemPeakPickerHiRes_RandomAccess + algorithm:report_FWHM_unit string relative(ppm) absolute,relative(ppm)
LuciphorAdapter + java_executable input-file java
LuciphorAdapter - selection_method string Peptide Prophet probability Peptide Prophet probability,Mascot Ion Score,-log(E-value),X!Tandem Hyperscore,Sequest Xcorr
MSGFPlusAdapter + java_executable input-file java
MapAlignerIdentification + model:lowess:delta double -1
MapAlignerIdentification + model:lowess:extrapolation_type string four-point-linear two-point-linear,four-point-linear,global-linear
MapAlignerIdentification + model:lowess:interpolation_type string cspline linear,cspline,akima
MapAlignerIdentification + model:lowess:num_iterations int 3 0:
MapAlignerIdentification + model:lowess:span double 0.666666666666667 0:1
MapAlignerIdentification - algorithm:peptide_score_threshold double 0
MapAlignerSpectrum + model:lowess:delta double -1
MapAlignerSpectrum + model:lowess:extrapolation_type string four-point-linear two-point-linear,four-point-linear,global-linear
MapAlignerSpectrum + model:lowess:interpolation_type string cspline linear,cspline,akima
MapAlignerSpectrum + model:lowess:num_iterations int 3 0:
MapAlignerSpectrum + model:lowess:span double 0.666666666666667 0:1
MapRTTransformer + model:lowess:delta double -1
MapRTTransformer + model:lowess:extrapolation_type string four-point-linear two-point-linear,four-point-linear,global-linear
MapRTTransformer + model:lowess:interpolation_type string cspline linear,cspline,akima
MapRTTransformer + model:lowess:num_iterations int 3 0:
MapRTTransformer + model:lowess:span double 0.666666666666667 0:1
MascotAdapterOnline + Mascot_server:export_params string _ignoreionsscorebelow=0&_sigthreshold=0.99&_showsubsets=1&show_same_sets=1&report=0&percolate=0&query_master=0
MascotAdapterOnline - Mascot_server:export_params string _sigthreshold=0.99&_showsubsets=1&show_same_sets=1&report=0&percolate=0&query_master=0
MassTraceExtractor + algorithm:mtd:quant_method string area area,median
MetaProSIP + labeling_element string C C,N,H,O
MetaProSIP + pattern_18O_TIC_threshold double 0.95
MetaProSIP - labeling_element string C C,N,H
OpenSwathAssayGenerator + enable_identification_ms2_precursors string false true,false
PeakPickerHiRes + algorithm:report_FWHM string false true,false
PeakPickerHiRes + algorithm:report_FWHM_unit string relative(ppm) absolute,relative(ppm)
PeptideIndexer + decoy_string string DECOY_
PeptideIndexer + decoy_string_position string prefix prefix,suffix
PeptideIndexer - decoy_string string _rev
PeptideIndexer - prefix string false true,false
------------------------------------------------------------------------------------------
---- OpenMS 2.0.1 ----
------------------------------------------------------------------------------------------
OpenMS 2.0.1 is a source only release of the core libraries and tools.
With over 300 merged pull requests, it introduces a considerable number of new features,
bug fixes and speed improvements.
Notable changes are:
File formats:
- Improved mzIdentML support (experimental)
- Improved mzTab support (experimental)
- Comet pepXML file reading support (experimental)
- Search parameter units are retained through id files
- Faster base64 decoding in XML files
Databases:
- HMDB has been updated to version 3.6
TOPPView:
- Added slight margin around data range (%2) for improved visualization
- Added FeatureFinderMultiplex to the tools accessible from TOPPView
- Some fixes to the scrollbar behaviour
Added tools:
- IDScoreSwitcher -- Switches between different scores of peptide or protein hits in identification data (UTIL)
- LuciphorAdapter -- Modification site localisation using LuciPHOr2 (TOPP)
- MetaProSIP -- Performs proteinSIP on peptide features for elemental flux analysis (UTIL)
- MzMLSplitter -- Splits an mzML file into multiple parts (UTIL)
- OpenSwathAssayGenerator -- Generates assays according to different models for a specific TraML (TOPP)
Removed tools:
- RTAnnotator -- Annotates identification files that are missing the RT field (UTIL)
Tools with major changes:
- OpenSWATH now outputs peak apices
- Improved iRT correction
- Assay generator
- UIS scoring
- Deuterium labeling in MetaProSIP (experimental)
- XTandemAdapter allows for external config file
- TextExporter can optionally export PeptideIdentification and PeptideHits meta-values
- FeatureLinkerUnlabeledQT speed improvements
- FileMerger allows to concatenate files in RT
- MzTabExporter supports protein IDs
- PeakPickerWavelet speedup
- HiResPrecursorMassCorrector supports correction of precursors to detected features
- FeatureFinderMultiplex speed improvements
Library:
- Support for user definable enzymes available in EnzymesDB.xml
- PeptideIndexing is now available as internal algorithm
- EnzymaticDigestion allows for minimum / maximum length constraints
- HyperScore and PScore implementations
- Fits allow extrapolation of data values
- QT clustering is now order independent
- Additional convinience functions to access the nearest spectrum peak in a mass tolerance window
- User defined averagine compositions
- A fast linear lowess implementation has been added
- MetaInfoInterface has been added to FeatureMap to store additional meta-values
- Calculation of Median Absolute Deviation
General:
- OpenMS writes indexed mzML by default
- OpenMS home directory can be configured through OPENMS_HOME_DIR environment variable
- Updated GenericWrapper definitions for MS-GF+ and Mascot
Third party software:
- LuciphorAdapter (experimental) PTM localization using the LuciPHOr2 algorithm (http://luciphor2.sourceforge.net/)
Changed tool parameters:
Tool name Added/removed Parameter name Type Default value Restrictions Supported formats
AccurateMassSearch + algorithm:mzTab:exportIsotopeIntensities int 0 0:
AccurateMassSearch - algorithm:report_mode string all all,top3,best
ConsensusID + algorithm string PEPMatrix PEPMatrix,PEPIons,best,worst,average,ranks
ConsensusID - algorithm:algorithm string PEPMatrix ranked,average,PEPMatrix,PEPIons,Minimum
ConsensusID + PEPIons:mass_tolerance double 0.5 0:
ConsensusID + PEPIons:min_shared int 2 1:
ConsensusID + PEPMatrix:matrix string identity identity,PAM30MS
ConsensusID + PEPMatrix:penalty int 5 1:
ConsensusID + filter:considered_hits int 0 0:
ConsensusID + filter:count_empty string false true,false
ConsensusID + filter:min_support double 0 0:1
ConsensusID - algorithm:PEPIons:MinNumberOfFragments int 2 0:
ConsensusID - algorithm:PEPIons:common double 1.1 0:1.1
ConsensusID - algorithm:PEPMatrix:common double 1.1 0:1.1
ConsensusID - algorithm:PEPMatrix:penalty int 5
ConsensusID - algorithm:considered_hits int 10 1:
ConsensusID - algorithm:number_of_runs int 0 0:
ConsensusID - min_length int 6 1:
ConsensusID - use_all_hits string false true,false
ConsensusMapNormalizer + accession_filter string
ConsensusMapNormalizer + algorithm_type string robust_regression robust_regression,median,median_shift,quantile
ConsensusMapNormalizer + description_filter string
ConsensusMapNormalizer - algorithm_type string robust_regression robust_regression,median,quantile
Digestor + enzyme string Trypsin V8-DE,V8-E,2-iodobenzoate,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,no cleavage,unspecific cleavage,Arg-C,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,CNBr,Formic_acid,Lys-C,Asp-N_ambic,Chymotrypsin,Asp-N,Trypsin
Digestor - enzyme string Trypsin Trypsin,none
DigestorMotif + enzyme string Trypsin Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,Formic_acid,Lys-C,Trypsin,Chymotrypsin,CNBr,leukocyte elastase,proline endopeptidase,2-iodobenzoate,glutamyl endopeptidase,no cleavage,unspecific cleavage,Arg-C,Asp-N_ambic,Asp-N
DigestorMotif - enzyme string Trypsin
FalseDiscoveryRate + algorithm:no_qvalues string false true,false
FalseDiscoveryRate + in_decoy input-file *.idXML
FalseDiscoveryRate + in_target input-file *.idXML
FalseDiscoveryRate - algorithm:decoy_string string _rev
FalseDiscoveryRate - algorithm:q_value string true true,false
FalseDiscoveryRate - fwd_in input-file *.idXML
FalseDiscoveryRate - rev_in input-file *.idXML
FeatureFinderMetabo + algorithm:ffm:enable_RT_filtering string true false,true
FeatureFinderMetabo + algorithm:ffm:quant_method string area area,median
FeatureFinderMetabo + algorithm:mtd:max_trace_length double -1
FeatureFinderMetabo - algorithm:mtd:max_trace_length double 300
FeatureFinderMultiplex + algorithm:averagine_type string peptide peptide,RNA,DNA
FeatureLinkerUnlabeledQT + algorithm:nr_partitions int 1 1:
FidoAdapter + greedy_group_resolution string false true,false
FidoAdapter - prob_param string Posterior Probability_score
FileFilter + algorithm:SignalToNoise:write_log_messages string true true,false
FileFilter + peak_options:pc_mz_list double
FileFilter + peak_options:pc_mz_range string :
FileFilter - pc_mz string :
FileMerger + raw:ms_level int 0
FileMerger + rt_concat:gap double 0
FileMerger + rt_concat:trafo_out output-file *.trafoXML
FileMerger - raw:ms_level int 2
FileMerger - raw:user_ms_level string false true,false
FuzzyDiff + matched_whitelist string
HighResPrecursorMassCorrector + feature:assign_all_matching string false true,false
HighResPrecursorMassCorrector + feature:believe_charge string false true,false
HighResPrecursorMassCorrector + feature:in input-file *.featureXML
HighResPrecursorMassCorrector + feature:keep_original string false true,false
HighResPrecursorMassCorrector + feature:max_trace int 2
HighResPrecursorMassCorrector + feature:mz_tolerance double 5
HighResPrecursorMassCorrector + feature:mz_tolerance_unit string ppm Da,ppm
HighResPrecursorMassCorrector + feature:rt_tolerance double 0
HighResPrecursorMassCorrector + nearest_peak:mz_tolerance double 0
HighResPrecursorMassCorrector + nearest_peak:mz_tolerance_unit string ppm Da,ppm
IDFileConverter + in input-file *.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.xml,*.psms,*.tsv,*.idXML,*.mzid
IDFileConverter + score_type string qvalue qvalue,PEP,score
IDFileConverter - in input-file *.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.xml,*.idXML,*.mzid
IDFileConverter - use_precursor_data string false true,false
IDFilter + blacklist:modifications string ...
IDFilter + blacklist:protein_accessions string
IDFilter + blacklist:proteins input-file *.fasta
IDFilter + charge string :
IDFilter + length string :
IDFilter + whitelist:ignore_modifications string false true,false
IDFilter + whitelist:modifications string ...
IDFilter + whitelist:peptides input-file *.idXML
IDFilter + whitelist:protein_accessions string
IDFilter - max_length int 0 0:
IDFilter - min_charge int 1 1:
IDFilter - min_length int 0 0:
IDFilter - precursor:allow_missing string false true,false
IDFilter - whitelist:by_seq_only string false true,false
IDPosteriorErrorProbability + fit_algorithm:max_nr_iterations int 1000
IDPosteriorErrorProbability - smallest_e_value double 1e-19
LowMemPeakPickerHiRes + algorithm:SignalToNoise:write_log_messages string true true,false
LowMemPeakPickerHiRes_RandomAccess + algorithm:SignalToNoise:write_log_messages string true true,false
MRMTransitionGroupPicker + algorithm:PeakPickerMRM:use_gauss string true false,true
MRMTransitionGroupPicker + algorithm:PeakPickerMRM:write_sn_log_messages string true true,false
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:use_gauss string true
MSGFPlusAdapter + legacy_conversion string false true,false
MSSimulator + algorithm:MSSim:Digestion:enzyme string Trypsin leukocyte elastase,proline endopeptidase,2-iodobenzoate,glutamyl endopeptidase,no cleavage,unspecific cleavage,Arg-C,Formic_acid,Lys-C,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,Chymotrypsin,CNBr,Asp-N,Asp-N_ambic,Trypsin
MSSimulator + algorithm:MSSim:RawTandemSignal:Precursor:min_mz_peak_distance double 2 0.0001:
MSSimulator + algorithm:MSSim:RawTandemSignal:Precursor:mz_isolation_window double 2 0:
MSSimulator - algorithm:MSSim:Digestion:enzyme string Trypsin Trypsin,none
MSSimulator - algorithm:MSSim:RawTandemSignal:Precursor:min_peak_distance double 3 0:
MSSimulator - algorithm:MSSim:RawTandemSignal:Precursor:selection_window double 2 0:
MapAlignerIdentification + model:interpolated:extrapolation_type string two-point-linear two-point-linear,four-point-linear,global-linear
MapAlignerSpectrum + model:interpolated:extrapolation_type string two-point-linear two-point-linear,four-point-linear,global-linear
MapRTTransformer + in input-file *.mzML,*.featureXML,*.consensusXML,*.idXML
MapRTTransformer + model:interpolated:extrapolation_type string two-point-linear two-point-linear,four-point-linear,global-linear
MapRTTransformer + out output-file *.mzML,*.featureXML,*.consensusXML,*.idXML
MapRTTransformer + store_original_rt string false true,false
MapRTTransformer + trafo_in input-file *.trafoXML
MapRTTransformer + trafo_out output-file *.trafoXML
MapRTTransformer - in input-file *.mzML,*.featureXML,*.consensusXML,*.idXML
MapRTTransformer - out output-file *.mzML,*.featureXML,*.consensusXML,*.idXML
MapRTTransformer - trafo_in input-file *.trafoXML
MapRTTransformer - trafo_out output-file *.trafoXML
MascotAdapterOnline + Mascot_server:skip_export string false true,false
MassTraceExtractor + algorithm:mtd:max_trace_length double -1
MassTraceExtractor - algorithm:mtd:max_trace_length double 300
MyriMatchAdapter + SpectrumListFilters string
MyriMatchAdapter + ignoreConfigErrors string false true,false
MyriMatchAdapter - max_precursor_charge int 3
MyriMatchAdapter - min_precursor_charge int 1
MzTabExporter + in input-file *.featureXML,*.consensusXML,*.idXML,*.mzid
MzTabExporter + out output-file *.tsv
MzTabExporter - in_consensus input-file *.consensusXML
MzTabExporter - in_feature input-file *.featureXML
MzTabExporter - in_id input-file *.idXML
MzTabExporter - out output-file *.csv
OMSSAAdapter + enzyme string Trypsin Trypsin,TrypChymo,Trypsin/P,Lys-C/P,PepsinA,Asp-N_ambic,Formic_acid,Arg-C,unspecific cleavage,CNBr,no cleavage,glutamyl endopeptidase,Lys-C,Chymotrypsin,Asp-N
OMSSAAdapter - e int 0
OpenSwathAnalyzer + algorithm:Scores:use_uis_scores string false true,false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss string true false,true
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages string true true,false
OpenSwathAnalyzer + algorithm:uis_threshold_peak_area int 0
OpenSwathAnalyzer + algorithm:uis_threshold_sn int -1
OpenSwathAnalyzer + model:type string linear linear,b_spline,interpolated,lowess
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss string true
OpenSwathAnalyzer - model:type string linear linear,b_spline,interpolated
OpenSwathChromatogramExtractor + model:type string linear linear,b_spline,interpolated,lowess
OpenSwathChromatogramExtractor - model:type string linear linear,b_spline,interpolated
OpenSwathDecoyGenerator + allowed_fragment_charges string 1,2,3,4
OpenSwathDecoyGenerator + allowed_fragment_types string b,y
OpenSwathDecoyGenerator + enable_detection_specific_losses string false true,false
OpenSwathDecoyGenerator + enable_detection_unspecific_losses string false true,false
OpenSwathDecoyGenerator - enable_losses string false true,false
OpenSwathDecoyGenerator - theoretical string false true,false
OpenSwathRTNormalizer + algorithm:Scores:use_uis_scores string false true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss string true false,true
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages string true true,false
OpenSwathRTNormalizer + algorithm:uis_threshold_peak_area int 0
OpenSwathRTNormalizer + algorithm:uis_threshold_sn int -1
OpenSwathRTNormalizer + outlierDetection:outlierMethod string iter_residual iter_residual,iter_jackknife,ransac,none
OpenSwathRTNormalizer + outlierDetection:useIterativeChauvenet string false true,false
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss string true
OpenSwathRTNormalizer - outlierDetection:outlierMethod string iter_residual
OpenSwathRTNormalizer - outlierDetection:useIterativeChauvenet string false
OpenSwathWorkflow + Scoring:Scores:use_uis_scores string false true,false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss string false false,true
OpenSwathWorkflow + Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages string false true,false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:background_subtraction string none none,smoothed,original
OpenSwathWorkflow + Scoring:uis_threshold_peak_area int 0
OpenSwathWorkflow + Scoring:uis_threshold_sn int -1
OpenSwathWorkflow + enable_uis_scoring string false true,false
OpenSwathWorkflow + mz_correction_function string none none,unweighted_regression,weighted_regression,quadratic_regression,weighted_quadratic_regression,weighted_quadratic_regression_delta_ppm,quadratic_regression_delta_ppm
OpenSwathWorkflow + outlierDetection:InitialQualityCutoff double 0.5
OpenSwathWorkflow + outlierDetection:MinBinsFilled int 8
OpenSwathWorkflow + outlierDetection:MinPeptidesPerBin int 1
OpenSwathWorkflow + outlierDetection:NrRTBins int 10
OpenSwathWorkflow + outlierDetection:OverallQualityCutoff double 5.5
OpenSwathWorkflow + outlierDetection:RANSACMaxIterations int 1000
OpenSwathWorkflow + outlierDetection:RANSACMaxPercentRTThreshold int 3
OpenSwathWorkflow + outlierDetection:RANSACSamplingSize int 10
OpenSwathWorkflow + outlierDetection:estimateBestPeptides string false true,false
OpenSwathWorkflow + outlierDetection:outlierMethod string iter_residual iter_residual,iter_jackknife,ransac,none
OpenSwathWorkflow + outlierDetection:useIterativeChauvenet string false true,false
OpenSwathWorkflow + readOptions string normal normal,cache,cacheWorkingInMemory
OpenSwathWorkflow - Scoring:EMGScoring:deltaRelError double 0.1
OpenSwathWorkflow - Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss string false
OpenSwathWorkflow - readOptions string normal normal,cache
PeakPickerHiRes + algorithm:SignalToNoise:write_log_messages string true true,false
PeptideIndexer + enzyme:name string Trypsin Chymotrypsin,CNBr,Formic_acid,Lys-C,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,2-iodobenzoate,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,no cleavage,unspecific cleavage,Trypsin,Arg-C,Asp-N,Asp-N_ambic
PeptideIndexer + filter_aaa_proteins string false true,false
PeptideIndexer + mismatches_max int 0 0:
PeptideIndexer + write_protein_description string false true,false
PeptideIndexer - annotate_proteins string false true,false
PeptideIndexer - enzyme:name string Trypsin Trypsin
PhosphoScoring + max_num_perm int 16384 1:
PhosphoScoring + max_peptide_length int 40 1:
RTEvaluation - sequences_file input-file *.fasta
Resampler + align_sampling string false true,false
Resampler + min_int_cutoff double -1
Resampler + ppm string false true,false
SimpleSearchEngine + enzyme string Trypsin Asp-N_ambic,Trypsin,PepsinA,TrypChymo,Arg-C,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,glutamyl endopeptidase,no cleavage,Lys-C/P,Asp-N,CNBr,Formic_acid,Lys-C,unspecific cleavage,Chymotrypsin
SimpleSearchEngine + peptide:max_size int 40
SpectraMerger + algorithm:average_gaussian:cutoff double 0.01 0:1
SpectraMerger + algorithm:average_gaussian:ms_level int 1 1:
SpectraMerger + algorithm:average_gaussian:rt_FWHM double 5 0:100000000000
SpectraMerger + algorithm:average_gaussian:spectrum_type string automatic profile,centroid,automatic
SpectraMerger + algorithm:average_tophat:ms_level int 1 1:
SpectraMerger + algorithm:average_tophat:rt_range double 5 0:100000000000
SpectraMerger + algorithm:average_tophat:rt_unit string scans scans,seconds
SpectraMerger + algorithm:average_tophat:spectrum_type string automatic profile,centroid,automatic
SpectraMerger + algorithm:mz_binning_width double 5 0:
SpectraMerger + algorithm:mz_binning_width_unit string ppm Da,ppm
SpectraMerger + merging_method string average_gaussian average_gaussian,average_tophat,precursor_method,block_method
SpectraMerger - algorithm:mz_binning_width double 0.0001 0:
SpectraMerger - algorithm:mz_binning_width_unit string Da Da,ppm
SpectraMerger - merging_method string block_method precursor_method,block_method
TextExporter + feature:add_metavalues int -1 -1:100
TextExporter + id:add_hit_metavalues int -1 -1:100
TextExporter + id:add_metavalues int -1 -1:100
XTandemAdapter + cleavage_site string Trypsin Trypsin,Asp-N_ambic,Lys-C/P,PepsinA,V8-E,unspecific cleavage,Asp-N,TrypChymo,leukocyte elastase,Formic_acid,Trypsin/P,V8-DE,CNBr,2-iodobenzoate,glutamyl endopeptidase,Lys-C,Chymotrypsin,Arg-C
XTandemAdapter + default_config_file input-file CHEMISTRY/XTandem_default_input.xml
XTandemAdapter + ignore_adapter_param string false true,false
XTandemAdapter + min_precursor_charge int 2
XTandemAdapter + precursor_mass_tolerance double 10
XTandemAdapter + use_noise_suppression string false true,false
XTandemAdapter - cleavage_site string [RK]|{P}
XTandemAdapter - default_input_file input-file
XTandemAdapter - min_precursor_charge int 1
XTandemAdapter - precursor_mass_tolerance double 1.5
Note: If you are interested in details on the number of merged pull requests or the state of individual issues.
You can simple query this information from our github repository (see e.g. https://help.github.com/articles/searching-issues/).
------------------------------------------------------------------------------------------
---- OpenMS 2.0 ----
------------------------------------------------------------------------------------------
Release date: February 2015
OpenMS 2.0 is the first release after the switch to git and a complete overhaul of the
build system. It introduces a considerable number of new features and bug fixes.
Furthermore, we removed the dependency to GSL and replaced the functionality using
Eigen3 and Wildmagic. Thus, the OpenMS core and the full build are now under a more
permissive non-GPL (e.g., Apache or BSD) license.
File formats:
- mzQuantML support (experimental)
- mzIdentML support (experimental)
- mzTab support (experimental)
- Indexed mzML support
- Support for numpress encoding in mzML
- Major speed improvement in mzML / mzXML parsing (up to 4x for some setups)
TOPPView:
- Support for visualizing mass fingerprinting hits from featureXML along with their raw spectra in MS1
- Improved "Tools" -> "Goto" dialog
- Improved display of m/z, RT, and intensity values 1D and 2D view
New tools:
- FeatureFinderIdentification -- Detects features in MS1 data based on peptide identifications (TOPP)
- FeatureFinderMultiplex -- Determination of peak ratios in LC-MS data (TOPP)
- FidoAdapter -- Runs the protein inference engine Fido (TOPP)
- LowMemPeakPickerHiRes -- Finds mass spectrometric peaks in profile mass spectra (UTIL)
- LowMemPeakPickerHiRes_RandomAccess -- Finds mass spectrometric peaks in profile mass spectra (UTIL)
- MRMTransitionGroupPicker (UTIL)
- MSGFPlusAdapter -- MS/MS database search using MS-GF+ (TOPP)
- MetaboliteSpectralMatcher -- Find potential HMDB ids within the given mass error window (UTIL)
- OpenSwathWorkflow -- Complete workflow to run OpenSWATH (UTIL)
- PeakPickerIterative -- Finds mass spectrometric peaks in profile mass spectra (UTIL)
- RTAnnotator -- Annotates identification files that are missing the RT field (UTIL)
- SimpleSearchEngine -- Annotates MS/MS spectra using SimpleSearchEngine (UTIL)
- TopPerc -- Facilitate input to Percolator and reintegrate (UTIL)
Deprecated tools:
- DBExporter -- Exports data from an OpenMS database to a file (TOPP)
- DBImporter -- Imports data to an OpenMS database (TOPP)
- FeatureFinderRaw -- Determination of peak ratios in LC-MS data (TOPP)
- SILACAnalyzer -- Determination of peak ratios in LC-MS data (TOPP)
Status changes:
- PhosphoScoring (UTIL -> TOPP)
Tools with major changes:
- OpenSWATH now supports MS1 extraction and labelled workflows
- OpenSWATHWorkflow single binary (high performance integrated workflow)
- IsobaricAnalyzer now supports TMT 10-plex
General:
- Removed GSL dependencies
- Introduced low memory versions of various algorithms
- OpenMS now offers a single interface for different implementations to access mass spectrometric data
- in memory
- on disk with index
- cached on disc for fast access
as well as a chainable, low memory sequential processor of MS data (using a separate interface)
- pyOpenMS now supports python 3.x
- Refactored AASequence, major speed improvement (~40x) for construction of unmodified sequences
Third party software:
- Added Fido support
- Added MS-GF+ support
Changes to the Build System / Package System:
- Restructured repository layout and build system
- Added support for Travis CI
- Simplified pyOpenMS build system
- Support for Visual Studio 2013
Changed parameters:
Tool name Added/removed Parameter name Type Default value Restrictions Supported formats
AccurateMassSearch + algorithm:ionization_mode string positive positive,negative,auto
AccurateMassSearch + algorithm:keep_unidentified_masses string false false,true
AccurateMassSearch + db:mapping input-file CHEMISTRY/HMDBMappingFile.tsv *.tsv
AccurateMassSearch + db:struct input-file CHEMISTRY/HMDB2StructMapping.tsv *.tsv
AccurateMassSearch + force string false true,false
AccurateMassSearch + negative_adducts_file input-file CHEMISTRY/NegativeAdducts.tsv *.tsv
AccurateMassSearch + out_annotation output-file *.featureXML,*.consensusXML
AccurateMassSearch + positive_adducts_file input-file CHEMISTRY/PositiveAdducts.tsv *.tsv
AccurateMassSearch - algorithm:ionization_mode string positive positive,negative
AccurateMassSearch - algorithm:negative_adducts_file string
AccurateMassSearch - algorithm:positive_adducts_file string
AdditiveSeries + force string false true,false
BaselineFilter + force string false true,false
CVInspector + force string false true,false
CompNovo + force string false true,false
CompNovoCID + force string false true,false
ConsensusID + force string false true,false
ConsensusMapNormalizer + force string false true,false
ConvertTSVToTraML + algorithm:override_group_label_check string false true,false
ConvertTSVToTraML + algorithm:retentionTimeInterpretation string iRT iRT,seconds,minutes
ConvertTSVToTraML + force string false true,false
ConvertTSVToTraML + in input-file *.tsv,*.csv,*.mrm
ConvertTSVToTraML + in_type string tsv,csv,mrm
ConvertTSVToTraML - in input-file *.csv
ConvertTraMLToTSV + force string false true,false
DTAExtractor + force string false true,false
DeMeanderize + force string false true,false
Decharger + force string false true,false
DecoyDatabase + force string false true,false
Digestor + force string false true,false
DigestorMotif + force string false true,false
EICExtractor + auto_rt:FHWM double 5
EICExtractor + auto_rt:SNThreshold double 5
EICExtractor + auto_rt:enabled string false true,false
EICExtractor + auto_rt:out_debug_TIC output-file *.mzML
EICExtractor + force string false true,false
EICExtractor + in_header input-file *.txt
EICExtractor + out output-file *.csv
EICExtractor + out_separator string ,
EICExtractor - out output-file *.txt
EICExtractor - out_detail output-file *.txt
ERPairFinder + force string false true,false
ExecutePipeline + force string false true,false
FFEval + force string false true,false
FalseDiscoveryRate + force string false true,false
FeatureFinderCentroided + force string false true,false
FeatureFinderCentroided + out_mzq output-file *.mzq
FeatureFinderCentroided - algorithm:fit:epsilon_abs double 0.0001 0:
FeatureFinderCentroided - algorithm:fit:epsilon_rel double 0.0001 0:
FeatureFinderIsotopeWavelet + force string false true,false
FeatureFinderMRM + force string false true,false
FeatureFinderMetabo + algorithm:epd:enabled string true true,false
FeatureFinderMetabo + force string false true,false
FeatureFinderSuperHirn + force string false true,false
FeatureLinkerLabeled + force string false true,false
FeatureLinkerUnlabeled + force string false true,false
FeatureLinkerUnlabeledQT + force string false true,false
FileConverter + MGF_compact string false true,false
FileConverter + UID_postprocessing string ensure none,ensure,reassign
FileConverter + force string false true,false
FileConverter + out output-file *.mzData,*.mzXML,*.mzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta,*.csv
FileConverter + out_type string mzData,mzXML,mzML,dta2d,mgf,featureXML,consensusXML,edta,csv
FileConverter + process_lowmemory string false true,false
FileConverter + write_mzML_index string false true,false
FileConverter - out output-file *.mzData,*.mzXML,*.mzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta
FileConverter - out_type string mzData,mzXML,mzML,dta2d,mgf,featureXML,consensusXML,edta
FileFilter + force string false true,false
FileFilter + peak_options:indexed_file string false true,false
FileFilter + peak_options:numpress:intensity string none none,linear,pic,slof
FileFilter + peak_options:numpress:intensity_error double 0.0001
FileFilter + peak_options:numpress:masstime string none none,linear,pic,slof
FileFilter + peak_options:numpress:masstime_error double 0.0001
FileFilter + spectra:select_polarity string unknown,positive,negative
FileInfo + force string false true,false
FileInfo + i string false true,false
FileInfo + in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid
FileInfo + in_type string mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid
FileInfo - in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid
FileInfo - in_type string mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid
FileMerger + force string false true,false
FuzzyDiff + force string false true,false
HighResPrecursorMassCorrector + force string false true,false
IDConflictResolver + force string false true,false
IDDecoyProbability + force string false true,false
IDEvaluator + force string false true,false
IDEvaluatorGUI + force string false true,false
IDExtractor + force string false true,false
IDFileConverter + force string false true,false
IDFileConverter + in input-file *.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.xml,*.idXML,*.mzid
IDFileConverter + peptideprophet_analyzed string false true,false
IDFileConverter - in input-file *.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.idXML
IDFilter + blacklist:ignore_modifications string false true,false
IDFilter + delete_unreferenced_peptide_hits string false true,false
IDFilter + force string false true,false
IDFilter + max_length int 0 0:
IDFilter + precursor:allow_missing string false true,false
IDFilter + precursor:mz string :
IDFilter + precursor:rt string :
IDFilter + remove_decoys string false true,false
IDFilter - max_length int 0 :0
IDMapper + consensus:annotate_ids_with_subelements string false true,false
IDMapper + force string false true,false
IDMapper + id input-file *.mzid,*.idXML
IDMapper - id input-file *.idXML
IDMassAccuracy + force string false true,false
IDMerger + add_to input-file *.idXML
IDMerger + force string false true,false
IDPosteriorErrorProbability + force string false true,false
IDPosteriorErrorProbability + out_plot output-file *.txt
IDPosteriorErrorProbability - fit_algorithm:output_name output-file
IDPosteriorErrorProbability - fit_algorithm:output_plots string false true,false
IDPosteriorErrorProbability - output_name output-file *.txt
IDRTCalibration + force string false true,false
IDRipper + force string false true,false
IDSplitter + force string false true,false
INIUpdater + force string false true,false
ITRAQAnalyzer + force string false true,false
ImageCreator + force string false true,false
InclusionExclusionListCreator + algorithm:PrecursorSelection:feature_based:max_number_precursors_per_feature int 1 1:
InclusionExclusionListCreator + algorithm:PrecursorSelection:feature_based:no_intensity_normalization string false true,false
InclusionExclusionListCreator + force string false true,false
InclusionExclusionListCreator - algorithm:PrecursorSelection:min_peak_distance double 3 0:
InclusionExclusionListCreator - algorithm:PrecursorSelection:selection_window double 2 0:
InspectAdapter + force string false true,false
InternalCalibration + force string false true,false
IsobaricAnalyzer + extraction:precursor_isotope_deviation double 10 0:
IsobaricAnalyzer + extraction:purity_interpolation string true true,false
IsobaricAnalyzer + force string false true,false
IsobaricAnalyzer + tmt10plex:channel_126_description string
IsobaricAnalyzer + tmt10plex:channel_127C_description string
IsobaricAnalyzer + tmt10plex:channel_127N_description string
IsobaricAnalyzer + tmt10plex:channel_128C_description string
IsobaricAnalyzer + tmt10plex:channel_128N_description string
IsobaricAnalyzer + tmt10plex:channel_129C_description string
IsobaricAnalyzer + tmt10plex:channel_129N_description string
IsobaricAnalyzer + tmt10plex:channel_130C_description string
IsobaricAnalyzer + tmt10plex:channel_130N_description string
IsobaricAnalyzer + tmt10plex:channel_131_description string
IsobaricAnalyzer + tmt10plex:correction_matrix string
IsobaricAnalyzer + tmt10plex:reference_channel string 126 126,127N,127C,128N,128C,129N,129C,130N,130C,131
IsobaricAnalyzer + type string itraq4plex itraq4plex,itraq8plex,tmt10plex,tmt6plex
IsobaricAnalyzer - extraction:precursor_isotope_deviation double 0.02 0:
IsobaricAnalyzer - type string itraq4plex itraq4plex,itraq8plex,tmt6plex
LabeledEval + force string false true,false
MRMMapper + force string false true,false
MRMPairFinder + force string false true,false
MSSimulator + force string false true,false
MSSimulator + in input-file *.FASTA
MSSimulator + out_id output-file *.idXML
MSSimulator - in input-file *.fasta
MapAlignerIdentification + force string false true,false
MapAlignerIdentification + model:b_spline:boundary_condition int 2 0:2
MapAlignerIdentification + model:b_spline:extrapolate string linear linear,b_spline,constant,global_linear
MapAlignerIdentification + model:b_spline:num_nodes int 5 0:
MapAlignerIdentification + model:b_spline:wavelength double 0 0:
MapAlignerIdentification - model:b_spline:break_positions string uniform uniform,quantiles
MapAlignerIdentification - model:b_spline:num_breakpoints int 5 2:
MapAlignerPoseClustering + force string false true,false
MapAlignerSpectrum + force string false true,false
MapAlignerSpectrum + model:b_spline:boundary_condition int 2 0:2
MapAlignerSpectrum + model:b_spline:extrapolate string linear linear,b_spline,constant,global_linear
MapAlignerSpectrum + model:b_spline:num_nodes int 5 0:
MapAlignerSpectrum + model:b_spline:wavelength double 0 0:
MapAlignerSpectrum - model:b_spline:break_positions string uniform uniform,quantiles
MapAlignerSpectrum - model:b_spline:num_breakpoints int 5 2:
MapAlignmentEvaluation + force string false true,false
MapNormalizer + force string false true,false
MapRTTransformer + force string false true,false
MapRTTransformer + model:b_spline:boundary_condition int 2 0:2
MapRTTransformer + model:b_spline:extrapolate string linear linear,b_spline,constant,global_linear
MapRTTransformer + model:b_spline:num_nodes int 5 0:
MapRTTransformer + model:b_spline:wavelength double 0 0:
MapRTTransformer - model:b_spline:break_positions string uniform uniform,quantiles
MapRTTransformer - model:b_spline:num_breakpoints int 5 2:
MapStatistics + force string false true,false
MascotAdapter + force string false true,false
MascotAdapterOnline + Mascot_parameters:special_modifications string Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)
MascotAdapterOnline + Mascot_server:export_params string _sigthreshold=0.99&_showsubsets=1&show_same_sets=1&report=0&percolate=0&query_master=0
MascotAdapterOnline + force string false true,false
MascotAdapterOnline - Mascot_server:max_hits int 0 0:
MascotAdapterOnline - Mascot_server:query_master string false true,false
MassCalculator + force string false true,false
MassTraceExtractor + force string false true,false
MyriMatchAdapter + CleavageRules string Trypsin,Trypsin/P,Arg-C,Asp-N,Asp-N_ambic,CNBr,Chymotrypsin,Formic_acid,Lys-C,Lys-C/P,PepsinA,TrypChymo,V8-DE,V8-E,glutamyl endopeptidase,leukocyte elastase,no cleavage,proline endopeptidase,unspecific cleavage
MyriMatchAdapter + MonoisotopeAdjustmentSet string 0
MyriMatchAdapter + force string false true,false
MyriMatchAdapter - CleavageRules string Trypsin,Trypsin/P,Chymotrypsin,TrypChymo,Lys-C,Lys-C/P,Asp-N,PepsinA,CNBr,Formic_acid,NoEnzyme
MyriMatchAdapter - MonoisotopeAdjustmentSet string [-1,2]
MzTabExporter + force string false true,false
MzTabExporter + in_consensus input-file *.consensusXML
MzTabExporter + in_feature input-file *.featureXML
MzTabExporter + in_id input-file *.idXML
MzTabExporter - in input-file *.idXML
NoiseFilterGaussian + force string false true,false
NoiseFilterGaussian + processOption string inmemory inmemory,lowmemory
NoiseFilterSGolay + force string false true,false
NoiseFilterSGolay + processOption string inmemory inmemory,lowmemory
OMSSAAdapter + chunk_size int 0
OMSSAAdapter + force string false true,false
OpenSwathAnalyzer + algorithm:DIAScoring:peak_before_mono_max_ppm_diff double 20 0:
OpenSwathAnalyzer + algorithm:Scores:use_dia_scores string true true,false
OpenSwathAnalyzer + algorithm:Scores:use_ms1_correlation string false true,false
OpenSwathAnalyzer + algorithm:Scores:use_ms1_fullscan string false true,false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width double 50
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:method string legacy legacy,corrected,crawdad
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width double 40
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks string false false,true
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length int 15
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order int 3
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise double 1 0:
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count int 30
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len double 1000
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss string true
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:compute_peak_quality string false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:min_peak_width double -1
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:minimal_quality double -10000
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:recalculate_peaks string false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:recalculate_peaks_max_z double 1
OpenSwathAnalyzer + force string false true,false
OpenSwathAnalyzer - algorithm:EMGScoring:deltaAbsError double 0.0001
OpenSwathAnalyzer - algorithm:EMGScoring:deltaRelError double 0.0001
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:gauss_width double 50
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:peak_width double 40 0:
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:sgolay_frame_length int 15
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:sgolay_polynomial_order int 3
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:signal_to_noise double 1 0:
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:sn_bin_count int 30
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:sn_win_len double 1000
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:use_gauss string true
OpenSwathAnalyzer - model:interpolation_type string cspline
OpenSwathAnalyzer - model:num_breakpoints int 5 2:
OpenSwathChromatogramExtractor + extract_MS1 string false true,false