https://github.com/grosenberger/OpenMS
Tip revision: bfb26979a2915643a01be494f6befcd5387b5223 authored by M Bernt on 20 February 2020, 15:46:22 UTC
TOFCalibration: be more precise in input formats (#4525)
TOFCalibration: be more precise in input formats (#4525)
Tip revision: bfb2697
CHANGELOG
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
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---- OpenMS 2.4 ----
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OpenMS 2.4 introduces changes from 322 pull requests including new features and bug fixes.
Notable changes since version 2.3 are:
Dependencies:
- Switch to Qt 5 (>= 5.5)
Documentation:
- New developer documentation to get started developing tools with OpenMS
Library:
- Improved mass calculations for isotope distributions
- Moved tool code from the tool to the library
- BinnedSpectrum now also supports offsets
- Improved peak type estimation
- Improved adduct grouping
- New EMG fitter for peak intensity imputation
- Targeted / untargeted spectra extraction and matching
- Spectra matching against a spectra library, using contrast angle similary function
- More precise peak integration (trapezoid, simpson)
New tools:
- AssayGeneratorMetabo -- Assay library generation from DDA data (Metabolomics) (UTIL)
- ClusterMassTraces -- Creates pseudo spectra (UTIL)
- ClusterMassTracesByPrecursor -- Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile (UTIL)
- CruxAdapter -- Identifies MS/MS spectra using Crux (TOPP)
- MSFraggerAdapter -- Peptide Identification with MSFragger (UTIL)
- MSstatsConverter -- Converter to input for MSstats (UTIL)
- MaRaClusterAdapter -- Facilitate input to MaRaCluster and reintegrate (TOPP)
- NovorAdapter -- Template for Tool creation (UTIL)
- RNADigestor -- Digests an RNA sequence database in-silico (UTIL)
Deprecated and removed tools:
- AdditiveSeries -- Computes an additive series to quantify a peptide in a set of samples (TOPP)
- IDEvaluator -- Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value (UTIL)
- IDEvaluatorGUI -- Computes a 'q-value vs. #PSM' plot to visualize the number identifications for a certain q-value (UTIL)
- RNPxl -- Tool for RNP cross linking experiment analysis (UTIL) (superseded by RNPxlSearch)
Changed Tools:
- SiriusAdapter now supports several input data
- FileFilter now supports filtering spectra by similarity
- PeptideIndexer now supports automatic detection of decoy suffix/prefix string and position
- PeakPickerHiRes now supports automatic detection and picking of profile spectra
- Support for MSFragger search engine through MSFraggerAdapter
- Support for Crux search engine through CruxAdapter
- Support for Maracluster through MaraClusterAdapter
- OpenPepXL was improved in efficiency and usability
- IDFileConverter now supports the Cross-Linking MS specific xquest.xml format
TOPPView:
- Improved visualization of identification results and ion annotations
- Support for visualization of Ion Mobility and DIA data
Major changes in functionality:
- None
File formats:
- Importer for MSP files
Scripts:
- None
Databases:
- None
Third-party software:
- New: maracluster (0.05)
- Update: MS-GF+ to Release (2018.01.30)
- Update: Sirius 4 for Windows 64bit, Linux 64bit, and MacOS 64bit
- Update: Crux (crux-3.1.8b78546) on all 64bit platforms.
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
------------------------------------------------------------------------------------------
---- OpenMS 2.3 ----
------------------------------------------------------------------------------------------
OpenMS 2.3 introduces a considerable number of new features and bug fixes.
Notable changes since version 2.2 are:
TOPPView:
- Deletion of selections of Peak Annotations is reflected in the Peptide Hit
- Buttons for saving ID files were merged to one single button. Format is determined by file extension or selected filter
- Clicking on a data point in 2D view, the search range for close fragment ion spectra is extended if no spectra are found initially
New tools:
- CometAdapter -- Annotates MS/MS spectra using Comet (TOPP)
- MetaboliteAdductDecharger -- Decharges and merges different feature charge variants of the same metabolite (UTIL)
- OpenPepXL -- Tool for protein-protein cross-linking identification using labeled linkers (UTIL)
- OpenPepXLLF -- Tool for protein-protein cross linking with label-free linkers (UTIL)
- PSMFeatureExtractor -- Computes extra features for each input PSM (UTIL)
- SiriusAdapter -- Tool for metabolite identification using single and tandem mass spectrometry (UTIL)
- XFDR -- Calculates false discovery rate estimates on protein-protein-crosslink identifications (UTIL)
Deprecated and removed tools:
- None
Renamed tool:
- LowMemPeakPickerHiRes_RandomAccess was renamed to LowMemPeakPickerHiResRandomAccess
Major changes in functionality:
- Experimental design
- Add support for fractions
- FeatureLinkerUnlabeledKD
- m/z and retention time tolerances for warping and linking are now separate parameters
- IsobaricAnalyzer
- Support for TMT11plex (https://www.thermofisher.com/order/catalog/product/A34808)
- FileInfo
- For idXML files, the tool computes the average length of contained peptides
- TopPerc
- Renamed in PercolatorAdapter (still experimental)
- OpenSWATH:
- RT normalization now allows more models
- Add S/N ratio for each ion trace
- Support for C++11 (requires a compiler that supports C++11)
Library:
- TOPP tools report their peak memory usage when using -debug 1 (or higher)
- idXML files can now be written faster (about 10%)
- pyOpenMS bindings for DataArrayByName getters
- Python build are now split in compilation units and can thus run in parallel
- FASTA files can now be written
- Allow String values to be passed to EnzymaticDigestion::isValidProduct
File formats:
- consensusXML now supports both channels and MS runs. Information will also be exported in mzTab
Scripts:
- None
Databases:
- None
Third-party software:
- New: Comet "2016.01 rev. 3" for Windows 32bit/64bit, Linux 64bit, and MacOS 64bit
- New: Percolator 3.1.2 for Windows 32bit/64bit, Linux 64bit, and MacOS 64bit (still experimental)
- New: Sirius 3.5.1 for Windows 64bit, Linux 64bit, and MacOS 64bit
- New: SpectraST 5.0 for Windows 64bit, Linux 64bit, and MacOS 64bit
- Update MS-GF+ to Release (v2017.07.21)
Changed tool parameters:
Tool name Added/removed Parameter name Type Default value Restrictions Supported formats
AccurateMassSearch + negative_adducts input-file CHEMISTRY/NegativeAdducts.tsv *.tsv
AccurateMassSearch + out output-file *.tsv
AccurateMassSearch + positive_adducts input-file CHEMISTRY/PositiveAdducts.tsv *.tsv
AccurateMassSearch - negative_adducts_file input-file CHEMISTRY/NegativeAdducts.tsv *.tsv
AccurateMassSearch - out output-file *.csv
AccurateMassSearch - positive_adducts_file input-file CHEMISTRY/PositiveAdducts.tsv *.tsv
Digestor + enzyme string Trypsin Arg-C/P,glutamyl endopeptidase,2-iodobenzoate,no cleavage,unspecific cleavage,Arg-C,Lys-N,Chymotrypsin,Asp-N/B,Asp-N_ambic,CNBr,Formic_acid,proline endopeptidase,Lys-C/P,Chymotrypsin/P,Asp-N,Lys-C,Trypsin,V8-DE,V8-E,Alpha-lytic protease,leukocyte elastase,PepsinA,TrypChymo,Trypsin/P
Digestor - enzyme string Trypsin Asp-N,PepsinA,TrypChymo,Trypsin,Lys-C,Lys-C/P,Asp-N_ambic,Formic_acid,CNBr,Chymotrypsin,Arg-C,Trypsin/P,V8-DE,V8-E,2-iodobenzoate,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,no cleavage,unspecific cleavage
DigestorMotif + enzyme string Trypsin Chymotrypsin,CNBr,Asp-N_ambic,Lys-N,2-iodobenzoate,no cleavage,Trypsin/P,V8-DE,Arg-C/P,Formic_acid,Lys-C/P,Lys-C,Arg-C,Alpha-lytic protease,glutamyl endopeptidase,V8-E,proline endopeptidase,leukocyte elastase,unspecific cleavage,Asp-N/B,TrypChymo,Asp-N,Chymotrypsin/P,PepsinA,Trypsin
DigestorMotif - enzyme string Trypsin Formic_acid,Lys-C,Lys-C/P,PepsinA,TrypChymo,leukocyte elastase,proline endopeptidase,2-iodobenzoate,glutamyl endopeptidase,Asp-N,Asp-N_ambic,Chymotrypsin,unspecific cleavage,Arg-C,V8-E,no cleavage,Trypsin,Trypsin/P,V8-DE,CNBr
FeatureFinderMetabo + out_chrom output-file *.mzML
FeatureLinkerUnlabeled + design input-file *.tsv
FeatureLinkerUnlabeledKD + algorithm:link:mz_tol double 10 0:
FeatureLinkerUnlabeledKD + algorithm:link:rt_tol double 30 0:
FeatureLinkerUnlabeledKD + algorithm:warp:enabled string true true,false
FeatureLinkerUnlabeledKD + algorithm:warp:max_nr_conflicts int 0 -1:
FeatureLinkerUnlabeledKD + algorithm:warp:max_pairwise_log_fc double 0.5
FeatureLinkerUnlabeledKD + algorithm:warp:min_rel_cc_size double 0.5 0:1
FeatureLinkerUnlabeledKD + algorithm:warp:mz_tol double 5 0:
FeatureLinkerUnlabeledKD + algorithm:warp:rt_tol double 100 0:
FeatureLinkerUnlabeledKD + design input-file *.tsv
FeatureLinkerUnlabeledKD - algorithm:max_nr_conflicts int 0 -1:
FeatureLinkerUnlabeledKD - algorithm:max_pairwise_log_fc double 0.5
FeatureLinkerUnlabeledKD - algorithm:min_rel_cc_size double 0.5 0:1
FeatureLinkerUnlabeledKD - algorithm:mz_tol double 15 0:
FeatureLinkerUnlabeledKD - algorithm:rt_tol double 60 0:
FeatureLinkerUnlabeledKD - algorithm:warp string true true,false
FeatureLinkerUnlabeledQT + design input-file *.tsv
FileInfo + in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML,*.fasta
FileInfo - in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid,*.trafoXML
FileMerger + in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.fid,*.traML,*.FASTA
FileMerger + in_type string mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,fid,traML,FASTA
FileMerger - in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.fid,*.traML
FileMerger - in_type string mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,fid,traML
IDFileConverter + add_ionmatch_annotation double 0
IDFilter + digest:enzyme string Trypsin unspecific cleavage,PepsinA,Trypsin/P,Lys-N,2-iodobenzoate,no cleavage,glutamyl endopeptidase,Asp-N,Lys-C/P,Lys-C,CNBr,Asp-N_ambic,leukocyte elastase,V8-DE,Arg-C,Trypsin,V8-E,Alpha-lytic protease,proline endopeptidase,Asp-N/B,Arg-C/P,Formic_acid,Chymotrypsin/P,TrypChymo,Chymotrypsin
IDFilter - digest:enzyme string Trypsin proline endopeptidase,2-iodobenzoate,CNBr,Arg-C,Chymotrypsin,Asp-N_ambic,Asp-N,Formic_acid,glutamyl endopeptidase,no cleavage,leukocyte elastase,V8-E,Lys-C/P,unspecific cleavage,TrypChymo,Trypsin/P,Lys-C,Trypsin,V8-DE,PepsinA
IsobaricAnalyzer + tmt11plex:channel_126_description string
IsobaricAnalyzer + tmt11plex:channel_127C_description string
IsobaricAnalyzer + tmt11plex:channel_127N_description string
IsobaricAnalyzer + tmt11plex:channel_128C_description string
IsobaricAnalyzer + tmt11plex:channel_128N_description string
IsobaricAnalyzer + tmt11plex:channel_129C_description string
IsobaricAnalyzer + tmt11plex:channel_129N_description string
IsobaricAnalyzer + tmt11plex:channel_130C_description string
IsobaricAnalyzer + tmt11plex:channel_130N_description string
IsobaricAnalyzer + tmt11plex:channel_131C_description string
IsobaricAnalyzer + tmt11plex:channel_131N_description string
IsobaricAnalyzer + tmt11plex:correction_matrix string
IsobaricAnalyzer + tmt11plex:reference_channel string 126 126,127N,127C,128N,128C,129N,129C,130N,130C,131N,131C
IsobaricAnalyzer + type string itraq4plex itraq4plex,itraq8plex,tmt10plex,tmt11plex,tmt6plex
IsobaricAnalyzer - type string itraq4plex itraq4plex,itraq8plex,tmt10plex,tmt6plex
MRMMapper + allow_multiple_mappings string false true,false
MRMTransitionGroupPicker + algorithm:PeakPickerMRM:method string corrected legacy,corrected,crawdad
MRMTransitionGroupPicker + algorithm:PeakPickerMRM:peak_width double -1
MRMTransitionGroupPicker + algorithm:resample_boundary double 15
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:method string legacy legacy,corrected,crawdad
MRMTransitionGroupPicker - algorithm:PeakPickerMRM:peak_width double 40
MSGFPlusAdapter + enzyme string Trypsin/P Alpha-lytic protease,Arg-C/P,Asp-N/B,Chymotrypsin/P,Lys-C/P,Lys-N,Trypsin/P,glutamyl endopeptidase,no cleavage,unspecific cleavage
MSGFPlusAdapter + precursor_mass_tolerance double 10
MSGFPlusAdapter - enzyme string trypsin unspecific,trypsin,chymotrypsin,LysC,LysN,GluC,ArgC,AspN,alphaLP,no_cleavage
MSGFPlusAdapter - precursor_mass_tolerance double 20
MSSimulator + algorithm:MSSim:Digestion:enzyme string Trypsin no cleavage,unspecific cleavage,glutamyl endopeptidase,Arg-C,Formic_acid,Asp-N_ambic,Asp-N,Asp-N/B,V8-DE,proline endopeptidase,Alpha-lytic protease,Lys-C,Lys-N,Chymotrypsin,Arg-C/P,CNBr,Chymotrypsin/P,Trypsin,Trypsin/P,V8-E,2-iodobenzoate,leukocyte elastase,Lys-C/P,PepsinA,TrypChymo
MSSimulator - algorithm:MSSim:Digestion:enzyme string Trypsin Lys-C,Lys-C/P,Trypsin,CNBr,Formic_acid,Asp-N,Chymotrypsin,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,2-iodobenzoate,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,no cleavage,unspecific cleavage,Asp-N_ambic,Arg-C
MapAlignerIdentification + design input-file *.tsv
MyriMatchAdapter + precursor_mass_tolerance double 10
MyriMatchAdapter + precursor_mass_tolerance_unit string ppm Da,ppm
MyriMatchAdapter - precursor_mass_tolerance double 1.5
MyriMatchAdapter - precursor_mass_tolerance_unit string Da Da,ppm
OMSSAAdapter + enzyme string Trypsin Trypsin,Lys-C/P,Lys-C,Arg-C,CNBr,PepsinA,no cleavage,glutamyl endopeptidase,Chymotrypsin,Formic_acid,Asp-N,Asp-N_ambic,Trypsin/P,unspecific cleavage,TrypChymo
OMSSAAdapter + precursor_error_units string ppm Da,ppm
OMSSAAdapter + precursor_mass_tolerance double 10
OMSSAAdapter - enzyme string Trypsin Trypsin,Asp-N_ambic,unspecific cleavage,Chymotrypsin,glutamyl endopeptidase,no cleavage,TrypChymo,Trypsin/P,CNBr,Formic_acid,Arg-C,Asp-N,Lys-C,Lys-C/P,PepsinA
OMSSAAdapter - precursor_mass_tolerance double 1.5
OMSSAAdapter - precursor_mass_tolerance_unit_ppm string false true,false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:method string corrected legacy,corrected,crawdad
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width double -1
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:resample_boundary double 15
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:method string legacy legacy,corrected,crawdad
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width double 40
OpenSwathRTNormalizer + RTNormalization:RANSACMaxIterations int 1000
OpenSwathRTNormalizer + RTNormalization:RANSACMaxPercentRTThreshold int 3
OpenSwathRTNormalizer + RTNormalization:RANSACSamplingSize int 10
OpenSwathRTNormalizer + RTNormalization:outlierMethod string iter_residual iter_residual,iter_jackknife,ransac,none
OpenSwathRTNormalizer + RTNormalization:useIterativeChauvenet string false true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:method string corrected legacy,corrected,crawdad
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width double -1
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:resample_boundary double 15
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:method string legacy legacy,corrected,crawdad
OpenSwathRTNormalizer - algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width double 40
OpenSwathRTNormalizer - outlierDetection:RANSACMaxIterations int 1000
OpenSwathRTNormalizer - outlierDetection:RANSACMaxPercentRTThreshold int 3
OpenSwathRTNormalizer - outlierDetection:RANSACSamplingSize int 10
OpenSwathRTNormalizer - outlierDetection:outlierMethod string iter_residual iter_residual,iter_jackknife,ransac,none
OpenSwathRTNormalizer - outlierDetection:useIterativeChauvenet string false true,false
OpenSwathWorkflow + RTNormalization:InitialQualityCutoff double 0.5
OpenSwathWorkflow + RTNormalization:MinBinsFilled int 8
OpenSwathWorkflow + RTNormalization:MinPeptidesPerBin int 1
OpenSwathWorkflow + RTNormalization:NrRTBins int 10
OpenSwathWorkflow + RTNormalization:OverallQualityCutoff double 5.5
OpenSwathWorkflow + RTNormalization:RANSACMaxIterations int 1000
OpenSwathWorkflow + RTNormalization:RANSACMaxPercentRTThreshold int 3
OpenSwathWorkflow + RTNormalization:RANSACSamplingSize int 10
OpenSwathWorkflow + RTNormalization:alignmentMethod string linear linear,interpolated,lowess,b_spline
OpenSwathWorkflow + RTNormalization:b_spline:num_nodes int 5 0:
OpenSwathWorkflow + RTNormalization:estimateBestPeptides string false true,false
OpenSwathWorkflow + RTNormalization:lowess:span double 0.666666666666667 0:1
OpenSwathWorkflow + RTNormalization:outlierMethod string iter_residual iter_residual,iter_jackknife,ransac,none
OpenSwathWorkflow + RTNormalization:useIterativeChauvenet string false true,false
OpenSwathWorkflow + Scoring:TransitionGroupPicker:resample_boundary double 15
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
PeptideIndexer + enzyme:name string Trypsin proline endopeptidase,Alpha-lytic protease,glutamyl endopeptidase,Asp-N,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,Asp-N_ambic,Asp-N/B,2-iodobenzoate,no cleavage,unspecific cleavage,Arg-C/P,Arg-C,Trypsin
PeptideIndexer - enzyme:name string Trypsin Lys-C/P,Trypsin,Formic_acid,Lys-C,Arg-C,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,glutamyl endopeptidase,no cleavage,unspecific cleavage,Chymotrypsin,CNBr,Asp-N,Asp-N_ambic
RNPxlSearch + peptide:enzyme string Trypsin Trypsin,proline endopeptidase,Alpha-lytic protease,Lys-C/P,leukocyte elastase,Chymotrypsin,no cleavage,Chymotrypsin/P,Lys-N,Asp-N_ambic,PepsinA,Arg-C/P,V8-DE,V8-E,Trypsin/P,unspecific cleavage,2-iodobenzoate,CNBr,Formic_acid,Asp-N,Lys-C,Asp-N/B,Arg-C,glutamyl endopeptidase,TrypChymo
RNPxlSearch + precursor:isotopes int
RNPxlSearch - peptide:enzyme string Trypsin Lys-C,Trypsin,Formic_acid,Lys-C/P,PepsinA,glutamyl endopeptidase,no cleavage,Chymotrypsin,CNBr,2-iodobenzoate,leukocyte elastase,proline endopeptidase,Asp-N,Arg-C,TrypChymo,Trypsin/P,V8-DE,V8-E,unspecific cleavage,Asp-N_ambic
SimpleSearchEngine + enzyme string Trypsin Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,proline endopeptidase,leukocyte elastase,unspecific cleavage,Asp-N/B,Chymotrypsin,Trypsin,Asp-N_ambic,Formic_acid,Lys-N,CNBr,Chymotrypsin/P,Arg-C/P,Asp-N,Lys-C,no cleavage,Alpha-lytic protease,glutamyl endopeptidase,2-iodobenzoate,Arg-C
SimpleSearchEngine + precursor:isotopes int
SimpleSearchEngine - enzyme string Trypsin glutamyl endopeptidase,no cleavage,unspecific cleavage,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,2-iodobenzoate,Asp-N,Asp-N_ambic,Chymotrypsin,Arg-C,Lys-C/P,PepsinA,CNBr,Formic_acid,Lys-C,Trypsin
XTandemAdapter + enzyme string Trypsin Trypsin/P,Arg-C/P,V8-DE,Formic_acid,Asp-N,Chymotrypsin/P,CNBr,Lys-C/P,unspecific cleavage,Asp-N/B,Lys-C,Chymotrypsin,PepsinA,Lys-N,Trypsin,glutamyl endopeptidase,2-iodobenzoate,leukocyte elastase,Alpha-lytic protease,V8-E,Arg-C,TrypChymo,Asp-N_ambic
XTandemAdapter - enzyme string Trypsin Trypsin,Formic_acid,Lys-C,Chymotrypsin,CNBr,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,2-iodobenzoate,leukocyte elastase,glutamyl endopeptidase,unspecific cleavage,Asp-N_ambic,Asp-N,Arg-C
------------------------------------------------------------------------------------------
---- 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
OpenSwathChromatogramExtractor + force string false true,false
OpenSwathChromatogramExtractor + mz_window double 0.05 0:
OpenSwathChromatogramExtractor + rt_window double -1
OpenSwathChromatogramExtractor - extraction_window double 0.05 0:
OpenSwathChromatogramExtractor - model:interpolation_type string cspline
OpenSwathChromatogramExtractor - model:num_breakpoints int 5 2:
OpenSwathChromatogramExtractor - rt_extraction_window double -1
OpenSwathConfidenceScoring + force string false true,false
OpenSwathDIAPreScoring + force string false true,false
OpenSwathDecoyGenerator + enable_losses string false true,false
OpenSwathDecoyGenerator + force string false true,false
OpenSwathDecoyGenerator + mz_threshold double 0.05
OpenSwathDecoyGenerator + remove_unannotated string false true,false
OpenSwathDecoyGenerator - max_transitions int 6
OpenSwathDecoyGenerator - min_transitions int 2
OpenSwathDecoyGenerator - mz_threshold double 0.8
OpenSwathFeatureXMLToTSV + force string false true,false
OpenSwathMzMLFileCacher + force string false true,false
OpenSwathRTNormalizer + algorithm:DIAScoring:dia_byseries_intensity_min double 300 0:
OpenSwathRTNormalizer + algorithm:DIAScoring:dia_byseries_ppm_diff double 10 0:
OpenSwathRTNormalizer + algorithm:DIAScoring:dia_centroided string false true,false
OpenSwathRTNormalizer + algorithm:DIAScoring:dia_extraction_window double 0.05 0:
OpenSwathRTNormalizer + algorithm:DIAScoring:dia_nr_charges int 4 0:
OpenSwathRTNormalizer + algorithm:DIAScoring:dia_nr_isotopes int 4 0:
OpenSwathRTNormalizer + algorithm:DIAScoring:peak_before_mono_max_ppm_diff double 20 0:
OpenSwathRTNormalizer + algorithm:EMGScoring:interpolation_step double 0.2
OpenSwathRTNormalizer + algorithm:EMGScoring:max_iteration int 500
OpenSwathRTNormalizer + algorithm:EMGScoring:statistics:mean double 1
OpenSwathRTNormalizer + algorithm:EMGScoring:statistics:variance double 1
OpenSwathRTNormalizer + algorithm:EMGScoring:tolerance_stdev_bounding_box double 3
OpenSwathRTNormalizer + algorithm:Scores:use_coelution_score string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_dia_scores string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_elution_model_score string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_intensity_score string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_library_score string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_ms1_correlation string false true,false
OpenSwathRTNormalizer + algorithm:Scores:use_ms1_fullscan string false true,false
OpenSwathRTNormalizer + algorithm:Scores:use_nr_peaks_score string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_rt_score string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_shape_score string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_sn_score string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_total_xic_score string true true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width double 50
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:method string legacy legacy,corrected,crawdad
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width double 40
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks string false false,true
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length int 15
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order int 3
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise double 1 0:
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count int 30
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len double 1000
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss string true
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:background_subtraction string none none,smoothed,original
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:compute_peak_quality string false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:min_peak_width double -1
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:minimal_quality double -10000
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:recalculate_peaks string false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:recalculate_peaks_max_z double 1
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:stop_after_feature int -1
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:stop_after_intensity_ratio double 0.0001
OpenSwathRTNormalizer + algorithm:add_up_spectra int 1 1:
OpenSwathRTNormalizer + algorithm:quantification_cutoff double 0 0:
OpenSwathRTNormalizer + algorithm:rt_extraction_window double -1
OpenSwathRTNormalizer + algorithm:rt_normalization_factor double 1
OpenSwathRTNormalizer + algorithm:spacing_for_spectra_resampling double 0.005 0:
OpenSwathRTNormalizer + algorithm:stop_report_after_feature int -1
OpenSwathRTNormalizer + algorithm:write_convex_hull string false true,false
OpenSwathRTNormalizer + estimateBestPeptides string false true,false
OpenSwathRTNormalizer + force string false true,false
OpenSwathRTNormalizer + outlierDetection:RANSACMaxIterations int 1000
OpenSwathRTNormalizer + outlierDetection:RANSACMaxPercentRTThreshold int 3
OpenSwathRTNormalizer + outlierDetection:RANSACSamplingSize int 10
OpenSwathRTNormalizer + outlierDetection:outlierMethod string iter_residual
OpenSwathRTNormalizer + outlierDetection:useIterativeChauvenet string false
OpenSwathRTNormalizer + peptideEstimation:InitialQualityCutoff double 0.5
OpenSwathRTNormalizer + peptideEstimation:MinBinsFilled int 8
OpenSwathRTNormalizer + peptideEstimation:MinPeptidesPerBin int 1
OpenSwathRTNormalizer + peptideEstimation:NrRTBins int 10
OpenSwathRTNormalizer + peptideEstimation:OverallQualityCutoff double 5.5
OpenSwathRewriteToFeatureXML + force string false true,false
PILISIdentification + force string false true,false
PILISModelCV + force string false true,false
PILISModelTrainer + force string false true,false
PILISSpectraGenerator + force string false true,false
PTModel + force string false true,false
PTPredict + force string false true,false
PeakPickerHiRes + algorithm:SignalToNoise:auto_max_percentile int 95 0:100
PeakPickerHiRes + algorithm:SignalToNoise:auto_max_stdev_factor double 3 0:999
PeakPickerHiRes + algorithm:SignalToNoise:auto_mode int 0 -1:1
PeakPickerHiRes + algorithm:SignalToNoise:bin_count int 30 3:
PeakPickerHiRes + algorithm:SignalToNoise:max_intensity int -1 -1:
PeakPickerHiRes + algorithm:SignalToNoise:min_required_elements int 10 1:
PeakPickerHiRes + algorithm:SignalToNoise:noise_for_empty_window double 1e+20
PeakPickerHiRes + algorithm:SignalToNoise:win_len double 200 1:
PeakPickerHiRes + algorithm:missing int 1 0:
PeakPickerHiRes + algorithm:ms_levels int 1:
PeakPickerHiRes + algorithm:spacing_difference double 1.5 0:
PeakPickerHiRes + algorithm:spacing_difference_gap double 4 0:
PeakPickerHiRes + force string false true,false
PeakPickerHiRes + processOption string inmemory inmemory,lowmemory
PeakPickerHiRes - algorithm:ms1_only string false true,false
PeakPickerWavelet + algorithm:optimization:iterations int 400 1:
PeakPickerWavelet + force string false true,false
PeakPickerWavelet - algorithm:optimization:delta_abs_error double 9.99999974737875e-05 0:
PeakPickerWavelet - algorithm:optimization:delta_rel_error double 9.99999974737875e-05 0:
PeakPickerWavelet - algorithm:optimization:iterations int 15 1:
PepNovoAdapter + force string false true,false
PeptideIndexer + IL_equivalent string false true,false
PeptideIndexer + annotate_proteins string false true,false
PeptideIndexer + force string false true,false
PeptideIndexer + write_protein_sequence string false true,false
PeptideIndexer - write_protein_sequence string false true,false
PhosphoScoring + force string false true,false
PhosphoScoring + fragment_mass_tolerance double 0.05
PhosphoScoring + fragment_mass_unit string Da Da,ppm
PhosphoScoring + out output-file *.idXML
PhosphoScoring - fragment_mass_tolerance double 0.5
PhosphoScoring - out output-file
PrecursorIonSelector + algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature int 1 1:
PrecursorIonSelector + algorithm:MIPFormulation:feature_based:no_intensity_normalization string false true,false
PrecursorIonSelector + force string false true,false
PrecursorIonSelector + ids input-file *.idXML
PrecursorIonSelector - ids string
PrecursorMassCorrector + force string false true,false
ProteinInference + force string false true,false
ProteinQuantifier + average string median median,mean,weighted_mean,sum
ProteinQuantifier + force string false true,false
ProteinQuantifier + protein_groups input-file *.idXML
ProteinQuantifier - average string median median,mean,sum
ProteinQuantifier - mzTab_out output-file *.csv
ProteinQuantifier - protxml input-file *.idXML
ProteinResolver + force string false true,false
QCCalculator + force string false true,false
QCEmbedder + force string false true,false
QCExporter + force string false true,false
QCExtractor + force string false true,false
QCImporter + force string false true,false
QCMerger + force string false true,false
QCShrinker + force string false true,false
RNPxl + continue string false true,false
RNPxl + force string false true,false
RNPxlXICFilter + force string false true,false
RTEvaluation + force string false true,false
RTModel + force string false true,false
RTPredict + force string false true,false
Resampler + force string false true,false
SeedListGenerator + force string false true,false
SemanticValidator + cv input-file *.obo
SemanticValidator + force string false true,false
SemanticValidator + in input-file *.analysisXML,*.mzML,*.TraML,*.mzid,*.mzData,*.xml
SemanticValidator - in input-file *.analysisXML,*.mzML
SequenceCoverageCalculator + force string false true,false
SpecLibCreator + force string false true,false
SpecLibSearcher + compare_function string ZhangSimilarityScore PeakAlignment,SpectrumAlignmentScore,SpectrumCheapDPCorr,SpectrumPrecursorComparator,SteinScottImproveScore,ZhangSimilarityScore
SpecLibSearcher + force string false true,false
SpecLibSearcher - compare_function string ZhangSimilarityScore CompareFouriertransform,PeakAlignment,SpectrumAlignmentScore,SpectrumCheapDPCorr,SpectrumPrecursorComparator,SteinScottImproveScore,ZhangSimilarityScore
SpectraFilterBernNorm + force string false true,false
SpectraFilterMarkerMower + force string false true,false
SpectraFilterNLargest + force string false true,false
SpectraFilterNormalizer + force string false true,false
SpectraFilterParentPeakMower + force string false true,false
SpectraFilterScaler + force string false true,false
SpectraFilterSqrtMower + force string false true,false
SpectraFilterThresholdMower + force string false true,false
SpectraFilterWindowMower + force string false true,false
SpectraMerger + force string false true,false
SvmTheoreticalSpectrumGeneratorTrainer + force string false true,false
TMTAnalyzer + force string false true,false
TOFCalibration + algorithm:PeakPicker:optimization:iterations int 400 1:
TOFCalibration + force string false true,false
TOFCalibration - algorithm:PeakPicker:optimization:delta_abs_error double 9.99999974737875e-05 0:
TOFCalibration - algorithm:PeakPicker:optimization:delta_rel_error double 9.99999974737875e-05 0:
TOFCalibration - algorithm:PeakPicker:optimization:iterations int 15 1:
TextExporter + force string false true,false
TransformationEvaluation + force string false true,false
XMLValidator + force string false true,false
XMLValidator + in input-file *.mzML,*.mzData,*.featureXML,*.mzid,*.idXML,*.consensusXML,*.mzXML,*.ini,*.pepXML,*.TraML,*.xml
XMLValidator - in input-file *.mzML,*.mzData,*.featureXML,*.idXML,*.consensusXML,*.mzXML,*.ini,*.pepXML
XTandemAdapter + allow_isotope_error string yes yes,no
XTandemAdapter + force string false true,false
XTandemAdapter + output_results string all all,valid,stochastic
Resolved issues and merged pull requests:
#644 Fix header macros
#649 Fix ms numpress
#651 [INTERNAL,API] Removal of the GSL
#656 Repository layout restructuring
#657 [FIX, INTERNAL]
#658 [FIX] PeptideIndexer crashes on empty idXML (#653)
#659 [NOP] replaced c like file ending C with cpp
#660 [FIX] fix Cython 0.20 compatibility issue
#661 [BUILD,PYOPENMS] simplify pyOpenMS build system
#662 CMake and docu cleanups w.r.t. to the new layout
#664 [BUILD] build system fixes / cleanups
#665 Fix coverity errors
#666 [FEATURE] ib spectra format export
#667 [BUILD] improved handling of boost in OpenMS build system
#668 [NOP] added support for travis-ci to OpenMS
#669 [FIX] fixed AccurateMassSearch_test
#673 [FEATURE,FIX] Added min/max values to go-to dialog
#675 Checker/Test fixes and adds test for CTD writing
#677 [PYOPENMS] setup.py as minimal as possible + other improvements
#678 [FIX] fix how swath files are annotated
#679 [FIX,TEST] fixed OpenSwathDecoyGenerator / MRMDecoy
#680 [INTERNAL] Feature/CachedMzML fixes
#684 [FIX] Bugfix for threading issue in MascotGenericFile
#685 Typo fixes in documentation and licence files
#688 Fix/file size limit
#689 [FIX] disable OpenMP again for ILPDCWrapper
#690 Fix/misc
#691 further improvements to MGF::load()
#693 Major speedup of String --> Double conversion
#694 added missing index file for OMSSA test, which gets recreated when runni...
#696 [FIX] fix RAM usage when adding dataprocessing to chromatograms
#697 [FIX] proper usage of map in ControlledVocabulary
#698 Updates to FeatureFinderIdentification and the ...TraceFitter classes
#702 Feature/parallel reader
#703 Feature/aa sequence tpp
#705 [FIX] Propagate metadata in OpenSwathWorkflow
#707 [FEATURE] variable stylesheet support for qcml
#708 [BUILD] fix build system bug
#711 [FEATURE,BUILD] fix install target
#713 Fix for pepXML loading bug (#710)
#715 Feature/pyopenms wrapping improvements neu
#716 [NOP,TEST] clean up MRMDecoy, add more tests
#717 fixed 32bit memory limitation of OMSSA by chunking input data
#718 [FIX] fixed misleading warning ("Removed x peptide identifications...
#719 [CI,FIX] fix travis contrib clone problems
#721 [INTERNAL] cleanup of iostream includes
#722 Feature/mz xml consumer
#724 Feature/pyopenms mzxml consumer
#725 Fix/misc
#726 IDPosteriorErrorProbability fix
#729 Fix/coverity
#730 Feature/peak picker sn performance
#734 Feature/more pyopenms improvements
#735 [FEATURE] clang warning level
#737 [FIX] several minor fixes
#739 Feature/uids fileconverter
#741 ProteinResolver fix
#742 svn cleanup
#743 [FIX] fixed compilation error on vs2013
#747 Speedup OMSSA-XML parsing and some stats for OMSSA&XTandem
#749 Feature/python3
#750 [PYOPENMS,FIX] fixed streampos->long conversion
#751 [FEATURE] track base name when reading pep.xml files
#752 [FIX] fixed missing adaption PeptideIdentification::empty()
#754 [PYOPENMS] changed extra methods on MSSpectrum
#755 [FIX] fixed shadow warning
#756 Unity Builds
#760 [FIX-#618] fix spelling errors in headers
#761 Feature/header fixes
#764 [FEATURE] lib superhirn
#765 Feature/db removal
#768 [FIX] fixed warnings in CONCEPTS
#770 [FIX] fixed some clang warnings in stream manipulation
#771 New warnings
#773 [BUILD,PYOPENMS] fix pyOpenMS build
#775 [FIX] typos in the CMake file
#776 Fix for IDPosteriorErrorProbability on Mascot search results (#740)
#777 Memory profiling class
#779 [FIX] replaced DoubleReal and Real by double and float.
#780 [FIX] fix Swath window estimation
#781 Fix/open swath fixes
#784 [FEATURE] fix macosx pyopenms errors
#785 [FIX] VS2013 compile fixes
#786 [FEATURE] added openms_add_library function
#787 [FEATURE,BUILD] move pyOpenMS to src
#789 small fix to Win install doc for VS2013
#790 Remove "RT"; and "MZ"; metavalues from PeptideIdentification
#791 [FIX] forgot writtenDigits fixes in tests VS2013
#792 [FIX] AASequence refactoring
#794 Generic Wrapping of R scripts using GenericWrapper
#797 [NOP,DOC] removed all remaining references to FeatureFinderRaw and SILAC...
#798 Fix/py open ms testfix
#799 [DOC] removed migrated pages from doxygen. replaced by link to wiki
#800 spline interpolation of MS1 spectra
#801 RTPredict: fixed order of parameters and doc
#802 [FIX] fixed copy-paste mistake in error message
#804 [FIX] MRMDecoy: Fix neutral losses for higher charge states
#805 [PYOPENMS] added getters/setters for MZ and RT in PeptideIdentification....
#807 cubic spline implementation
#810 cubic spline interpolation
#811 [NOP] add better debug information and error handling
#812 [FIX] per cppcheck
#813 Fix/openswath
#814 [FEATURE] ConvertTSVToTraML: Support for SpectraST MRM Transition Lists
#816 Feature/cached mz ml format change
#817 [FIX] fix spline derivative for cubic spline
#819 Feature/custom i rt
#820 Fix/warnings
#821 [FIX] suppress clang warnings
#823 Feature/update numpress
#824 Fix/coverity
#826 Feature/funny pictures
#827 [FIX] fixes export macro warnings
#831 [FEATURE] fix all gcc warnings and turn warnings into errors
#832 several pyopenms fixes + updates
#833 Feature/visibility hidden
#834 Fix/fix werror
#835 Fix spline spectrum
#836 [FIX,TEST] MRMRTNormalizer_test: Windows compatibility
#838 [FIX] fixed uninitialized pointer warning
#840 [FIX] fix pyOpenMS test
#841 [BUILD] disable -Werror by default
#842 [FIX] fix dereference of iterator
#843 [FIX] fixes tests failing win debug mode
#844 [FIX] evaluation at m/z in first package now possible
#845 [FEATURE] replace String classes with StringUtils
#846 Fix/fixes from822
#847 peak boundaries and new cubic splines for PeakPickerHiRes
#850 [FEATURE] modified tests to reflect X!Tandem SLEDGEHAMMER as default
#851 Fix and tests for a bug in reading Mascot XML files
#852 [FIX] fix windows compile error
#854 [FIX] ConsensusID doesn't sort peptide hits before processing (idXML)
#855 [FIX] FalseDiscoveryRate "target+decoy"; hits should be considered as targets
#856 [FEATURE] KNIME package generation updates
#857 Fix/py open ms fix
#858 [FEATURE] ~40x speedup for constructions of unmodified AASequence
#859 Feature/SystemWildMagic
#863 [BUILD] added test for x!tandem version to enable tests only with newer ...
#865 Work-around for special modifications in Mascot (fixes #864)
#866 [FEATURE] git version embedding
#867 [FIX-#861,DOC] fixed eigen 3.2.1 problems with GammaDistributionFitter
#868 multiplex filtering
#869 [FIX] fixed problems with negative sizeof values in CachedMzML
#870 [FIX,DOC] doxygen 1.8.7 fixes
#873 [FIX] fixed macosx version query
#875 Rewrite of 'AASequence::parseString_', increasing robustness of parsing (fixes #818)
#876 [DOC] added new doc_class_only target
#880 PeakPickerHiRes peak boundaries fixed
#881 [FEATURE] mzTab 1.0
#882 [FEATURE] coding style improvements
#884 [FIX] Convert XTandem search results into .pepXML by IDFileConverter
#885 [NOP] added moc files to gitignore
#888 [FIX-#887] IDFilter errornousely removed peptidhits in multiple run files
#889 multiplex clustering
#891 [FIX] converting uniform distributed generators with normal distributions
#892 Enable loading of some pepXML files that used to cause crashes
#894 [FEATURE] improved 3rd party lib finding
#895 [FEATURE] simple search engine
#896 added scan-polarity filter to FileFilter ...
#897 (feature for Windows developers) added a small Windows .reg file
#898 More compact format for MGF files (fixes #890)
#899 [DOC] some minor documentation addition
#901 [FIX] fix MS level for DTA file reader
#902 [FIX,PYOPENMS] fix pyOpenMS after #875
#903 [FIX] mzXML fix (filterLine, basePeakMz)
#904 Feature/fix peak boundaries
#910 [FIX] fixed unity build error introduced in #845
#911 [FIX] FFCentroided replace exception handling with proper check
#914 fix index in CubicSpline2d
#916 IDMapper extension for featureMaps
#917 AccurateMassSearchEngine annotation of input map (not only mzTab output)
#919 [FIX] libc++ test fixes
#920 [FIX] fixed minor problem with knime package generation and cmake versions >2.8.11
#921 MS1 annotation in TOPPView
#922 [FIX] build system improvements
#923 EmpiricalFormula: fix (negative counts were casted away)
#924 Switch to disable tracking of Git version within OpenMS
#925 Fix/small docu improvement
#926 Feature/spellcheck
#927 PeptideIndexer: support for treating isoleucine/leucine as equivalent (resolves #872)
#928 Build System
#929 TextFile feature (skip empty lines) and docu fix
#930 check for missing peaks
#931 fix for evaluation at last node
#936 [FIX] fixed the 'variable' consumption of xslt files for a QcML file.
#938 [FEATURE] precursor scoring
#939 [FIX] fix compile error
#940 coding convention violations in MultiplexClustering fixed
#943 [FIX,PYOPENMS] fix pyOpenMS after #889
#944 [FIX,TOOLS] pyopenms parser fix
#945 [FEATURE] pyopenms wrap improved
#946 OPENMS_DLLAPI removed from GridBasedClustering
#947 [FEATURE] FeatureFinderMultiplex
#949 Fix/xml escape
#950 Feature/traml heavylight
#951 [FIX] add setOptions method for FileHandler
#955 Fix/xml escape
#958 [FIX] disallow concurrent access to the static PRNG
#959 Feature/pyopenms copyconstr
#960 [FEATURE] peptide group label new
#962 [FIX] QCCalculator now computes TIC only on MS1 spectra (fixes #96)
#964 [FIX] check for invalid charge ranges in search engine adapters (see #963)
#965 [FEATURE] tmt 10plex support
#966 [FEATURE] chaining consumer
#967 [FEATURE,TEST] mssim more ground truth in id xml
#968 [FEATURE] export PT value analogous to predicted rt value in TextExporte...
#969 [FEATURE] add a low memory FileConverter option
#970 [FEATURE] test if java can be executed
#972 Fix/file cleanup
#973 [FIX] validate presence of input file before starting executable
#977 [FEATURE] replaced pphires ms1_only flag with ms_levels parameter
#981 Feature/TextExporter_mzML
#983 [FEATURE] add library check on Windows for correct lib arch
#984 [NOP] add heavy methyl SILAC labels to unimod.xml
#985 [FEATURE] bspline support using eol bsplines implementation
#988 [FIX] simplified EmpiricalFormula
#990 [FIX,FEATURE] TransformationModelInterpolated readded
#993 Feature/sort on load (mzML, mzXML)
#994 fixes mass traces in featureXML output
#995 fixes CubicSpline2d constructor exceptions
#996 allow for SplinePackages based on just two data points
#1000 fixes problems with ">>" generated in nested C++ templates
#1001 Fix/py open ms test
#1002 [pyOPENMS] features
#1003 [FIX] fixes random fails of MSSim_test
#1006 [FEATURE] enable gui less OpenMS
#1009 update unimod.xml with newest version from unimod.org
#1010 [FIX] external code tests updated/fixed
#1011 [FIX] external project doc
#1012 [FEATURE] decreased memory footprint of Feature class by up to 44%
#1014 TOPPView: group separator for mz,rt and int values in 1D and 2D canvas
#1019 [FIX] fixed unitybuild problem on win32 with eol-bsplines
#1020 [NOP] updated copyright/license header to 2014
#1021 Feature/py open ms fixes and wraps
#1024 sorting mass shifts in FeatureFinderMultiplex
#1025 Fix/checker fixes
#1026 additional example in SplineSpectrum test
#1027 Adapter for Fido (protein inference engine), solves #808
#1029 [FIX-#184] remove public vector/map inheritance
#1032 fixes peak boundaries in PeakPickerHiRes (resolves #1022)
#1034 [FIX] improve set_peaks documentation
#1035 B-spline interpolation for peak width estimation in MultiplexClustering class
#1036 [FEATURE,API] Removed template parameter from FeatureMap
#1037 Fix/ TraML load/store
#1038 Feature/py open ms wraps
#1039 Fix/debug fix
#1040 Fix/spellcheck
#1044 [FIX:#1043]fixed featureXML reading spectrum_reference as String
#1045 [FIX] fix compile issue on win32 systems
#1046 Fix/py open ms wrap
#1047 [FIX] first probe install path, then the build path for share/OpenMS
#1048 Feature/peptide hit protein locations
#1050 Re-added B-spline transformation for non-linear RT alignment in MapAlignerIdentification
#1051 [FIX] made arguments and functions in BSpline2d const (if possible)
#1055 [FEATURE] improved purity computation for IsobaricAnalyzer
#1056 [FIX] UniqueIdGenerator susceptible to identical RNG seeds
#1057 GenericWrapper doc has minor quirks
#1058 Feature/openswathwf add
#1059 Switch to version 2.0
#1061 FeatureFinderIdentification: documentation, tests, parameter improvements
#1063 Fix/accession nr
#1065 PeakPickerHiRes docu updated
#1067 Testing/mzid
#1069 Fix and test for issue #1068 (bug in "AASequence::operator<" involving N-terminal modifications)
#1070 removing zeros in profile data caused by Thermo bug
#1072 PeakPickerHiRes: disable spacing constraints for chromatograms (fixes #1060)
#1074 'intensity weighted mean'; averaging added to ProteinQuantifier, solves #830
#1076 Adapter for MS-GF+ search engine
#1077 [TESTING] download and add MSGFPlus in travis-ci
#1078 [FEATURE] export aabefore and aaafter in peptideindexer
#1079 Linear extrapolation (and other options) for B-spline transformation
#1080 [NOP] refactored PeptideHit protein accession extraction to true member
#1082 [NOP] removed index file as these are recreated by MSGF+ anyways
#1083 Feature/mz tab fixes
#1084 [FIX] compile fixes
#1086 Update (indistinguishable) protein groups when filtering protein identifications (fixes #748)
#1087 centroided input data for FeatureFinderMultiplex
#1088 Fix FileConverter's "write_mzML_index" flag
#1089 Fix/mzid
#1090 Enable mzIdentML input in IDFileConverter
#1091 Feature/mz tab cleanup
#1092 [NOP] removed unnecessary index files
#1094 [FIX] fixed small bugs preventing a build on windows
#1097 [FIX] consistent use of wildmagic
#1098 Revert "[FIX] consistent use of wildmagic"
#1099 [FIX,BUILD] fix Windows build
#1100 Fix/windows fix
#1101 optimisation for knockout searches in FeatureFinderMultiplex
#1102 Fix/fix spellcheck
#1104 [FIX] fix compile warning from unused variables
#1108 [FIX] fix compile warnings and increase QT min version to 4.6
#1109 [FIX] removed support for multiple id formats in tools without
#1115 fix some windows compile warnings
#1116 fix segfaults in XTandemXMLFile and IsobaricChannelExtractor
#1118 Feature/swath window loader
#1121 [FIX] some VC 2013 static tests fixed
#1122 Fix PeakPicker Wavelet
#1123 [FEATURE] remove PeakType template argument from FeatureFinder
#1124 [NOP] addendum to #1123
#1125 optimisations in FeatureFinderMultiplex
#1126 [FIX] intermediate fix for win32 systems
#1127 [FEATURE] create uncrustify branch
#1128 Fix/RT meta value related bug, removed unused comment
#1131 Make BuildSystem's LibCheck fail-safe
#1135 Fix/ams mz tab export
#1136 [NOP] uncrustified
#1137 [FIX] added -b option to create new branch
#1140 [FIX] fixed bugs in AScore implementation and added deisotoping as
#1141 Fix AccurateMassSearch and visualization
#1145 Fix/spellchecks
#1147 Fix/copyright update
#1150 Added PhosphoScoring tool to TOPP documentation
#1151 Changelog 2.0
#1152 [FIX,PYOPENMS] fix and adopt pyOpenMS
#1153 minor amendmend to last fix (better console output)
#1154 [TEST] fix test
#1156 [FIX-#618] fix spelling errors
#1157 [NOP] correct version in LICENSE file
#1158 [FIX] make identifier of multiple identification runs unique
#1161 pyOpenMS 2.0 features
#1162 [FIX] fixed study variable index start at 1. Added global identifiert to
#1164 [FIX] pepXML does on some occassion contain very small fixed
#1165 Added minimal test cases for checker.php Missing test errors
#1169 [FIX] fixed segfault if searchparam requested on empty proteinids
#1170 [FIX,TEST] FidoAdapter test
#1172 [FIX] fix for the write out of mzid
#1173 [FIX] changed path String parameter to input files
#1174 [TRAVIS] added Fido executables and adapted to new directory structure
#1175 [FEATURE] add ConsensusMap push_back
#1176 [BUILD] added support for new thirdparty executables in KNIME
#1179 [FIX] added missing option to apply e-value filtering
#1180 [FIX] fix toolnames for KNIME packaging
#1181 fixed minor typo in error message
#1184 [FIX] we decided to add the missing struct mapping file and in the
#1185 [FIX] added missing elements and spike ins
#1186 Fix/docu qc mzid
#1187 [FIX] AMS: export observed-Mass in mzTab as well
#1188 [Build] Added support for new third party binaries for dmg packaging. Adapted Li...
#1189 Feature/sn
#1190 [TEST] fix test
#1192 [FIX] HMDB: removed duplicates introduced by including spike ins
#1194 [NOP] removed deprecated qc toppas workflow
#1195 [STYLE] Changed header guards mentioned by checker.php
#1196 [FIX] XTandemAdapter added option to disable isotope error flag
#1198 [TEST] fix
#1199 [TEST,FIX] changing the order of the test fixes the issue
#1201 Fix/lp wrapper param file
#1203 [TEST,FIX] set reasonable comparison tolerance
#1204 Removes debug code from FeatureFinderMultiplex
#1206 [TEST] fix test error
#1212 [FIX] and/or extension to IDFilter: Added support for old target_decoy user param in decoy filtering.
#1213 [DOC] improve linux install doc
#1215 [FIX] export AMS result as valid mzTab
#1218 [FIX] consistent use of wildmagic: TransformationModelLinear
#1219 [FIX] Map index stored as meta value in peptide identification
#1220 change parameter ranges in FeatureFinderMultiplex
#1224 updated KNIME license
#1225 [FIX][TEST] Fido replacing scores
#1226 Ammend to pull request #1212
#1228 [FIX, PYOPENMS] fixed pxd file
#1229 [DOC] merged License.txt and LICENSE for more complete description
#1230 Updated ACTIVE_MAINTAINERS with people commiting, starting in 2012. Remo...
#1231 Added Deuterium and Tritium to Elements.xml, as LIPIDMAPS contains sum f...
#1232 Fix amt
#1237 [FIX] minimum value for max_length should be 0 not -Inf
#1240 [FIX] Fix/id filter blacklist
#1242 Fix amt
#1243 fixes INIUpdater test
#1246 Updated problematic FidoAdapter test (fixes #1171)
#1247 [FIX] added missing function
#1248 [FIX, PYOPENMS] ammend to last commit
#1249 Documentation improvements (and minor fixes)
#1250 Another FidoAdapter test fix
#1253 [FIX] IsobaricAnalyzer: set charge states of consensus features
#1254 [DOC,FIX] Updated CHANGELOG, changelog_helper.sh
#1256 Fix MSGFPlusAdapter running in TOPPAS (mzid output)
#1257 Clean-up of UTILS documentation
#1261 [KNIME] adapted parameter naming for FidoAdapter in KNIME
#1262 IDFilter reports empty results
#1263 [FIX] moved TopPerc to UTILS and changed experimental status of MSGFPlus
#1266 [FIX] ammend to last commit
#1267 [FIX] fix conversion from Feature with Masstraces to MSExperiment
#1269 IsobaricAnalyzer: documentation, warning fix
#1270 [FIX] lexical cast is discouraged. Use of build in functions.
#1273 [FIX][BUILD] Fixes linking issue with boost in UTILS #1272
#1275 [FEATURE] [FIX] mass trace RT spacing
#1283 [PYOPENMS] Better PepXMLFile write support
#1284 [FIX] KNIME execution of MSGFPlusAdapter
#1286 [FIX] set low memory log type correctly
#1290 [FIX, PYOPENMS] fix python binding for MassTrace
#1305 [FIX] Fix/id mapper statistics
#1307 remove OS X specific code for opening folders
#1309 [FIX] Ammend to #1284
#1315 sync develop additions
------------------------------------------------------------------------------------------
---- OpenMS 1.11.1 ----
------------------------------------------------------------------------------------------
Release date: November 2013
OpenMS 1.11.1 is a bugfix release resolving the following issues with OpenMS 1.11:
TOPPAS:
- fixed bug that caused TOPPAS to crash when a connection between nodes was added under certain circumstances
TOPP:
- XMLValidator can now be used on mzML files
- fixed bug in MSSimulator/EnzymaticDigestion where amino acid "U" was leading to crash
- fixed some problems with protein modifications in MascotAdapterOnline
- fixed potential problems of TOPP help screens on small screens / small terminal windows
Build system:
- fixed issues with CMake 2.8.12
- fixed potential clang compile errors
General:
- fixed issues with MIME types in KNIME
Resolved issues:
#606 TOPPAS crashes during creation of certain edges.
#609 MascotAdapterOnline: Problems with modifications
#614 Amino acid "U" leads to crash in MSSimulator/EnzymaticDigestion
#629 OpenMS is incompatible with CMake 2.8.12
#630 Knime mime.types file should have lower case mime type names
#633 ConsoleUtils::breakString triggers uncaught exception if terminal size is too small
------------------------------------------------------------------------------------------
---- OpenMS 1.11 ----
------------------------------------------------------------------------------------------
Release date: August 2013
OpenMS 1.11 is the first release with fully integrated Python bindings (termed pyOpenMS).
For further details, please refer to https://pypi.python.org/pypi/pyopenms
File formats:
- QcML support
- pepXML exported from Mascot (added support)
- mzTab updated to 1.0RC3
- ParamXML updated to v 1.6.2
- support for CTD schema 0.3
- full support of sourceFile tag in mzML (all source files are written, SHA1 support)
TOPPView:
- handle .mzML file with mixed spectra and chromatograms (prefer spectra)
- chromatograms of all types can be displayed (not just SRM)
- link to documentation and webpage fixed
- fix a segfault when loading empty chromatograms into TOPPView
TOPPAS:
- link to documentation and webpage fixed
TOPP tools:
- MODIFIED:
- FeatureLinkerUnlabeledQT: performance (speed and memory) improvement
- FeatureLinkerUnlabeled: performance (memory) improvement (now constant in number of input maps)
- MapAlignerPoseClustering: performance (memory) improvement (now constant in number of input maps)
- EICExtractor: critical bugfix if the input map was not sorted
- PeptideIndexer: by default now demands that the peptide is fully tryptic ("-enzyme:specificity none" restores the old behavior)
- FileFilter: filter MS2 spectra by consensus map feature overlap, collision energy, isolation window width
- ProteinResolver: documentation and interface improvements
- QCCalculator/QCEmbedder/QCExtractor: multiple improvements
- WindowMower: speed improvement (movetype either slide or jump [faster])
- ADDED
- AccurateMassSearch: AccurateMassSearch assembles metabolite features from singleton mass traces.
- IsobaricAnalyzer: Extracts and normalizes isobaric labeling information from an MS experiment. This merges the previous TMTAnalyzer and ITRAQAnalyzer functionality
- QCExtractor: Extracts a table attachment to a given qc parameter
- QCImporter: Embed tables or pictures in QcML
General:
- Python bindings allow full access to the OpenMS API from Python
- TOPPTools now support passing of all parameters on the command line (use --helphelp)
- Better chromatogram support (for NoiseFilterGaussian, NoiseFilterSGolay, PeakPickerHiRes)
Search engine support:
- Mascot 2.4 is now supported
- OMSSAAdapter with improved memory footprint
- N-terminal modifications work now with X!Tandem
Changes to the Build System / Package System:
- shared linking works for all contrib packages with automated detection using CMake find modules
- upgrade of xerces to version 3.1.1
- upgrade of libsvm to version 3.12
Development:
- public inheritance from std::vector and std::set has been reduced in the
OpenMS codebase (removed from ConsensusFeature, FeatureMap, ConsensusMap,
MSExperiment)
- addition of the OpenMS/INTERFACES folder which contains proposed OpenMS
interfaces for reading/writing spectra
Deprecated:
- TMTAnalyzer, ITRAQAnalyzer -> please use IsobaricAnalyzer instead
- Several functions provided by std::vector in the MSSpectrum interface are now
deprecated (e.g. push_back, reserve etc.)
Resolved issues:
#120 Improve visual representation of edges
#151 Optimize time/memory efficiency of critical tools/algorithms
#184 Some OpenMS classes are derived from std::vector
#309 FileConverter puts incorrect/incomplete information in <sourceFile>
#343 OpenMS build system should allow searching for contrib libs also in system paths (e.g., /opt/local/..)
#382 Excessive memory usage by MapAligners and FeatureLinkers
#398 INIFileEditor doesn't save modified values if still in edit mode
#457 Use system libraries instead of contrib
#465 "-debug" option in TOPP tools doesn't show LOG_DEBUG messages
#497 Non-intuitive way to edit parameters in TOPPView/TOPPAS/INIFileEditor
#516 TOPPAS: "Refresh parameters" complains if no input files are present
#517 MSQuantification::load declared but not implemented
#519 Merge ITRAQAnalyzer and TMTAnalyzer
#520 Support linking against shared libs
#521 Upgrade contrib libsvm
#522 Make parameters from subsections addressable from command line
#523 Link to OpenMS website from within TOPPAS/TOPPView broken
#524 PeptideIndexer does not honor cleavage sites
#525 EICExtractor will report wrong intensities if input map is not sorted
#527 pyOpenMS compile issue with clang
#529 Strange naming of TextExporter parameters
#531 Upgrade xerces-c version in contrib to 3.1.1
#533 pyOpenMS
#534 MascotAdapterOnline does not support Mascot 2.4
#535 mzML with Spectra and Chromatograms
#536 MascotAdapterOnline SSL and Mascot 2.4
#537 Invalid Doxygen XML Files
#540 IsobaricAnalyzer
#541 AccurateMassSearch
#542 TOPPView: switch to 3D view should pick the data layer automatically
#544 featureXML version at 1.4 while 1.6 is the current version
#549 Problems converting Mascot XML to idXML
#552 pyOpenMS build system
#553 TOPPView's "Apply TOPP tool" functionality is broken
#554 FeatureLinkerUnlabeled(QT) - speed/memory enhancements
#556 Setting parameter may not take effect
#557 XTandemAdapter/mz-out scramble
#562 cmake doesn't check for MSBuild.exe location on Windows
#565 XTandemAdapter fails to add terminal modifications correctly to X!Tandem search
#569 Segfault of IDEvaluator and IDEvaluatorGUI
#570 FeatureLinkerUnlabeledQT regression
#574 Update ParamXMLHandler to support v1.6.2 of Param schema
#575 Upgrade TOPPBase's CTD support to new version of CTD schema
#576 Cython 0.19 does not compile current pyOpenMS
#578 Add qcML CV terms
#580 XTandemAdapter finds non-tryptic peptides although cleavage rule is set to "[RK]|{P}"
#582 Compile error with Boost 1.46
#583 MascotAdapterOnline with Mascot 2.4.0 may never finish
#584 FileFilter parameter -mz (mz range to extract) applies to all MS levels and not to a specified level
#586 ModificationsDB_test relies on raw memory addresses
#587 MascotAdapterOnline does not support SSL connections
#588 MascotAdapterOnline does not support connections to public MatrixScience Mascot instance
#591 Detection of MGF format via file content fails on our own files
#593 Parameter default of 'tab' will be returned as single space
#598 SILACAnalyzer (no label) crash
#603 TOPPView: showing peptide annotations of feature maps also shows feature indexes
------------------------------------------------------------------------------------------
---- OpenMS 1.10 ----
------------------------------------------------------------------------------------------
Release date: March 2013
OpenMS 1.10 is the first release integrated into KNIME (www.knime.org).
To use OpenMS in KNIME please refer to the www.OpenMS.de for additional information.
File formats:
- TraML 1.0.0 support
- Initial mzQuantML, mzIdentML and mzTab support (not fully supported)
TOPPView:
- Concurrent zoom
- SRM data visualization
New tools:
- Superhirn
- OpenSWATH
- QCCalculator
- IDRipper
- FeatureFinderMetabo
- IDEvaluation
- RNPxl
General:
- Better chromatogram support
- Decoy strings can now be prepended
- Filter modified peptides
- Many memory and speed improvements
- TMT-6plex support
- EDTA conversion from feature and consensusXML in FileConverter
- Filtering of MS2 spectra by identifications
Search engine support:
- MyriMatch adapter
Changes to the Build System / Package System:
- Cpplint coding convention check integrated into build system
- Integration of OMSSA search engine in Windows and Mac installers
- Integration of X!Tandem search engine in Windows and Mac installers
- Integration of MyriMatch search engine in Windows and Mac installers
Development:
- Style corrections of the OpenMS source base using uncrustify
Deprecated:
- Conversion of Sequest files in IDFileConverter
Resolved issues:
#513 Commented out the functionality of smartFileNames_() (not mature enough for the 1.10 release)
#508 allow free columns for TSV
#473 change in/out types again to csv
#507 TOPPDocumenter now expects the path to the executables and can generate doc for TOPPView/TOPPAS on mac osx
#506 added custom info.plist containing the path to OMSSA/XTandem for the GUI tools
#505 goto dialogs now act with error tolerance
#504 Fixed XTandemXMLFile loading when no encoding is given by XTandemXML file by enforcing ISO-Latin-1 (default would be utf-8, breaking the aminoacid sequence readin). Introduced enforceEncoding(encoding) to XMLFile.
#316 SpectraViewWidget is not cleaned up when last layer is deleted
#283 TOPPView: Scan view widget does not clear after closing last file
#379 MapAlignerPoseClustering: -reference:index has no effect
#384 replace zip libraries with The Boost Iostreams Library (already in contrib)
#280 IonizationSimulation_test can not be compiled with OpenMP support on Mac OS X (Unit) Tests
#368 Check Example pipelines and tutorials if they still contain the Tools using the type parameters
#341 Move IMS Mass Decomposition Code to OpenMS and remove IMS from contrib
#330 Remove static references to 10.5 SDK in OpenMS and contrib builds
#135 Remove temporary files after completion
#301 IDExtractor has no documentation
#78 Write generic Nightly Testing Script
#355 Adapt documentation to the changes in the contrib handling of the build system
#348 Update TOPP tool names in documentation
#383 iTRAQ isotope correction & simulation broken for 8plex
#333 CMake returning incorrect configurations.
#378 Intensity issue for simulation of MS2 signals
#264 PrecursorIonSelector crashs (SegFault) with minimal input
#322 PeakPicker (wavelet) writes lots of "dataProcessing" junk to mzML file
#327 Feature width not stored in featureXML
#372 Calculation of rank correlation coefficient buggy
#376 Command line parser does not recognize --help and --helphelp
#374 IonizationSimulation takes ages to complete on very high abundance peptides
#371 FileFilter should support filtering by meta values
#359 Remove type argument from SpectrumFilter
#346 Implement mechanism to convert pre1.9 toppas workflows to 1.9 workflows
#345 Implement mechanism to convert pre1.9 ini files to 1.9 workflows
#212 Nicer formatting of parameter listings in documentation
#356 PeakPickerWavelet fails for broad peaks
#332 TOPPAS: QWebView for downloading pipelines does not work behind proxy
#366 SILACLabeler should adjust all channels to have the same RT elution profiles
#365 Sampling of RT parameters in RTSimulation can produces abnormal RT parameters
#364 Improve handling of user input while downloading workflows from the online repository
#363 TOPP test need to define their dependencies to avoid wrong execution
#360 Remove type argument from FeatureFinder
#357 IDPosteriorError Prob crashes with small number of peptides
#354 Adapt documentation to the changes in the contrib handling of the build system
#344 remove TOPPBase type argument from MSSimulator
#347 Contaminant simulation might produce wrong masses when used in unintended way
#41 AndiMS for 32/64bit Windows and 64bit Linux.
#326 PepXMLFile: use RT of MS2 spectra for peptide RT
#321 Update Seqan to 1.3 Build System
#331 TOPPAS: Active tab changes all the time under MacOSX (10.6 and 10.7)
#106 Export for Workflows as image
#325 No HTML for Internal FAQ
#324 DecoyDatabase should support shuffling and contaminants TOPP
#323 MapAligner -apply_given_trafo's "invert" option only works from commandline TOPP
#209 Reading Bruker XMassFile failes with invalid DateTime String
#236 TOPP tool API change will crash existing TOPPAS pipelines
#282 TOPPAS updateParameters() might create invalid Pipeline
#298 "Open in TOPPView" broken for MacOSX
#320 TOPPAS Workflows should support a short documentation
#318 FuzzyStringComparator::compareLines_ throws exception on gcc-4.6
#317 ostream::operator<< for MSSpectrum is not working
#314 Crash when selecting empty window
#227 TOPPAS tmp directory not multi-user friendly
#178 Warn if merger node is followed by a tool for single files, not lists
#313 MascotAdapterOnline does not support Mascot 2.3
#312 FilterFilter should support filtering by precursor charge
#226 Specific isotopes in ElementsDB are generated with wrong masses
#308 AASequence(iterator, iterator) constructor is invalid, since it ignores terminal modifications
#305 TOPPView fails while opening mzML with intensities stored in an int32 array
#234 File forwarding/merging broken
#303 TOPPAS, TOPPView and ExecutePipeline: looking for TOPP tools
#302 Simulator should support picked peak Ground Truth
#300 Allow input node recycling TOPPAS closed fixed
#299 Enable automatic static code analysis of OpenMS using cppcheck
#205 TOPPAS crashes
#210 TOPPAS Merger nodes are buggy
#259 Resume button broken
#43 Discuss overhaul of OpenMS web site and possible migration to CMS Website, FAQs, Screencasts
#297 Simulation: Ionization does not consider n-term to carry charge
#295 Split OpenMS library in two or more parts
#296 PeptideIndexer might keep 1 old ProteinAccession
------------------------------------------------------------------------------------------
---- OpenMS 1.9 ----
------------------------------------------------------------------------------------------
Release date: February 2012
OpenMS 1.9 has some major changes in TOPP tool names and usage. Therefore all .ini files
for "typed" TOPP tools (i.e. those with a "type" parameter) built with OpenMS 1.8 and below
are incompatible! To fix your old .ini and .toppas files use the new
INIUpdater tool (see its documentation and the TOPP documentation in general).
OpenMS 1.9 removed support for Mac OS X 10.5.
Documentation:
- new Quickstart tutorial
- dedicated and reworked TOPPAS tutorial
TOPPView improvements:
-MODIFIED:
- ConsensusFeatures can now be colored using MetaValues
- better grid line drawing/calculation, extracted AxisPainter class
- IdentificationView:
- added automatic labeling with peptide fragment sequence
- theoretical spectrum is now hidden by default (labeling contains relevant information for most use cases)
- automatic zoom to measured MS2 data range
TOPPAS improvements:
- TOPPAS allows for interactive download of preconfigured TOPPAS pipelines from OpenMS homepage
- "Recycling" mode for nodes, useful for database input files (see docu for details)
- more flexible pipeline design for Merger nodes
- Merger nodes (merge, merge all) renamed to "Merge" (one round) and "Collect" (all rounds)
TOPP tools:
- ADDED:
- MapStatistics: statistics for low level quality control
- EICExtractor: quantify known RT, m/z locations in one or many LC/MS maps and align them
- MassTraceExtractor: annotate mass traces in centroided LC/MS maps - useful for metabolomics and top-down proteomics (use FeatureFinder tools for peptides)
- FeatureFinderRaw: feature finding on raw data
- FeatureFinderMetabo: feature finding for metabolites
- IDConflictResolver: resolve ambiguous annotations of features with peptide identifications
- MODIFIED:
- FeatureFinder: split into FeatureFinderMRM, FeatureFinderCentroided, FeatureFinderIsotopeWavelet
- FeatureLinker: split into FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT
- FeatureLinker tools remove unneeded data after loading featureXML files to conserve memory
- MapAligner: split into MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, and MapRTTransformer
- model parameters of MapAligner tools are now set in the INI file
- MapAlignerIdentification: don't fail if parameter "min_run_occur" is set too high, warn and use possible maximum instead
- NoiseFilter: split into NoiseFilterGaussian and NoiseFilterSGolay
- PeakPicker: split into PeakPickerWavelet and PeakPickerHiRes
- PILISModel: split into PILISModelCV, PILISModelTrainer, and PILISSpectraGenerator
- MascotAdapterOnline: now supports Mascot 2.3 servers
- ProteinQuantifier: added support for writing idXML (suitable for export to mzTab)
- IDFileConverter: when reading pepXML, fail if the requested experiment (parameters "mz_file"/"mz_name") could not be found in the file
- REMOVED:
- AndiMS/NetCDF is no longer supported on any platform
- removed IDDecoyProbability tool
UTIL tools:
- ADDED:
- INIUpdater: update INI and TOPPAS files
- TransformationEvaluation: evaluate a (RT) transformation by applying it to a range of values
- REMOVED:
- CaapConvert
- UniqueIdAssigner
- HistView
Changes to the Build System:
- TOPPAS now requires Qt's Webkit library
- Use CMAKE_BUILD_TYPE instead of OPENMS_BUILD_TYPE (removed)
- Use CMAKE_FIND_ROOT_PATH instead of CONTRIB_CUSTOM_DIR (deprecated)
- Removed AndiMS, NetCDF and dependencies
- Removed dependency to imslib, relevant classes were moved directly to OpenMS/CHEMISTRY/MASSDECOMPOSITION/IMS
- OpenMS now supports ctests functionality for optimized and parallel testing (see ticket #363)
Fixed Issues: (see also http://sourceforge.net/apps/trac/open-ms/report)
#341 Move IMS Mass Decomposition Code to OpenMS and remove IMS from contrib
#330 Remove static references to 10.5 SDK in OpenMS and contrib builds
#301 IDExtractor has no documentation
#78 Write generic Nightly Testing Script
#355 Adapt documentation to the changes in the contrib handling of the build system
#348 Update TOPP tool names in documentation
#333 CMake returning incorrect configurations
#264 PrecursorIonSelector crashs (SegFault) with minimal input
#280 IonizationSimulation_test can not be compiled with OpenMP support on Mac OS X
#322 PeakPicker (wavelet) writes lots of "dataProcessing" junk to mzML file
#327 Feature width not stored in featureXML
#372 Calculation of rank correlation coefficient buggy
#376 Command line parser does not recognize --help and --helphelp
#371 FileFilter should support filtering by meta values
#359 Remove type argument from SpectrumFilter
#346 Implement mechanism to convert pre1.9 toppas workflows to 1.9 workflows
#345 Implement mechanism to convert pre1.9 ini files to 1.9 workflows
#212 Nicer formatting of parameter listings in documentation
#356 PeakPickerWavelet fails for broad peaks
#363 TOPP test need to define their dependencies to avoid wrong execution
#360 Remove type argument from FeatureFinder
#357 IDPosteriorErrorProb crashes with small number of peptides
#354 Adapt documentation to the changes in the contrib handling of the build system
#41 AndiMS for 32/64bit Windows and 64bit Linux..
#326 PepXMLFile: use RT of MS2 spectra for peptide RT
#321 Update to Seqan 1.3
#324 DecoyDatabase should support shuffling and contaminants
#323 MapAligner -apply_given_trafo's "invert" option only works from commandline
#209 Reading Bruker XMassFile failes with invalid DateTime String
#236 TOPP tool API change will crash existing TOPPAS pipelines
#318 FuzzyStringComparator::compareLines_ throws exception on gcc-4.6
#317 ostream::operator<< for MSSpectrum is not working
#297 Simulation: Ionization does not consider n-term to carry charge
#383 Simulation: iTRAQ isotope correction & simulation broken for 8plex
#378 Simulation: Intensity issue for simulation of MS2 signals
#374 Simulation: IonizationSimulation takes ages to complete on very high abundance peptides
#366 Simulation: SILACLabeler should adjust all channels to have the same RT elution profiles
#365 Simulation: Sampling of RT parameters in RTSimulation can produces abnormal RT parameters
#344 Simulation: remove TOPPBase type argument from MSSimulator
#347 Simulation: Contaminant simulation might produce wrong masses when used in unintended way
#303 TOPPAS, TOPPView and ExecutePipeline: looking for TOPP tools
#305 TOPPView fails while opening mzML with intensities stored in an int32 array
#314 TOPPView: Crash when selecting empty window
#205 TOPPAS crashes
#227 TOPPAS: tmp directory not multi-user friendly
#282 TOPPAS: updateParameters() might create invalid Pipeline
#332 TOPPAS: QWebView for downloading pipelines does not work behind proxy
#135 TOPPAS: Remove temporary files after completion
#320 TOPPAS: Workflows should support a short documentation
#298 TOPPAS: "Open in TOPPView" broken for MacOSX
#106 TOPPAS: Export for Workflows as image
#364 TOPPAS: Improve handling of user input while downloading workflows from the online repository
#331 TOPPAS: Active tab changes all the time under MacOSX (10.6 and 10.7)
#210 TOPPAS: Merger nodes are buggy
#259 TOPPAS: Resume button broken
#300 TOPPAS: Allow input node recycling
#234 TOPPAS: File forwarding/merging broken
#178 TOPPAS: Warn if merger node is followed by a tool for single files, not lists
#313 MascotAdapterOnline does not support Mascot 2.3
#312 FilterFilter should support filtering by precursor charge
#226 Specific isotopes in ElementsDB are generated with wrong masses
#308 AASequence(iterator, iterator) constructor is invalid, since it ignores terminal modifications
#302 Simulator should support picked peak Ground Truth
#299 Enable automatic static code analysis of OpenMS using cppcheck
#43 Discuss overhaul of OpenMS web site and possible migration to CMS
#295 Split OpenMS library in two or more parts
#296 PeptideIndexer might keep 1 old ProteinAccession
#379 MapAlignerPoseClustering: -reference:index has no effect
Detailed list of changes to specific OpenMS classes:
- NEW:
- compose_f_gx_hy_t (from imslib)
- compose_f_gx_t (from imslib)
- IMSAlphabet (from imslib)
- IMSAlphabetParser (from imslib)
- IMSAlphabetTextParser (from imslib)
- IMSElement (from imslib)
- IMSIsotopeDistribution (from imslib)
- IntegerMassDecomposer (from imslib)
- MassDecomposer (from imslib)
- RealMassDecomposer (from imslib)
- Weights (from imslib)
- sum/mean/median functions added to header "StatisticFunctions"
- PeptideAndProteinQuant: contains quantification code formerly included in ProteinQuantifier (TOPP tool)
- MODIFIED:
- AASequence: removed AASequence(ConstIterator, ConstIterator) constructor, since it ignored Terminal Modifications; since there was no way to enable correct construction from two Iterators, we removed it
- MapAlignmentAlgorithmIdentification: don't fail (exception: InvalidParameter) if value for "min_run_occur" is too high, warn and use possible maximum instead
- MSSimulator: "type" parameter moved to "MSSim:Labeling:type"
- Param: added new command line parser with improved functionality
- PepXMLFile:
- added reading support for pepXML version 1.17
- set RT's of peptide identifications based on MS2 spectra, not the MS1 precursors as before (flag "use_precursor_rt" switches to the old behavior)
- fail with ParseError if a requested experiment could not be found in a pepXML file
- ProtXMLFile: set score type for peptides
- TOPPBase: added methods to turn Param objects into command line parameters
- TransformationModel: simplified handling of parameters
- TransformationModelBSpline: new option to distribute breakpoints evenly at data quantiles (instead of uniformly over the data range)
- lots more... too much to list
------------------------------------------------------------------------------------------
---- OpenMS 1.8 ----
------------------------------------------------------------------------------------------
TOPP tools:
- MODIFIED:
- MapAligner: separated data extraction from transformation modelling - this allows to combine different algorithms and models; new option "invert"; reworked parameters (please see the MapAligner documentation and update your INI files)
- FeatureLinker: now able to link consensus maps; added new experimental algorithm "unabeled_qt"; improved quality calculation in "unlabeled" algorithm
- IDMapper, FeatureLinker ("unlabeled"/"unlabeled_qt" algorithms): now consider charge states by default (use parameter "ignore_charge" if you want to avoid this)
- FileInfo: improved formatting of output
- TextExporter: unified output formats
- FileConverter: added conversion to consensusXML
- ProteinQuantifier: redefined meaning of parameter combination "top 0"/"consensus:fix_peptides"
- ITRAQAnalyzer: isotope corrected quantitation result is written to "-out" instead of the uncorrected values
- GenericWrapper: now supports arbitrary external programs, when a .ttd file is present (see <OpenMS>/share/OpenMS/TOOLS/EXTERNAL)
UTIL tools:
TOPPView improvements:
- NEW:
- Identification View (load idXML through Tools->annotate with identifications)
- 1D view now supports vector graphics export when saving an image
- Peaks in 2D view are drawn as circles at a high zoom level
- TOPPAS pipelines can be edited and run directly from TOPPView
TOPPAS improvements:
- MODIFIED:
- improved stability when using longer filenames
- minor fixes (see bug tickets below)
OpenMS library improvements:
- Stability and consistency fixes mostly (see bug tickets below)
Changes to the Build System:
- minor only
Fixed Issues:
#277 Crash upon annotation with idXML
#271 Filename generation in TOPPAS broken
#278 TOPP tools update only values from INI files, not restrictions
#273 TOPPAS appends an extra "toppas" when saving files with uppercase TOPPAS extension
#272 TOPPAS doesn't update the tab title after saving a new pipeline
#261 ProteinQuantifier: handling of mod. peptides during protein quantification
#153 "Unlabeled" FeatureLinker produces quality values that make no sense
#220 TOPPAS: mzML.gz files are not recognized as correct input
#260 InclusionExclusionListCreator creates invalid lists for Thermo instruments
#269 OMSSAAdapter crashes when run from directory containing spaces
#267 bug in StablePairfinder (distances)
#266 TOPPAS "store" button for vertex' INI files always writes default INI
#129 TOPPAS: Allow opening files in one layer
#105 TOPPAS: Split TOPPAS.ini into Resource and Workflow files
#262 PrecursorIonSelector handles input/output arguments incorrectly
#100 TOPPView memory consumption high when copying data
#257 CLang++ crashes with "SCEVAddRecExpr operand is not loop-invariant!" on EnzymaticDigestion
#233 TOPPView's updateLayer does not reload all data
#247 TOPPView: crashes if file is deleted while opened
#66 "Tools -> Go to" coordinates should default to current view
#239 seg. fault when loading featureXML into TOPPView from the wrong context
#221 TOPPView: when loading a new layer, the zoom should not reset
#222 IDMapper should support mapping charge-matched entities only
#255 TOPPView's Projection is showing only single peaks at high zoom
#253 TOPP tools should be able to write their type into ini file, without knowing it a priori
#252 OMSSAAdapter crashes when v2.1.7 and 'precursor_mass_tolerance_unit_ppm' are used
#251 XTandem Adapter ignores "no_refinement" flag
#198 add Proteowizward to Windows binary installer
#246 TOPPView: Update Layer broken
#149 Support external tools not derived from TOPPBase
#245 PeptideIndexer fails on ambiguous AA's
#244 merging by Precursor in SpectraMerger
#242 Protein coverage should be reported
#237 RT corrections via BSpline transformation is unreliable for sparse regions (e.g. borders and extrapolation)
#235 TOPPAS input file name lists should be sorted
#231 FeatureFinder has faulty Averagine model
#229 Digestor UTIL cannot write FASTA output
#27 generate publication ready figures in SVG format - 1D view
#215 FeatureFinder crashes with Segmentation fault
#213 TOPPView crashs when loading mzML and featureXML
#224 PepXMLFile produces invalid files (mod_aminoacid_mass position is 1-based)
#225 msInspect pepXML parser can not handle OpenMS pepXML due to massdiff attribute
#223 TOPPAS restores wrong parameter name when deleting an input/output edge
#217 Caching in LogStream is not thread safe
#218 FF should work on non-sorted data, but gracefully exit on negative m/z values
#214 MapAligner crashes on certain data
#211 TOPPAS: IDFilter RTPredict linking not possible
#150 TOPPAS does not use user environment to find executables
#208 Windows: hide extra console window when starting GUI apps
#207 Projections show wrong axis names
#179 adapt to command/console width
#206 Parameter names should include subsection
#204 TOPPView "Go To" Dialog should support UniqueID's
#202 "Open file" dialog: "readable files" should include .gz files
#191 changing from 1D to 2D,3D View and 3D to 2D if MS1 spectra are present
#196 NoiseFilter, PeakPicker, BaselineFilter crash on certain input-data
Detailed list of changes to specific OpenMS classes:
- NEW:
- BaseFeature: parent of Feature and ConsensusFeature
- FeatureGroupingAlgorithmQT, QTClusterFinder, QTCluster, GridFeature: feature grouping for unlabeled data based on QT clustering
- FeatureDistance: distance measure for features
- TransformationModel: different models for retention time transformations
- SvmTheoreticalSpectrumGenerator: simulator for MS/MS spectra
- MODIFIED:
- Feature, ConsensusFeature: moved common parts to BaseFeature
- StablePairFinder: moved distance calculation to FeatureDistance
- TransformationDescription: reworked, some functionality moved to TransformationModel
- all MapAlignmentAlgorithm... classes, PoseClustering[Affine/Shift]Superimposer, TransformationXMLFile, InternalCalibration: adapted to changes in RT alignment/transformation modelling
- FeatureGroupingAlgorithm: support linking of consensus maps; new algorithm "unlabeled_qt"
- BaseGroupFinder: new algorithm "qt"
- IDMapper: consider charge states for matching
- PepXMLFile: use E-value (instead of hyperscore) as score for X! Tandem results
- FileHandler: accept endings ".pep.xml" and ".prot.xml" for pepXML/protXML
- FeatureMap, ConsensusMap: "clear" also clears meta data by default
- ConsensusMap: adapted signature of "convert" for feature maps (to mirror that for peak maps)
- Param: remove() and ::removeAll() now delete empty nodes which have no subnodes nor entries (otherwise writing paramXML breaks)
- TheoreticalSpectrumGenerator: getSpectrum() now generates all selected ion types not only b- and y-ions
------------------------------------------------------------------------------------------
---- OpenMS 1.7 ----
------------------------------------------------------------------------------------------
Release date: Sep 5th 2010
TOPP tools:
- TOPP tool categories have been reorganized
- TOPP documentation now has a predecessor/successor tool section and uniform algorithms subsection parameter documentation
- MODIFIED:
- IDFilter: reworked parameter names and documentation (please see the IDFilter documentation and update your INI files)
- IDMapper: reworked parameter handling (please see the IDMapper documentation and update your INI files)
- FileMerger: can now merge featureXML
- IDMerger: new option to integrate data from pepXML and protXML
- MapAligner: improved handling of reference files, added several options to the "identification" algorithm
- SeedListGenerator: new option to use monoisotopic peptide mass instead of precursor m/z for seeds from idXML input
- Resampler: PNG image creation functionality removed and transferred to ImageCreator UTIL
- FeatureFinder: deprecated algorithms "simple" and "simplest"
- FeatureLinker: deprected algorithm "identification"
- NEW:
- ProteinQuantifier: compute protein/peptide abundances from annotated featureXML or consensusXML files
- GenericWrapper: wrap external programs (e.g. ProteinProphet) in TOPPAS
- ConsensusID: [rewritten] combine several peptide search engine results to improve precision and recall
- InclusionExclusionListCreator: creates inclusion or exclusion lists for MS/MS based on identifications, feature maps or protein databases
- REMOVED:
- TextImporter (functionality moved to FileConverter)
UTIL tools:
- MODIFIED:
- DecoyDatabase now uses "_rev" as decoy string by default (previously: "_ref"), as required by PeptideIndexer by default
- MSSimulator provides a framework for the simulation of labeled data (#88)
- NEW:
- ImageCreator: creates PNG's from MS maps
- IDSplitter: splits peptide/protein annotations off of data files (inverse operation as IDMapper)
- MassCalculator: calculates masses and mass-to-charge ratios of peptide sequences
OpenMS library improvements:
- read protXML files
- support protein groups in ProteinIdentification/idXML
- line numbers in errors of Textbased files (most formats: dta, dta2D, FASTAFile, PepNovoOutfile, MascotGenericFile, MS2File, MSPFile, OMSSACSVFile, TextImporter (csv, msInspect, SpecArray?, Kroenik))
- FeatureFinderAlgorithmPicked is now able to fit asymmetric retention time profiles (experimental)
- added generic labeling framework to SIMULATION (#88) (experimental)
TOPPView improvements:
- basic visualization of peptide identifications in idXML
- when the amount of loaded data causes memory depletion, an error is issued and TOPPView does not crash (only a problem on 32bit systems)
- zooming beyond the last zoom stack item using the mouse wheel or CTRL+
TOPPAS improvements:
- added copy/paste for workflow items
- workflows can now include other workflows (File>Include)
- several bug fixes
- split TOPPAS in TOPPAS and PipelineExecute TOPP-tool
Changes to the Build System:
- external code support for CMake 2.8:
External code using "include (${OpenMS_USE_FILE})" in its CMakeLists.txt cannot be configured against OpenMS 1.7, however, only minor changes are required to fix this. See the documentation for "Programming with OpenMS".
- nightly tests for external code
- SVN revision used to build the lib is remembered (finer version tracking)
- nightly coverage builds
- GUI testing (experimental)
- Visual Studio 2010 support
- building on Mac OS X requires CMake 2.8.1 due to bugs in CMake < 2.8.1
Fixed Issues:
[new tracker: http://sourceforge.net/apps/trac/open-ms/query?status=closed&group=resolution&milestone=Release+1.7]
- #23 implement protXML
- #44 TOPPView warning "Cannot show projections!"
- #46 All TOPP/UTILS segfault if /share is not found
- #53 TOPPAS select directory has save as dialog
- #54 TOPPAS select directory has save as dialog
- #56 TOPPAS context menu "open in TOPPView" does not work under MacOSX
- #58 Unit tests for nested classes
- #59 Test of external Code
- #61 automatic ini file Version number update
- #62 nightly tests for external code
- #63 rename methods named min() or max() to something else...
- #64 TOPPView - update_layer reload is incomplete
- #69 FileMerger needs ability to merge featureXML
- #73 Resampler: can't create PNGs with TOPPAS
- #74 Default parameters of PTModel cause infinite loop
- #76 Add deployment target for compatibility with older MacOSX versions
- #77 FuzzyDiff always returns 'true' when comparing any two PNG images
- #81 Terminal modification with residue specificity
- #85 IDMapper will crash on negative RT's or big deltas
- #87 Gzipped files work as input, but arrow stays red
- #88 Implement Labeling Framework for MSSimulator
- #90 Quantification on protein level
- #91 Simple FF crashes on very sparse data
- #92 Encoding of XML files (invalid multcharacter)
- #93 TOPPAS layer bug
- #98 display RT value when viewing 1D data
- #104 Split TOPPAS in TOPPAS and PipelineExecute TOPP-tool
- #110 "Copy&paste, include workflows in current window"
- #121 Tool categories and menu items in context menus have arbitrary order
- #122 Projection view: mouse-over text on RT projection says "m/z"
- #123 Reorganize TOPP tool categories
- #124 TOPPAS fails to load files correctly
- #127 catch out-of-memory exceptions in TOPPView
- #131 TOPP input files check too restrictive...
- #132 check all system calls
- #133 Textexporter runs indefinitely when input has no IDs and -consensus_features as output
- #134 [Windows] failure of TOPP tools in TOPPAS due to _out and _temp directory not writeable
- #136 TOPPView: #of Isotopes in TheoreticalSpectrumGenerator not forwarded
- #137 Implement asymmetric elution profile shapes for model fitting in FeatureFinderAlgorithmPicked
- #141 CMake 2.8.1 causes linker errors on Mac OS 10.6.3
- #143 Incompatibility between String and string methods
- #147 Internal Compiler Error with gcc 4.3
- #152 Remove/hide deprecated algorithms
- #154 Update TOPPAS workflows params
- #155 linking OpenMS.so using a relative contrib directory fails
- #156 use MSBuild instead of devenv for contrib building on Windows
- #158 FeatureFinder (centroided) might crash on certain input
- #159 IDMapper will crash when given empty FeatureMap
- #161 TOPPAS Output file naming can lead to wrong "merge all" behaviour
- #163 rework IDFilter
- #164 DecoyDatabase creates faulty protein names by default
- #170 TheoreticalSpectrumGenerator computes wrong prefix/suffix masses
- #171 Remove/hide entire deprecated tools
- #175 Internal Compiler error in BaseModel/FeatureFinder
- #182 INIFileEditor crashes upon execution
For more minor bugfixes visit the above URL.
Detailed list of changes to specific OpenMS classes:
- ConsensusMap, FeatureHandle, ConsensusFeature:
- element index replaced by unique id
- DPosition:
- min() renamed to minPositive()
- min_negative() to minNegative()
- DIntervalBase
- min() renamed to minPosition()
- max() renamed to maxPosition()
- String
- removed:
String substr(SignedSize start, SignedSize n) const;
String substr(SignedSize start) const;
- added:
String substr(size_t pos = 0, size_t n = npos) const;
String chop(Size n) const;
------------------------------------------------------------------------------------------
---- OpenMS 1.6 ----
------------------------------------------------------------------------------------------
Release date: Nov 19th 2009
Main improvements of TOPPView:
- Storing peak data is now possible in mzData, mzXML and mzML format
- Feature and consensus feature peaks are now configurable (icon and size)
- Added new label mode for feature layers: all peptide hits of a feature are displayed
- Added visualization of unassigned peptide hits for feature layers
- Measuring to arbitrary end points is now supported in 1D and 2D view
- file load progress bar stays responsive under load on Windows
- rudimentary chromatogram support
Main improvements of TOPP-Framework:
- Major update of TOPPAS
- TOPP tools now warn when used with parameter files from a different version
- Combining '-write_ini' and '-ini' option now allows to transfer settings with identical
path and names from an old ini file into a new one.
New TOPP tools:
- SeedListGenerator
- generates seed lists for feature detection (still experimental)
- PrecursorMassCorrector
- update precursor m/z information of MS/MS spectra based on MS1 peptide isotope fits
(still experimental)
Main improvements of TOPP-Tools:
- all tools:
- gzipped and bzipped XML files (e.g. mzML) can be directly read
- FeatureFinder
- Centroided
- supports parallel execution now
- supports user-specified seeds now
- Wavelet: removed (Isotope-Wavelet is still available)
- FileMerger: accumulated processingMethod entries, which all contained the same
information
- IDMapper
- has new default m/z tolerance and uses ppm as new default measure! Da is still
supported.
- referenze m/z of ID can now be either: 1) precursor mass, 2) [new] mass of identified
peptide
- assigns more peptides to features with convex hulls (the deltas are used)
- InternalCalibration
- supports calibration functions calculated seperately for each spectrum or one global
function
- supports peptide ids as reference peaks
- works on peak or feature data now
- MapAligner
- new "identification" algorithm for alignment based on identified peptides
(still experimental)
- PeakPicker
- support for automatic estimation of peak width
- TextImporter can now import Koenik(Hardkloer) feature files
- TextExporter
- added option for string quoting
- improved export of consensusXML
- PepNovoAdapter: complete rewrite of the code, including classes
New UTILS:
- UniqueIdAssigner can be used to assign unique ids to FeatureXML and ConsensusXML files
Main improvements of UTILS:
Main improvements of OpenMS C++ library:
- MGF file creation speedup (also affects some TOPP tools)
- removed FeatureFinder-Wavelet (IsotopeWavelet is still available)
- support for bzip2 and gzip compressed XML files
- chromatogram support
- comments and other strings of XML writers are now escaped to prevent reading problems
- fixed IdXMLFile segmentation fault if no protein identification given
Detailed list of changes to specific OpenMS classes
- [New classes]:
- UniqueIdGenerator, UniqueIdInterface, UniqueIdIndexer
- SVOutStream
- MapAlignmentAlgorithmIdentification
- SeedListGenerator
- [Removed classes]:
- FeatureFinderAlgorithmWavelet
- [Renamed classes]:
- IDTagger -> DocumentIDTagger
- String:
- improved behaviour of split(...) method
- added support for quoting and unquoting of strings
- ConsensusMap: added clear(...) method
- IDMapper:
- uses bounding boxes of mass traces instead of convex hulls now
- the given deltas are used for features with convex hulls as well
- PoseClusteringShiftSuperimposer:
- full rewrite, uses a similar algorithm like PoseClusteringAffineSuperimposer now
- TranformationDescription:
- added cubic b-spline transformation
- PairsType uses DoubleReal instead of Real now, thus can be used for m/z as well
- VersionInfo:
- includes (if available) SVN revision number that the library is build upon via support
by the build system
- SVN revision information is displayed in the TOPP tools help text
- PepXMLFile: improved handling of PTMs
Changes to the Build System:
- unit tests are now in a separate sub-project in <OpenMS/source/TEST/> avoiding huge
Solution files in MSVC IDE
- new targets: test_build, tutorials_build, tutorials_exec
- SVN revision (if available) is determined and compiled into OpenMS before the library is
built
- added real install prefix and install target to be able to do a 'make install'
Changes to OpenMS XML formats:
- FeatureXML and ConsensusXML files use unique ids now instead of running indices. New XML
Schema versions: 1.4
Changes to the contrib package:
- updated GSL to version 1.13
- updated SVM to version 2.89
- added Z lib and bz2 lib
Bug fixes:
[old tracker: http://sourceforge.net/tracker/?func=detail&aid=2857130&group_id=90558&atid=1059012]
- [2857042]: RTModel/PTModel unable to find modification
- [2857040]: Modification names with brackets fail to parse
- [2849215]: OMSSAAdapter fails with Acetlyation not found
- [2849201]: Parameters in INI files are duplicated
- [2849439]: Compilation error with Qt 4.3.x
- [2900457]: idXML files with more than ProteinIdentification might be incorrect
[new tracker: http://sourceforge.net/apps/trac/open-ms/query?status=closed&group=resolution&milestone=Release+1.6]
- #29: FilerMerger accumulates processingMethod entries
- #28: Segfault if idXML file does not contain a protein identification.
- #24: XML formats are written with unescaped special chars like "&"
------------------------------------------------------------------------------------------
---- OpenMS 1.5 ----
------------------------------------------------------------------------------------------
Main improvements of TOPPView:
- Added new labeling options for feature data
- Fixed crash when zooming in snap-mode
- Added context menu to spectra selection bar
- Feature editing mode can be enabled/disabled in the context menu (to avoid accidental editing)
- Several minor fixes and improvements
Main improvements of TOPP:
- Made mzML 1.1.0 the default format for all TOPP tools
- Added data processing information to all output files to improve traceability
- FileFilter:
- added 'sort_peaks' option
- added filtering according to scan type
- added filtering according to activation type
- FileInfo:
- added flag for data processing output
- corrupt data checks: sorting is checked now, improved speed
- Added new tool IDFileConverter, which can convert between identification file formats
- Added TOPPAS, a tool for visual creation and execution of TOPP pipelines (beta)
- TextImporter can now import SpecArray and msInspect feature files
- Added CompNovo, a de novo identification tool for combined CID/ETD experiments
- MapAligner uses a new algorithm for pose clustering with less parameters
Main improvements of UTILS:
- Added PeptideIndexer, assign proteins to peptides including target/decoy specification
- Added MRMPairFinder, ERPairFinder to extract ratios of labeled experiments
- Added IDMassAccurracy, given mzML files and identification, it calculates distributions of mass deviations
- Added MapAlignmentEvaluation, a tool to evaluate alignment results
- Added MSSimulator, a highly configurable simulator for mass spectrometry experiments
Main improvements of OpenMS C++ library:
- mzML 1.1.0 support
- Improved the precision of mass values in several file formats
Detailed list of changes to specific OpenMS classes
- New classes:
- CompNovo-classes
- StablePairFinder, which is now used by MapAligner and FeatureLinker
- Simulation-classes
- Removed classes:
- FeatureFinderAlgorithmWatershed
- PeakIcon
- FactoryProduct (replaced by DefaultParamHandler)
- DSpectrum (all the functionalty was moved to MSSpectrum)
- Renamed and moved classes:
- moved PersistentObject from FORMAT/ to FORMAT/DB/
- renamed PepXMLFile to PepXMLFileMascot
- Changes to Classes:
- MSExperiment: added 'isSorted' method
- MSSpectrum:
- added 'isSorted' method
- renamed MetaDataArray to FloatDataArray
- added IntegerDataArrays
- added StringDataArrays
- DataValue: added constructor for 'std::string' and QString
- MetaInfo: 'setValue' method takes only DataValue now
- MetaInfoInterface: 'setMetaValue' method takes only DataValue now
- Param: 'setValue' method takes only DataValue now
- ExperimentalSettings: moved DataProcessing to SpectrumSettings (for mzML)
- Precursor: supports multiple dissociation methods now (for mzML)
- MetaInfoDescription: removed comment and source file; added data processing (for MzML)
- ElementDB: isotopes are now possible
- EmpiricalFormula: isotopes are now possible (e.g. (2)H for deuterium)
- ModificationsDB: switched completely to UniMod (www.unimod.org). PSI-MOD still provided for convenience
- PepXMLFile: added new 'load' method (moved the old 'load' method to PepXMLFileMascot)
- TextFile:
- is now derived from StringList
- the 'asString' method was replaced by 'concatenate' from StringList
- MzMLFile:
- added support for integer and string binary arrays
- added support for compressed binary data arrays
- loading a file with unknown CV terms in certain tags no longer causes an error
- DBConnection:
- The 'executeQuery' method no longer sets the internal pointer to the first record of the result.
It is now positioned before the first record. A boolean flag can be used to switch to the old behaviour.
- SourceFile: changed native ID type to string
- PoseClusteringAffineSuperimposer: full rewrite, not using CGAL
Changes to the contrib package:
- Added CoinMP 1.3.3
- Added IMSlib 0.1.0
- Update Xerces-C to revision 806068 of SVN trunk
Bug fixes:
- [2778461]: mzData files containing 'supDataArray' elements no longer crash OpenMS
- [2777173]: TOPPView 2D view projections no longer forget the draw mode on repaint
- [2776386]: TOPPView snap-to-max intensity mode no longer crashes with empty spectra
- [2775912]: PeakPickerCWT no longer assigns RT=-1 to MS/MS spectra
------------------------------------------------------------------------------------------
---- OpenMS 1.4 ----
------------------------------------------------------------------------------------------
Main improvements of TOPPView:
- Drag-and-drop is now supported from the layer bar, spectrum bar and for files from the operating system
- Improved visualization of very high-resolution data
- Improved painting speed of 2D view
Main improvements of TOPP:
- Added new tool TextImporter, which can convert text files to featureXML
- TextExporter can now export peptide/protein information stored in consensusXML
- PeakPicker: reduced the number of parameters, added parallization support
- FeatureFinder: added new MRM algorithm and removed the tool 'FeatureFinderMRM'
- FileInfo: added support for idXML
Main improvements of OpenMS C++ library:
- mzML 1.1.0 RC5 support
- removed support for external memory (use the 64bit builds if you want to process large datasets)
- added support for three kinds of parallization architectures
- OpenMP
- Intel Threading Building Blocks
- Nvidia Cuda
Detailed list of changes to specific OpenMS classes:
- SpectrumSettings: several precursor peaks are now supported, added product list
- Precursor: complete rewrite for better support of mzData, mzXML and mzML
- PeakPickerCWT: cleaned up interface, improved meta data handling, improved parameters, added parallelization support
- GaussFilter: cleaned up interface, improved meta data handling
- SavitzkyGolayFilter: cleaned up interface, improved meta data handling
- MorphologicalFilter: cleaned up interface
- LinearResampler: cleaned up interface
- LabeledPairFinder: estimated negative sigma values are now treated as positive values
- FeatureFinder: added new algorithm 'MRM' for MRM feature detection; replaces FeatureFinderMRM
- ExperimentalSettings: remove native ID type (for mzML support)
- SourceFile: added native ID type (for mzML support)
- File: replaced vector<String> by StringList in all methods
Bug fixes:
- [2645436]: TOPPView - Data Filter for "Size" not available
- [2645510]: OpenMS - libOpenMS.so is built but linking fails (TOPP, tests) (on Debian "Lenny")
- [2665055]: FileFilter ignores -sort option for FeatureXML and Consensus
- [2659013]: windows contrib can fail when copying compiled libraries
- [2606068]: TOPP tools with list parameters do not work with INI files
- [2690367]: Protein references missing on peptide identifications
------------------------------------------------------------------------------------------
---- OpenMS 1.3 ----
------------------------------------------------------------------------------------------
New features and improvements of OpenMS:
- The build system is now based on CMake - supporting Linux, MacOS and Windows.
- Finalized mzML implementation (version 1.1.0 RC4)
- previously unsupported parts
- indexed mzML
- semantic validation (see FileInfo)
- Kernel: Replaced comparators NthPositionLess by the comparator(s) RTLess and/or MZLess.
- Kernel: Replaced methods sortByNthPosition() by the method(s) sortByRT() and/or sortByMZ().
- Improved the framework for meta data visualization.
- Several extensions to the meta data classes were made for mzML compliance.
- The macros used for unit testing in source/TEST have been revised.
- More consistent handling of single vs. double numeric precision, esp. in file output.
- Added ANALYSIS/PIP/PeakIntensityPredictor class for peak intensity prediction (contributed by Alexandra Scherbart).
- Added support for Intel Compiler versions 10 and 11
- Added support for Qt up to 4.5 rc1
New features and improvements of TOPP:
- Added SILACAnalyzer: A specialized tool for quantitation of SILAC experiments (contributed by Lars Nilse).
- Added ITRAQAnalyzer: A specialized tool for quantitation of ITRAQ experiments.
- Added IDMapper: Assigns protein/peptide identifications to features or consensus features.
- FeatureLinker: Added automated RT parameter estimation for 'labeled' algorithm.
- MapAligner: Added spectrum_alignment and apply_given_trafo, IdXML is supported.
- Resampler: This tool is now used for resampling raw data instead of resampling in NoiseFilter or BaselineFilter.
- FileInfo: The option '-v' now also does a semantic validation of mzML files.
- FileMerger: Improved interface
- ConsensusID: Now also supports consensus identification of features and consensus features.
- INIFileEditor: Support for string/int/double lists and input/output files was added.
- Added PrecursorIonSelector: A tool for result-driven precursor ion selection.
- FalseDiscoveryRate: corrected FDR calculations and added optional support for q-values
- Added MascotAdapterOnline: which allows queries to Mascot via network (together with Daniel Jameson)
New features and improvements of TOPPView:
- Added functionality for editing feature data
- Added support for consensus features (consensusXML)
- Added measuring and generic annotations to 1D view
- Several minor interface improvements and bugfixes
Changes to OpenMS XML formats:
- ParamXML:
- Restrictions in Param .ini files are represented by 'min:max' instead
of 'min-max' now, to avoid issues with small (1e-06) and negative numbers.
- Replaced 'advanced' attribute by the more general 'tags' attribute.
- Added support for float, int and string lists
- featureXML:
- Added tag <subordinate> to store competing features that did not qualify for the final map
- Removed <description> section
- Added document identifier
- Added protein and peptide information
- consensusXML:
- Added document identifier
- Added protein and peptide information
- idXML:
- Added document identifier
Changes to the contrib package:
- The build system is now based on CMake - supporting Linux, MacOS and Windows.
- Updated SeqAn package to revision 2666 (this fixes the STL debug error)
- Updated xerces-c to version 3.0.0
- Updated boost to version 1.37.0
- Downgraded GSL to 1.8 (because of Mac/Windows support)
Detailed list of changes to specific OpenMS classes:
- Renamed and moved classes
- Renamed MSMetaDataExplorer to MetaDataBrowser
- Renamed ProcessingMethod to DataProcessing
- Moved XMLValidator from FORMAT/ to FORMAT/VALIDATORS/
- Removed classes
- DPeakArray (moved the functionality to the classes that inherited from it)
- IDSpectrumMapper (replaced by IDMapper)
- IDFeatureMapper (replaced by IDMapper)
- FeatureXMLHandler (merged into FeatureXMLFile)
- ConsensusXMLHandler (merged into ConsensusXMLFile)
- PeakPicker (merged into PeakPickerCWT)
- MorphFilter (merged into MorphologicalFilter)
- TopHatFilter (merged into MorphologicalFilter)
- New classes
- DATASTRUCTURES/IntList
- DATASTRUCTURES/StringList
- ANALYSIS/ID/IDMapper
- ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmApplyGivenTrafo
- ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmSpectrumAlignment
- Changes to classes
- InstrumentSettings
- Revisited scan modes
- Added bool member for zoom scans (no longer a scan mode)
- MassAnalyzer: Removed tandem scanning method. This is stored in the ScanMode of InstrumentSettings.
- DataProcessing: Now contains Software and can handle multiple processing actions.
- Software: Only contains name and version now.
- SourceFile: Added MetaInfointerface and checksum type
- ContactPerson: Added URL and address
- Instrument:
- Can contain multiple detectors and multiple ion sources now
- Added Software
- Added ion optics type
- AcquisitionInfo: Added MetaInfoInterface
- Acquisition: integer 'number' member was changed to a string 'identifier' (for mzML)
- ExperimentalSettings
- Now contains multiple SourceFiles and DataProcessings
- ExperimentType was removed
- SpectrumSettings
- Added nativeID (from acquisition software)
- DSpectrum
- The peaks are no longer stored in a container member, but DSpectrum is derived
from std::vector<PeakType>.
- The container type is no longer a template argument. Peak type and allocator type
are the new template arguments.
- LabeledPairFinder: Added automated RT parameter estimation.
- GaussFitter: Removed several unneeded methods.
- GammaDistributionFitter: Removed several unneeded methods.
- DataValue: Added support for IntList and DoubleList types
- Param:
- Added a new remove(key) method, that removed only exact matches.
The old remove() method was renamed to removeAll(prefix)
- Replaced 'advanced' flag by a generic tagging mechanism
- Added support for IntList and DoubleList types
- File: find(...) now throws an exception, of the file is not found.
- DPeak and DRichPeak are metafunctions now, e.g. DPeak<1>::Type is a typedef for Peak1D.
- VersionInfo: Added support for SVN revision info. Slight interface changes.
- TOPPBase: Print revison info (if meaningful).
- MetaInfo: Uses double precision now.
- Date
- get() now returns a string instead of modifying a string reference.
- Made today() is static now and returns the current DateTime instead of modifying the object.
- DateTime
- get(), getDate() and getTime() now return a string instead of modifying a string reference.
- Made now() is static now and returns the current Date instead of modifying the object.
- MSExperiment: The date is now a DateTime object.
- ProgressLogger: Nested application uses indentation.
- XMLValidator: The output stream for error messages can now be set in the isValid(...) method
- XMLFile: The output stream for validation error messages can now be set in the isValid(...) method
- MzMLFile: The output stream for validation error messages can now be set in the isValid(...) method
- IdXMLFile: Adden document identifier to the load(...) and store(...) method
------------------------------------------------------------------------------------------
---- OpenMS 1.2 ----
------------------------------------------------------------------------------------------
New features and improvements of OpenMS:
- GCC 4.3 is now supported (GCC 3.4 and 4.0 are no longer supported)
- Added support for GCC STL debug mode (configure option --enable-stl-debug)
- Complete reimplementation of map alignment and feature grouping classes.
This affected some classes in KERNEL and nearly all classes in ANALYSIS/MAPMATCHING.
The affected classes are not listed in detail here.
- Added meta data arrays to spectra as the new standard way of handing peak meta information
- Improved interface of SpectrumCanvas and derived classes for easier reuse outside of TOPPView
- Added support for arbitrary modifications to peptide/protein modifications (based on PSI-MOD)
- Exceptions thrown by member functions are no longer declared in the header files.
They are however documented in the class documentation.
- Added *beta* support for the HUPO PSI format mzML
Currently only reading is supported and some features are not implemented yet
e.g. chromatograms, zlib compression of base64 data, base64 integer data, base64 16 bit data
- Added the UTILS package, a bundle of small helper tools.
- Changed handling of amino acid sequences and modifications. Modifications are taken from
PSI-MOD and are fully supported via the class AASequence.
- Added new framework for generic clustering
New features and improvements of TOPP:
- Replaced 'MapAlignment', 'UnlabeledMatcher' and 'LabeledMatcher' tools by 'MapAligner' and 'FeatureLinker' tools
- Added map alignment algorithm based on spectrum similarity to 'MapAlignment'
- Added 'PTModel' and 'PTPredict' tool for prediction of proteotypic peptides
- Added XTandemAdapter with a minimal interface (shared with OMSSAAdapter) all advanced option can be set using a
standard X!Tandem configuration file
- Changed OMSSAAdapter to same minimal interface as XTandemAdapter, advanced option are additionally available
- Added IDDecoyProbability which implements the transformation of a forward and reversed search into probability
scores (target-decoy approach)
- Added FalseDiscoveryRate, which implements FDR calculation from forward and reversed searches at peptide
and protein levels
New features and improvements of TOPPView:
- Major update to the user interface and functionality
- Speed improvements of the 2D view
- Many bug fixes
- Updated tutorial
Changes to OpenMS XML formats:
- Added TransformationXML which stores information about map alignment
- Removed map alignment information from ConsensusXML
- FeaturePairsXML is now deprecated (ConsensusXML is used instead)
Changes to the contrib package:
- Updated to NetCDF 3.6.3
- Updated to SeqAn 1.1 (r2416)
- Updated to CGAL 3.3.1
- Updated to GSL 1.11
- Updated to xerces-c 2.80
- Updated to boost 1.35.0
- Updated to libsvm 2.86
Detailed list of changes to specific OpenMS classes:
- Renamed and moved classes
- Renamed 'Exception::Base' to 'Exception::BaseException'
- Renamed all 'Peak' classes to 'RichPeak'
- Renamed all 'RawDataPoint' classes to 'Peak'
- Renamed 'KERNEL/DPeakConstRefArray' to 'DATASTRUCTURES/ConstRefVector'
- Removed classes
- KERNEL/PickedPeak1D
- DATASTRUCTURES/HashMap (replace by Map)
- ANALYSIS/MAPMATCHING/BaseAlignment (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/BaseMapMatcher (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/BasePairFinder (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/BasePairFinder_impl (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/BasePairwiseMapMatcher_impl (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/BaseSuperImposer_impl (restructuring of map alignment
- ANALYSIS/MAPMATCHING/ElementPair (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/Grid (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/GridCell (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/Group (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/IndexTuple (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/LinearMapping (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/MapDewarper (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/MapMatcherRegression (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/PairMatcher (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/PoseClusteringPairwiseMapMatcher (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/StarAlignment (restructuring of map alignment)
- ANALYSIS/CLUSTERING/BinnedRep (reimplemented in BinnedSpectrum)
- COMPARISON/SPECTRA/BinnedRepCompareFunctor (reimplemented in BinnedSpectrumCompareFunctor)
- COMPARISON/SPECTRA/BinnedRepMutualInformation (reimplemented in BinnedMutualInformation)
- COMPARISON/SPECTRA/BinnedRepSharedPeakCount (reimplemented in BinnedSharedPeakCount)
- COMPARISON/SPECTRA/BinnedRepSpectrumContrastAngle (reimplemented in BinnedSpectralContrastAngle)
- COMPARISON/SPECTRA/BinnedRepSumAgreeingIntensities (reimplemented in BinnedSumAgreeingIntensities)
- CONCEPT/Benchmark
- CONCEPT/HashFunction
- FILTERING/SMOOTHING/SmoothFilter
- FORMAT/FeaturePairsXMLFile (restructuring of map alignment)
- FORMAT/GridFile (restructuring of map alignment)
- FORMAT/HANDLER/FeaturePairsHandler (restructuring of map alignment)
- FORMAT/HANDLER/GridHandler (restructuring of map alignment)
- FORMAT/HANDLER/OMSAAXMLHandler (replaced by OMSSAXMLFile)
- KERNEL/ConsensusPeak (restructuring of map alignment)
- KERNEL/FeatureHandle
- KERNEL/MSExperimentExtern
- KERNEL/PeakIndex
- TRANSFORMATIONS/RAW2PEAK/PeakShapeType
- New classes
- CHEMISTRY/ModificationsDB which handles the PSI-MOD modifications
- CHEMISTRY/ModificationDefinition class, which specifies modification search options
- CHEMISTRY/ModificationDefinitionSet class, which specifies modification search options
- CHEMISTRY/ResidueModification which represents a PSI-MOD modification
- ANALYSIS/ID/FalseDiscoveryRate class, which calculates FDRs on peptide and protein level
- ANALYSIS/ID/IDDecoyProbability class, which implements a target decoy probability estimation
- DATASTRUCTURES/Map class and replaced HashMap usage with Map
- ANALYSIS/MAPMATCHING/BaseGroupFinder (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithm (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmLabeled (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmUnlabeled (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/LabeledPairFinder (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/MapAlignmentAlgorithm (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmPoseClustering (restructuring of map alignment)
- ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmSpectrumAlignment (new map alignment type using spectral alignments)
- ANALYSIS/MAPMATCHING/TransformationDescription (new map alignment type using spectral alignments)
- ANALYSIS/CLUSTERING/AverageLinkage (new framework for clustering)
- ANALYSIS/CLUSTERING/ClusterFunctor (new framework for clustering)
- ANALYSIS/CLUSTERING/ClusterHierachical (new framework for clustering)
- ANALYSIS/CLUSTERING/CompleteLinkage (new framework for clustering)
- ANALYSIS/CLUSTERING/SingleLinkage (new framework for clustering)
- COMPARISON/SPECTRA/BinnedSpectrum (Binned represenetation of a spectrum)
- COMPARISON/SPECTRA/BinnedMutualInformation
- COMPARISON/SPECTRA/BinnedSumAgreeingIntensities
- COMPARISON/SPECTRA/BinnedSpectralContrastAngle
- COMPARISON/SPECTRA/BinnedSharedPeakCount
- COMPARISON/SPECTRA/BinnedSpectrumCompareFunctor
- COMPARISON/SPECTRA/CompareFourierTransform
- COMPARISON/SPECTRA/PeakAlignment
- COMPARISON/SPECTRA/SteinScottImproveScore
- DATASTRUCTURE/DistanceMatrix
- FORMAT/ControlledVocabulary
- FORMAT/HANDLER/MzMLHandler
- FORMAT/HANDLER/UnimodXMLHandler
- FORMAT/HANDLER/XTandemInFileXMLHandler
- FORMAT/MSPFile
- FORMAT/MzMLFile
- FORMAT/OMSSACSVFile
- FORMAT/PepXMLFile (only for Mascot output, not complete implementation of pepXML)
- FORMAT/TransformationXMLFile
- FORMAT/XTandemInfile
- FORMAT/XTandemXMLFile
- MATH/STATISTICS/GammaDistributionFitter
- MATH/STATISTICS/GaussFitter
- TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmIsotopeWavelet
- TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmWavelet
- Changes to classes
- Changed AASequence to support PSI-MOD modifications
- Changed Residue to support PSI-MOD modifications
------------------------------------------------------------------------------------------
---- OpenMS 1.1.1 ----
------------------------------------------------------------------------------------------
Bug fixes:
- [1953335]: TOPP - TOPPView: Filter bar is not updated when deleting a layer
- [1953339]: TOPP - TOPPView: Crash when pressing cancel button of the DB password dialog
- [1948699]: TOPP - TOPPView: Opening a file from command-line containing spaces fails
- [1948080]: TOPP - MascotAdapter: Variable modification were added to fixed modifications
- [1941268]: TOPP - TOPPView: Crash when displaying files with intensity 0 peaks only
- [1941270]: TOPP - TOPPView: Recent file paths in TOPPView are wrong under certain conditions (Windows only)
- [1941273]: TOPP - TOPPView: Crash when loading an INI file without type in TOPP dialog
- [1934199]: OpenMS - SpectrumWidget: Crash when painted without layers
- [1933097]: OpenMS - TOPPBase: Invalid default values of string parameters were not handled correctly
------------------------------------------------------------------------------------------
---- OpenMS 1.1 ----
------------------------------------------------------------------------------------------
New features and improvements of OpenMS:
- Added support for Windows XP
- Improved configure
- prefix option now works as expected
- Fixed several bugs in handling of Qt
- Fixed several minor bugs
- Added support for large datasets through a custom allocator
- Added support for XML schemas, which allows validation of files
- Added optional schema version tag to all OpenMS XML formats
- Removed classes: DataReducer, MaxReducer, SumReducer, SavitzkyGolaySVDFilter,
MSExperimentExtern, BaseMapping
- Added classes: StringList, SuffixArray, DataFilters
- Renamed/moved classes:
- ExternalCalibraton -> TOFCalibration,
- SavitzkyGolayQRFilter -> SavitzkyGolayFilter
- FORMAT/Param.h -> DATASTRUCTURES/Param.h
- Refactoring of FeatureFinder framework
- Refactoring of MapAlignment framework
- Refactoring of XML parsing classes
- Refactoring of the visualization widgets
- Reorganization of the OpenMS documentation
- Lots of minor bug fixes and improvements to documentation
New features and improvements of TOPP:
- Added support for advanced parameters and parameter value restrictions
- Added file type/name checks before use of input/output files
- Improved parameter handling of the tools that offer different methods:
FeatureFinder, NoiseFilter and SpectraFilter
- Lots of minor bug fixes and improvements to documentation
- FileFilter: Added option to sort data points according to RT and m/z
- FileInfo: Added validation of files against the XML schema, added check for corrupt data
- Added TextExporter: exports featureXML, featurePairsXML, consensusXML and idXML to text
files for import to other tools
- Added FeatureFinderMRM: performs peptide quantitation using Multiple-Reaction-Monitoring (MRM)
New features and improvements of TOPPView:
- Refactoring of the interface: Moved a lot of functions to context menus
- Added data filters (intensity, quality, ...)
- Lots of minor bug fixes
- Added tutorial
Detailed list of changes to specific OpenMS classes:
- BoundingBox2D
- Added constructor from PointArrayType
- DataValue
- Simplified to Int, DoubleReal and String types only
- Direct cast to all data types is not possible anymore
- DefaultParamHandler
- Added support for restrictions
- Added support for advanced parameters
- String
- Improved implementations of implode and substr
- Renamed implode(...) method to concatenate(...)
- DSpectrum
- Added method to find the nearest peak to an m/z value (findNearest)
- Feature
- Added support for convex hulls of individual mass traces
- Param
- Added support for value restrictions
- Added support for advanced parameters
- Replaced STL iterator by Param-specific iterator, which is aware of the tree strucure
- The getValue method now throws an exception in case of a non-existing name.
Use exists(...) to check if a parameter exists
- FileHandler
- Added support for IdXML, ConsensusXML and mgf format
- Factory
- Added methods to find out which products are registered
- MetaInfo/MetaInfoInterface/MetaInfoRegistry
- Names are automatically registered now
- FileHandler
- Renamed some of the Type enum values to make them consistent
------------------------------------------------------------------------------------------
---- OpenMS 1.0 ----
------------------------------------------------------------------------------------------
- Kernel redesign (improvement of usability)
- Removed Boost dependencies
- Qt4 port
- Experimental support for MacOS 10
- Experimental support for Windows (XP & VISTA via MinGW)
- New OpenMS and TOPP tutorial
- Redesign of protein and peptide identification datastructures
- New format for protein and peptide identification: IdXML
- Release of annotated schemas for all OpenMS XML formats
- New features and improvements of TOPPView
- Visualization of peaks, feature and feature pairs has been speeded up
- Meta data browsing and editing
- TOPP tools can be invoked via TOPPView
- Visualization of protein/peptide identification annotated to LC-MS/MS data
- New features and improvements of TOPP
- Added INIFileEditor - A GUI editor for TOPP configuration files
- Added ConsensusID - A tool to unify protein and petide identification from several
search engines
- Added Decharger - Decharging feature maps
- Added MapAlignment - Multiple alignment of LC-MS maps
- Added MapNormalizer - Normalization of peak intensities
- Added InternalCalibration - Calibration of peak m/z using reference masses
- Added ExternalCalibration - Conversion of flight times into m/z using external
calibrant spectra
