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CHANGELOG
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CHANGELOG
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Glossary:
OpenMS - Name of the project and our C++ library
TOPP - "The OpenMS Proteomics Pipeline", collection of chainable tools for flexible HPLC/MS workflows
TOPPAS - "The OpenMS Proteomics Pipeline Assistant", graphical tool to interactively build and run HPLC/MS workflows
TOPPView - Versatile viewer for HPLC/MS data
INI file - parameter configuration file, holding custom parameter settings for TOPP tools
INIFileEditor - graphical parameter editor for INI files
Parameters - list of algorithm or TOPP tool parameters that changed in this release
------------------------------------------------------------------------------------------
---- OpenMS 2.1 ----
------------------------------------------------------------------------------------------
OpenMS 2.1 is the first release that provides an update notification functionality which
is also used to track usage statistics of OpenMS tools.
How it works:
At most once a day - on tool execution - a REST request to our update server is sent.
The REST server returns the most current version of the tool.
If the returned version is newer than the local one, the tool notifies the user that a software
update is available. By collecting this information we hope to improve the quality of OpenMS,
helps us to distribute development resources to e.g. heavily used tools
and is needed to calculate metrics required by our funding agency.
We will keep this information as confidential as possible and only provide summary
statistics to e.g. our funding agencies.
If you feel uncomfortable with this you can disable the update/usage tracking by:
1. disabling it in the build script (switch ENABLE_USAGE_STATISTICS to "OFF" ), or
2. setting the environment variable (OPENMS_DISABLE_USAGE_STATISTICS)
Notable changes are:
Databases:
- By default, decoy sequences are now denoted by a prefix 'DECOY_'.
------------------------------------------------------------------------------------------
---- 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.