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Contents:

  • Installation
    • Requirements
    • Installing from PyPI
    • Optional Dependencies
    • Installing from Source
    • Development Installation
  • Usage
    • Quick Start
    • Basic Peptide Ions
    • Other Ion Types
    • Modifications
    • Isotopes
    • Adducts
    • Charge States
    • Mass Errors and Confidence
    • Complex Annotations
    • Mass Calculations
    • Parsing Multiple Annotations
    • Creating Annotations Programmatically
      • Basic Factory Methods
      • Adding Modifications
      • Complex Annotations
      • With Sequences
      • Other Ion Types
    • Serialization (Round-trip)
    • Export to Dictionary
    • Peptacular Integration
  • API Reference
    • Annotation
      • CommonAnnotationParams
        • CommonAnnotationParams.adducts
        • CommonAnnotationParams.analyte_reference
        • CommonAnnotationParams.charge
        • CommonAnnotationParams.confidence
        • CommonAnnotationParams.is_auxiliary
        • CommonAnnotationParams.isotopes
        • CommonAnnotationParams.mass_error
        • CommonAnnotationParams.mass_error_unit
        • CommonAnnotationParams.neutral_losses
      • PafAnnotation
        • PafAnnotation.adducts
        • PafAnnotation.analyte_reference
        • PafAnnotation.as_dict()
        • PafAnnotation.charge
        • PafAnnotation.comp()
        • PafAnnotation.confidence
        • PafAnnotation.dict_composition()
        • PafAnnotation.formula()
        • PafAnnotation.ion_type
        • PafAnnotation.is_auxiliary
        • PafAnnotation.isotopes
        • PafAnnotation.make_formula()
        • PafAnnotation.make_immonium()
        • PafAnnotation.make_internal()
        • PafAnnotation.make_named_compound()
        • PafAnnotation.make_peptide()
        • PafAnnotation.make_precursor()
        • PafAnnotation.make_reference()
        • PafAnnotation.make_smiles()
        • PafAnnotation.make_unknown()
        • PafAnnotation.mass()
        • PafAnnotation.mass_error
        • PafAnnotation.mz()
        • PafAnnotation.neutral_losses
        • PafAnnotation.parse()
        • PafAnnotation.peptacular_ion_type
        • PafAnnotation.proforma_formula()
        • PafAnnotation.sequence
        • PafAnnotation.serialize()
    • Parser
      • mzPAFParser
        • mzPAFParser.parse()
        • mzPAFParser.parse_multi()
      • parse()
      • parse_multi()
      • parse_single()
    • Annotation Types
      • Adduct
        • Adduct.as_dict()
        • Adduct.base_formula
        • Adduct.count
        • Adduct.formula
        • Adduct.parse()
        • Adduct.proforma_formula
        • Adduct.serialize()
      • ChemicalFormula
        • ChemicalFormula.composition
        • ChemicalFormula.formula
        • ChemicalFormula.parse()
        • ChemicalFormula.proforma_formula
        • ChemicalFormula.serialize()
      • CompositionProvider
        • CompositionProvider.composition
        • CompositionProvider.dict_composition
        • CompositionProvider.mass()
      • ImmoniumIon
        • ImmoniumIon.amino_acid
        • ImmoniumIon.composition
        • ImmoniumIon.formula
        • ImmoniumIon.mass()
        • ImmoniumIon.modification
        • ImmoniumIon.parse()
        • ImmoniumIon.serialize()
      • InternalFragment
        • InternalFragment.composition
        • InternalFragment.cterm_ion_type
        • InternalFragment.end_position
        • InternalFragment.formula
        • InternalFragment.mass()
        • InternalFragment.nterm_ion_type
        • InternalFragment.parse()
        • InternalFragment.sequence
        • InternalFragment.serialize()
        • InternalFragment.start_position
      • IsotopeSpecification
        • IsotopeSpecification.as_dict()
        • IsotopeSpecification.composition
        • IsotopeSpecification.count
        • IsotopeSpecification.element
        • IsotopeSpecification.is_average
        • IsotopeSpecification.mass()
        • IsotopeSpecification.parse()
        • IsotopeSpecification.serialize()
      • MassError
        • MassError.parse()
        • MassError.serialize()
        • MassError.unit
        • MassError.value
      • MassProvider
        • MassProvider.average_mass
        • MassProvider.mass()
        • MassProvider.monoisotopic_mass
      • NamedCompound
        • NamedCompound.composition
        • NamedCompound.mass()
        • NamedCompound.name
        • NamedCompound.parse()
        • NamedCompound.serialize()
      • NeutralLoss
        • NeutralLoss.as_dict()
        • NeutralLoss.base_formula
        • NeutralLoss.base_mass
        • NeutralLoss.base_reference
        • NeutralLoss.count
        • NeutralLoss.formula
        • NeutralLoss.loss_type
        • NeutralLoss.mass()
        • NeutralLoss.parse()
        • NeutralLoss.proforma_formula
        • NeutralLoss.reference
        • NeutralLoss.serialize()
      • PeptideIon
        • PeptideIon.composition
        • PeptideIon.formula
        • PeptideIon.mass()
        • PeptideIon.parse()
        • PeptideIon.position
        • PeptideIon.sequence
        • PeptideIon.serialize()
        • PeptideIon.series
      • PrecursorIon
        • PrecursorIon.composition
        • PrecursorIon.formula
        • PrecursorIon.mass()
        • PrecursorIon.parse()
        • PrecursorIon.serialize()
      • ReferenceIon
        • ReferenceIon.composition
        • ReferenceIon.formula
        • ReferenceIon.mass()
        • ReferenceIon.name
        • ReferenceIon.parse()
        • ReferenceIon.reference
        • ReferenceIon.serialize()
      • SMILESCompound
        • SMILESCompound.composition
        • SMILESCompound.formula
        • SMILESCompound.parse()
        • SMILESCompound.proforma_formula
        • SMILESCompound.serialize()
        • SMILESCompound.smiles
      • ScalableComposition
        • ScalableComposition.composition
        • ScalableComposition.count
      • Serializable
        • Serializable.serialize()
      • UnknownIon
        • UnknownIon.composition
        • UnknownIon.label
        • UnknownIon.mass()
        • UnknownIon.parse()
        • UnknownIon.serialize()
      • composition_to_formula_string()
      • composition_to_proforma_formula_string()
      • formula_to_composition()
    • Constants
      • AminoAcids
        • AminoAcids.A
        • AminoAcids.C
        • AminoAcids.D
        • AminoAcids.E
        • AminoAcids.F
        • AminoAcids.G
        • AminoAcids.H
        • AminoAcids.I
        • AminoAcids.K
        • AminoAcids.L
        • AminoAcids.M
        • AminoAcids.N
        • AminoAcids.P
        • AminoAcids.Q
        • AminoAcids.R
        • AminoAcids.S
        • AminoAcids.T
        • AminoAcids.V
        • AminoAcids.W
        • AminoAcids.Y
      • AnnotationName
        • AnnotationName.FORMULA
        • AnnotationName.IMMONIUM
        • AnnotationName.INTERNAL
        • AnnotationName.NAMED_COMPOUND
        • AnnotationName.PRECURSOR
        • AnnotationName.REFERENCE
        • AnnotationName.SERIES
        • AnnotationName.SMILES
        • AnnotationName.UNANNOTATED
      • BackboneCleavageType
        • BackboneCleavageType.A
        • BackboneCleavageType.B
        • BackboneCleavageType.C
        • BackboneCleavageType.X
        • BackboneCleavageType.Y
        • BackboneCleavageType.Z
      • InternalSeries
        • InternalSeries.AX
        • InternalSeries.AY
        • InternalSeries.AZ
        • InternalSeries.BX
        • InternalSeries.BY
        • InternalSeries.BZ
        • InternalSeries.CX
        • InternalSeries.CY
        • InternalSeries.CZ
      • IonSeries
        • IonSeries.A
        • IonSeries.B
        • IonSeries.C
        • IonSeries.D
        • IonSeries.DA
        • IonSeries.DB
        • IonSeries.V
        • IonSeries.W
        • IonSeries.WA
        • IonSeries.WB
        • IonSeries.X
        • IonSeries.Y
        • IonSeries.Z
    • Utilities
      • parse_formula()
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