pyOpenMS
latest

Introduction

  • Introduction
  • Background

Getting started

  • Installation
  • Import pyopenms
  • Getting help
  • First look at data

Mass Spectrometry Concepts

  • MS Data
  • Chemistry
  • Peptides and Proteins
  • Oligonucleotides: RNA
  • Fragment spectrum generation
  • Spectrum alignment
  • Digestion
  • Identification Data
  • Quantitative Data

OpenMS Algorithms

  • Parameter Handling
  • Algorithms
  • Smoothing
  • Centroiding
  • Spectrum normalization
  • Charge and Isotope Deconvolution
  • Feature Detection
  • Map Alignment
  • Feature Linking
  • Peptide Search
  • Chromagraphic Analysis
  • Quality Control
  • Mass Decomposition
  • Export files for GNPS

Example Workflows

  • Identification by Accurate Mass
  • Untargeted Metabolomics Pre-Processing

How to contribute

  • Contribute

Advanced Topics

  • Reading Raw MS data
  • Other MS data formats
  • mzML files
  • Export to pandas DataFrame
  • Query MSExperiment with MassQL
  • Memory management
  • pyOpenMS in R
  • Build from source
  • Wrapping Workflow and wrapping new Classes
  • Interactive plots
  • Interfacing with ML libraries

Full API documentation

  • Full API documentation
    • pyopenms
      • pyopenms.free_mem
      • pyopenms.peptide_identifications_to_df
      • AAIndex
      • AASeqWithMass
      • AASequence
      • AMSE_AdductInfo
      • AQS_featureConcentration
      • AQS_runConcentration
      • AScore
      • AbsoluteQuantitation
      • AbsoluteQuantitationMethod
      • AbsoluteQuantitationMethodFile
      • AbsoluteQuantitationStandards
      • AbsoluteQuantitationStandardsFile
      • AccurateMassSearchEngine
      • AccurateMassSearchResult
      • Acquisition
      • AcquisitionInfo
      • ActivationMethod
      • Adduct
      • AggregationMethod
      • AnalysisSummary
      • AnnotationState
      • AnnotationStatistics
      • ArrayWrapperFloat
      • Assay
      • Attachment
      • AverageLinkage
      • BSpline2d
      • Base64
      • BaseFeature
      • BasicProteinInferenceAlgorithm
      • BayesianProteinInferenceAlgorithm
      • BernNorm
      • BiGaussFitter1D
      • BiGaussModel
      • BilinearInterpolation
      • BinnedSpectrum
      • BoundaryCondition
      • BoxElement
      • CV
      • CVMappingFile
      • CVMappingRule
      • CVMappingTerm
      • CVMappings
      • CVReference
      • CVTerm
      • CVTermList
      • CVTermListInterface
      • CVTerm_ControlledVocabulary
      • CachedMzMLHandler
      • CachedSwathFileConsumer
      • CachedmzML
      • CalibrationData
      • ChannelInfo
      • ChargePair
      • ChargedIndexSet
      • ChecksumType
      • ChromatogramExtractor
      • ChromatogramExtractorAlgorithm
      • ChromatogramPeak
      • ChromatogramSettings
      • ChromatogramTools
      • ChromeleonFile
      • ClusterProxyKD
      • ClusteringGrid
      • CoarseIsotopePatternGenerator
      • ColumnHeader
      • CompNovoIdentification
      • CompNovoIdentificationCID
      • CompNovoIonScoring
      • CompNovoIonScoringCID
      • ComplementFilter
      • ComplementMarker
      • Compomer
      • Compound
      • ConfidenceScoring
      • Configuration
      • ConsensusFeature
      • ConsensusIDAlgorithm
      • ConsensusIDAlgorithmAverage
      • ConsensusIDAlgorithmBest
      • ConsensusIDAlgorithmIdentity
      • ConsensusIDAlgorithmPEPIons
      • ConsensusIDAlgorithmPEPMatrix
      • ConsensusIDAlgorithmRanks
      • ConsensusIDAlgorithmSimilarity
      • ConsensusIDAlgorithmWorst
      • ConsensusMap
      • ConsensusMapNormalizerAlgorithmMedian
      • ConsensusMapNormalizerAlgorithmQuantile
      • ConsensusMapNormalizerAlgorithmThreshold
      • ConsensusXMLFile
      • Contact
      • ContactPerson
      • ContinuousWaveletTransform
      • ContinuousWaveletTransformNumIntegration
      • ControlledVocabulary
      • ConvexHull2D
      • CrossLinkSpectrumMatch
      • CrossLinksDB
      • CsiAdapterHit
      • CsiAdapterIdentification
      • CsiAdapterRun
      • CsiFingerIdMzTabWriter
      • CsvFile
      • CubicSpline2d
      • DBoundingBox2
      • DIAScoring
      • DPosition1
      • DPosition2
      • DRange1
      • DRange2
      • DRangeIntersection
      • DTA2DFile
      • DTAFile
      • DataFilter
      • DataFilters
      • DataProcessing
      • DataType
      • DataValue
      • Date
      • DateTime
      • DeNovoIonScore
      • DecoyGenerator
      • DecoyTransitionType
      • Deisotoper
      • DigestSimulation
      • Digestion
      • DigestionEnzyme
      • DigestionEnzymeProtein
      • DigestionEnzymeRNA
      • DimensionDescription
      • DistanceMatrix
      • DocumentIdentifier
      • DriftTimeUnit
      • EDTAFile
      • Element
      • ElementDB
      • ElutionModelFitter
      • ElutionPeakDetection
      • EmgFitter1D
      • EmgGradientDescent
      • EmgModel
      • EmgScoring
      • EmpiricalFormula
      • EnzymaticDigestion
      • EnzymaticDigestionLogModel
      • ExperimentalDesign
      • ExperimentalDesignFile
      • ExperimentalDesign_MSFileSectionEntry
      • ExperimentalDesign_SampleSection
      • ExperimentalSettings
      • ExtractionCoordinates
      • FASTAEntry
      • FASTAFile
      • FIAMSDataProcessor
      • FIAMSScheduler
      • FalseDiscoveryRate
      • Feature
      • FeatureDeconvolution
      • FeatureDistance
      • FeatureFileOptions
      • FeatureFinder
      • FeatureFinderAlgorithmIsotopeWavelet
      • FeatureFinderAlgorithmMetaboIdent
      • FeatureFinderAlgorithmPicked
      • FeatureFinderIdentificationAlgorithm
      • FeatureFinderMetaboIdentCompound
      • FeatureFinderMultiplexAlgorithm
      • FeatureFindingMetabo
      • FeatureGroupingAlgorithm
      • FeatureGroupingAlgorithmKD
      • FeatureGroupingAlgorithmLabeled
      • FeatureGroupingAlgorithmQT
      • FeatureGroupingAlgorithmUnlabeled
      • FeatureHandle
      • FeatureMap
      • FeatureMapping
      • FeatureMapping_FeatureMappingInfo
      • FeatureMapping_FeatureToMs2Indices
      • FeatureXMLFile
      • File
      • FileHandler
      • FileType
      • FileTypes
      • FilterFunctor
      • FineIsotopePatternGenerator
      • Fitter1D
      • FloatDataArray
      • GNPSMGFFile
      • GNPSMetaValueFile
      • GNPSQuantificationFile
      • GaussFilter
      • GaussFitResult
      • GaussFitter
      • GaussTraceFitter
      • GoodDiffFilter
      • Gradient
      • GridBasedCluster
      • HMMState
      • HPLC
      • HiddenMarkovModel
      • HyperScore
      • IBSpectraFile
      • IDConflictResolverAlgorithm
      • IDDecoyProbability
      • IDFilter
      • IDMapper
      • IDMapper_SpectraIdentificationState
      • IDRipper
      • ILPDCWrapper
      • IMFormat
      • IMSAlphabet
      • IMSElement
      • IMSIsotopeDistribution
      • IMSIsotopeDistribution_Peak
      • IMSWeights
      • IMTypes
      • ISDGroup
      • ITRAQ_TYPES
      • IdXMLFile
      • Identification
      • IdentificationData
      • IdentificationDataConverter
      • IdentificationHit
      • IdentificationRuns
      • IncludeExcludeTarget
      • InclusionExclusionList
      • IndexTriple
      • IndexedMzMLDecoder
      • IndexedMzMLFileLoader
      • IndexedMzMLHandler
      • InspectInfile
      • InspectOutfile
      • Instrument
      • InstrumentSettings
      • IntegerDataArray
      • IntensityBalanceFilter
      • Interfaces
      • InternalCalibration
      • InternalCalibration_LockMass
      • Internal_MzMLValidator
      • InterpolationModel
      • IonDetector
      • IonIdentityMolecularNetworking
      • IonOpticsType
      • IonSource
      • IonType
      • IsobaricChannelExtractor
      • IsobaricChannelInformation
      • IsobaricIsotopeCorrector
      • IsobaricNormalizer
      • IsobaricQuantifier
      • IsobaricQuantifierStatistics
      • IsotopeCluster
      • IsotopeDiffFilter
      • IsotopeDistribution
      • IsotopeDistributionCache
      • IsotopeFitter1D
      • IsotopeLabelingMDVs
      • IsotopeMarker
      • IsotopeModel
      • IsotopePattern
      • IsotopeVariant
      • IsotopeWavelet
      • IsotopeWaveletTransform
      • ItraqConstants
      • ItraqEightPlexQuantitationMethod
      • ItraqFourPlexQuantitationMethod
      • JavaInfo
      • KDTreeFeatureMaps
      • KDTreeFeatureNode
      • Kernel_MassTrace
      • KroenikFile
      • LLMParam
      • LPWrapper
      • LabeledPairFinder
      • LibSVMEncoder
      • LightCompound
      • LightMRMTransitionGroupCP
      • LightModification
      • LightProtein
      • LightTargetedExperiment
      • LightTransition
      • LinearInterpolation
      • LinearResampler
      • LinearResamplerAlign
      • LocalLinearMap
      • LogType
      • LowessSmoothing
      • MRMAssay
      • MRMDecoy
      • MRMFP_ComponentGroupParams
      • MRMFP_ComponentParams
      • MRMFQC_ComponentGroupPairQCs
      • MRMFQC_ComponentGroupQCs
      • MRMFQC_ComponentQCs
      • MRMFeature
      • MRMFeatureFilter
      • MRMFeatureFinderScoring
      • MRMFeaturePicker
      • MRMFeaturePickerFile
      • MRMFeatureQC
      • MRMFeatureQCFile
      • MRMFragmentSelection
      • MRMIonSeries
      • MRMMapping
      • MRMRTNormalizer
      • MRMScoring
      • MRMTransitionGroupCP
      • MRMTransitionGroupPicker
      • MS2File
      • MSChromatogram
      • MSDGroup
      • MSDataAggregatingConsumer
      • MSDataCachedConsumer
      • MSDataSqlConsumer
      • MSDataStoringConsumer
      • MSExperiment
      • MSNumpressCoder
      • MSPFile
      • MSPGenericFile
      • MSQuantifications
      • MSSim
      • MSSpectrum
      • MSstatsFile
      • MT_QUANTMETHOD
      • MZTrafoModel
      • MZTrafoModel_MODELTYPE
      • MapAlignmentAlgorithmIdentification
      • MapAlignmentAlgorithmKD
      • MapAlignmentAlgorithmPoseClustering
      • MapAlignmentAlgorithmSpectrumAlignment
      • MapAlignmentEvaluationAlgorithmPrecision
      • MapAlignmentEvaluationAlgorithmRecall
      • MapAlignmentTransformer
      • MapConversion
      • MarkerMower
      • MascotGenericFile
      • MascotInfile
      • MascotXMLFile
      • MassAnalyzer
      • MassDecomposition
      • MassDecompositionAlgorithm
      • MassExplainer
      • MassTrace
      • MassTraceDetection
      • MassTraces
      • MasstraceCorrelator
      • MatrixDouble
      • Measure
      • MetaInfo
      • MetaInfoDescription
      • MetaInfoInterface
      • MetaInfoRegistry
      • MetaboTargetedAssay
      • MetaboTargetedAssay_CompoundTargetDecoyPair
      • MetaboTargetedTargetDecoy
      • MetaboTargetedTargetDecoy_MetaboTargetDecoyMassMapping
      • MetaboliteFeatureDeconvolution
      • MetaboliteSpectralMatching
      • Modification
      • ModificationDefinition
      • ModificationDefinitionsSet
      • ModificationsDB
      • ModifiedPeptideGenerator
      • ModifiedPeptideGenerator_MapToResidueType
      • MorpheusScore
      • MorpheusScore_Result
      • MorphologicalFilter
      • MsInspectFile
      • MultiplexDeltaMasses
      • MultiplexDeltaMassesGenerator
      • MultiplexDeltaMassesGenerator_Label
      • MultiplexDeltaMasses_DeltaMass
      • MultiplexIsotopicPeakPattern
      • MzDataFile
      • MzIdentMLFile
      • MzMLFile
      • MzMLSpectrumDecoder
      • MzMLSqliteHandler
      • MzMLSwathFileConsumer
      • MzQCFile
      • MzQuantMLFile
      • MzTab
      • MzTabFile
      • MzTabM
      • MzTabMFile
      • MzXMLFile
      • NASequence
      • NLargest
      • NeutralLossDiffFilter
      • NeutralLossMarker
      • NoiseEstimator
      • NonNegativeLeastSquaresSolver
      • NoopMSDataWritingConsumer
      • NormalizationMethod
      • Normalizer
      • NumpressConfig
      • OMSSACSVFile
      • OMSSAXMLFile
      • OPXLDataStructs
      • OPXLHelper
      • OPXLSpectrumProcessingAlgorithms
      • OPXL_PreprocessedPairSpectra
      • OSBinaryDataArray
      • OSChromatogram
      • OSChromatogramMeta
      • OSSpectrum
      • OSSpectrumMeta
      • OSWFile
      • OSW_ChromExtractParams
      • OfflinePrecursorIonSelection
      • OnDiscMSExperiment
      • OpenMSBuildInfo
      • OpenMSOSInfo
      • OpenPepXLAlgorithm
      • OpenPepXLLFAlgorithm
      • OpenSwathDataAccessHelper
      • OpenSwathHelper
      • OpenSwathOSWWriter
      • OpenSwathScoring
      • OpenSwath_Scores
      • OpenSwath_Scores_Usage
      • OptimizationFunctions_PenaltyFactors
      • OptimizePeakDeconvolution
      • OptimizePeakDeconvolution_Data
      • OptimizePick
      • OptimizePick_Data
      • OriginAnnotationFormat
      • PI_PeakArea
      • PI_PeakBackground
      • PI_PeakShapeMetrics
      • PSLPFormulation
      • PSProteinInference
      • PScore
      • Param
      • ParamCTDFile
      • ParamEntry
      • ParamNode
      • ParamValue
      • ParamXMLFile
      • ParentPeakMower
      • Peak1D
      • Peak2D
      • PeakBoundary
      • PeakCandidate
      • PeakFileOptions
      • PeakIndex
      • PeakIntegrator
      • PeakIntensityPredictor
      • PeakMap
      • PeakMarker
      • PeakPickerCWT
      • PeakPickerHiRes
      • PeakPickerIterative
      • PeakPickerMRM
      • PeakPickerMaxima
      • PeakPickerSH
      • PeakShape
      • PeakSpectrum
      • PeakTypeEstimator
      • PeakWidthEstimator
      • PenaltyFactorsIntensity
      • PepXMLFile
      • PepXMLFileMascot
      • Peptide
      • PeptideAndProteinQuant
      • PeptideAndProteinQuant_PeptideData
      • PeptideAndProteinQuant_ProteinData
      • PeptideAndProteinQuant_Statistics
      • PeptideEntry
      • PeptideEvidence
      • PeptideHit
      • PeptideHit_AnalysisResult
      • PeptideHit_PeakAnnotation
      • PeptideIdentification
      • PeptideIndexing
      • PeptideProteinResolution
      • PeptideProteinResolution_ConnectedComponent
      • PercolatorFeatureSetHelper
      • PercolatorInfile
      • PercolatorOutfile
      • PlainMSDataWritingConsumer
      • PosteriorErrorProbabilityModel
      • Precursor
      • PrecursorCorrection
      • PrecursorIonSelection
      • PrecursorIonSelectionPreprocessing
      • PrecursorPurity
      • Prediction
      • ProbablePhosphoSites
      • Product
      • ProgressLogger
      • ProtXMLFile
      • ProteaseDB
      • ProteaseDigestion
      • Protein
      • ProteinEntry
      • ProteinGroup
      • ProteinHit
      • ProteinIdentification
      • ProteinInference
      • ProteinProteinCrossLink
      • ProteinResolver
      • ProteinResolverResult_Type
      • ProtonDistributionModel
      • Publication
      • PurityScores
      • QTCluster
      • QTClusterFinder
      • QcMLFile
      • QualityParameter
      • QuantitativeExperimentalDesign
      • QuotingMethod
      • RANSAC
      • RANSACParam
      • RANSACQuadratic
      • RNPxlMarkerIonExtractor
      • RNPxlModificationMassesResult
      • RNPxlModificationsGenerator
      • RNPxlReport
      • RNPxlReportRow
      • RNPxlReportRowHeader
      • RNaseDB
      • RNaseDigestion
      • RansacModelLinear
      • RansacModelQuadratic
      • Ratio
      • ReactionMonitoringTransition
      • RealMassDecomposer
      • RegularSwathFileConsumer
      • Residue
      • ResidueDB
      • ResidueModification
      • ResolverResult
      • RetentionTime
      • Ribonucleotide
      • RibonucleotideDB
      • RichPeak2D
      • RipFileContent
      • RipFileIdentifier
      • SIDE
      • SILACLabeler
      • SVMData
      • SVMPrediction
      • SVMWrapper
      • Sample
      • SavitzkyGolayFilter
      • Scaler
      • ScanMode
      • ScanWindow
      • SearchParameters
      • Seed
      • SeedListGenerator
      • SemanticValidator
      • SemanticValidator_CVTerm
      • SequestInfile
      • SequestOutfile
      • SignalToNoiseEstimatorMeanIterative
      • SignalToNoiseEstimatorMedian
      • SignalToNoiseEstimatorMedianChrom
      • SignalToNoiseEstimatorMedianRapid
      • SimProtein
      • SimRandomNumberGenerator
      • SimpleOpenMSSpectraFactory
      • SimplePairFinder
      • SimplePeak
      • SimpleSVM
      • SimpleSearchEngineAlgorithm
      • SimpleTSGXLMS
      • SiriusAdapterAlgorithm
      • SiriusAdapterHit
      • SiriusAdapterIdentification
      • SiriusAdapterRun
      • SiriusFragmentAnnotation
      • SiriusFragmentAnnotation_SiriusTargetDecoySpectra
      • SiriusMSFile
      • SiriusMSFile_AccessionInfo
      • SiriusMSFile_CompoundInfo
      • SiriusMzTabWriter
      • SiriusMzTabWriter_SiriusSpectrumMSInfo
      • SiriusTemporaryFileSystemObjects
      • Software
      • SolverParam
      • SourceFile
      • SpectraMerger
      • SpectraSTSimilarityScore
      • SpectralMatch
      • SpectrumAccessOpenMS
      • SpectrumAccessOpenMSCached
      • SpectrumAccessOpenMSInMemory
      • SpectrumAccessQuadMZTransforming
      • SpectrumAccessSqMass
      • SpectrumAccessTransforming
      • SpectrumAlignment
      • SpectrumAlignmentScore
      • SpectrumAnnotator
      • SpectrumHelper
      • SpectrumIdentification
      • SpectrumLookup
      • SpectrumMetaData
      • SpectrumMetaDataLookup
      • SpectrumSettings
      • SplineInterpolatedPeaks
      • SplinePackage
      • SplineSpectrum_Navigator
      • SqMassConfig
      • SqMassFile
      • SqrtMower
      • StablePairFinder
      • String
      • StringDataArray
      • StringView
      • SvmModelParameterSet
      • SvmTheoreticalSpectrumGenerator
      • SvmTheoreticalSpectrumGeneratorSet
      • SvmTheoreticalSpectrumGeneratorTrainer
      • SwathFile
      • SwathMap
      • SwathMapMassCorrection
      • SwathWindowLoader
      • SysInfo
      • TICFilter
      • TMTElevenPlexQuantitationMethod
      • TMTSixPlexQuantitationMethod
      • TMTSixteenPlexQuantitationMethod
      • TMTTenPlexQuantitationMethod
      • TM_DataPoint
      • TOFCalibration
      • TSE_Match
      • Tagger
      • Tagging
      • TargetedExperiment
      • TargetedExperiment_Instrument
      • TargetedExperiment_Interpretation
      • TargetedExperiment_Modification
      • TargetedSpectraExtractor
      • TermSpecificityNuc
      • TextFile
      • TheoreticalIsotopePattern
      • TheoreticalSpectrumGenerator
      • TheoreticalSpectrumGeneratorXLMS
      • ThresholdMower
      • ToolInfo
      • TraMLFile
      • TraMLProduct
      • TraceInfo
      • TransformationDescription
      • TransformationModelBSpline
      • TransformationModelInterpolated
      • TransformationModelLinear
      • TransformationModelLowess
      • TransformationStatistics
      • TransformationXMLFile
      • TransitionPQPFile
      • TransitionTSVFile
      • TwoDOptimization
      • UnimodXMLFile
      • UniqueIdGenerator
      • Unit
      • UnitType
      • ValueType
      • VersionDetails
      • VersionInfo
      • WindowMower
      • XFDRAlgorithm
      • XLPrecursor
      • XMLFile
      • XMLHandler
      • XQuestResultXMLFile
      • XQuestScores
      • XRefType_CVTerm_ControlledVocabulary
      • XTandemInfile
      • XTandemXMLFile
      • streampos
    • pyopenms.Constants
    • pyopenms.Plotting
    • pyopenms.dataframes
    • pyopenms.python_extras

Support

  • Support
  • Frequently Asked Questions
pyOpenMS
  • »
  • Full API documentation »
  • pyopenms »
  • ProteinProteinCrossLink
  • Launch Binder Edit on GitHub

ProteinProteinCrossLink

class pyopenms.ProteinProteinCrossLink

Bases: object

Cython implementation of _ProteinProteinCrossLink

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS::OPXLDataStructs_1_1ProteinProteinCrossLink.html

__init__()
  • Cython signature: void ProteinProteinCrossLink()

  • Cython signature: void ProteinProteinCrossLink(ProteinProteinCrossLink &)

Methods

__init__

  • Cython signature: void ProteinProteinCrossLink()

getType

Cython signature: ProteinProteinCrossLinkType getType()

Attributes

alpha

beta

cross_link_position

cross_linker_mass

cross_linker_name

precursor_correction

term_spec_alpha

term_spec_beta

alpha
beta
cross_link_position
cross_linker_mass
cross_linker_name
getType()

Cython signature: ProteinProteinCrossLinkType getType()

precursor_correction
term_spec_alpha
term_spec_beta
Previous Next

© Copyright 2022, OpenMS Team. Revision 63fb999f.

Built with Sphinx using a theme provided by Read the Docs.