Classes
class	AAIndex
	Representation of selected AAIndex properties. More...

class	AASequence
	Representation of a peptide/protein sequence. More...

class	DigestionEnzyme
	Base class for digestion enzymes. More...

class	DigestionEnzymeDB< DigestionEnzymeType, InstanceType >
	Digestion enzyme database (base class) More...

class	DigestionEnzymeProtein
	Representation of a digestion enzyme for proteins (protease) More...

class	DigestionEnzymeRNA
	Representation of a digestion enzyme for RNA (RNase) More...

class	Element
	Representation of an element. More...

class	ElementDB
	Singleton that stores elements and isotopes. More...

class	EmpiricalFormula
	Representation of an empirical formula. More...

class	EnzymaticDigestion
	Class for the enzymatic digestion of sequences. More...

class	CoarseIsotopePatternGenerator
	Isotope pattern generator for coarse isotope distributions. More...

class	FineIsotopePatternGenerator
	Isotope pattern generator for fine isotope distributions. More...

class	ModificationDefinition

class	ModificationDefinitionsSet

class	ModificationsDB
	database which holds all residue modifications from UniMod More...

class	MonosaccharideDB
	Singleton database of monosaccharides for glycan notation. More...

class	NASequence
	Representation of a nucleic acid sequence. More...

class	NucleicAcidSpectrumGenerator
	Generates theoretical spectra for nucleic acid sequences. More...

struct	ConversionIssue
	Description of a conversion issue from Peptidoform to AASequence. More...

struct	CvAccession
	Controlled vocabulary accession for a modification. More...

struct	NamedMod
	Named modification with optional CV prefix hint. More...

struct	MassDelta
	Mass delta modification with optional source hint. More...

struct	FormulaTag
	Chemical formula with optional charge. More...

struct	GlycanComposition
	Glycan composition specification. More...

struct	InfoTag
	Info tag for arbitrary text annotations. More...

struct	PositionConstraint
	Position constraint specifying allowed residues for a modification. More...

struct	Label
	Label for cross-links, branches, or ambiguous grouping. More...

struct	Modification
	A modification with one or more alternative tags. More...

struct	SequenceElement
	A single amino acid with its modifications. More...

struct	AmbiguousRegion
	Ambiguous amino acid region. More...

struct	ModifiedRange
	Modified sequence range with shared modifications. More...

struct	UnlocalisedMod
	Unlocalised modification with optional occurrence count. More...

struct	LabileModification
	Labile modification that may be lost during fragmentation. More...

struct	GlobalModification
	Global modification applied to specific locations. More...

struct	IsotopeReplacement
	Isotope replacement for stable isotope labeling. More...

struct	AdductIon
	Adduct ion specification for charge state. More...

struct	Peptidoform
	A single peptidoform (one peptide chain) More...

struct	PeptidoformIon
	A peptidoform ion (one or more chains with optional charge) More...

struct	CrossLinkGroup
	Cross-link group connecting sites across chains. More...

class	ProFormaParseError
	Structured parse error with context for ProForma parsing. More...

class	ProFormaParser
	Recursive descent parser for ProForma v2 peptidoform notation. More...

class	ProFormaTokenizer
	Tokenizer for ProForma v2 peptidoform notation. More...

class	ProFormaWriter
	Writer for ProForma v2 peptidoform notation. More...

class	ProteaseDB
	Database for enzymes that digest proteins (proteases) More...

class	ProteaseDigestion
	Class for the enzymatic digestion of proteins represented as AASequence or String. More...

class	Residue
	Representation of an amino acid residue. More...

class	ResidueDB
	OpenMS stores a central database of all residues in the ResidueDB. All (unmodified) residues are added to the database on construction. Modified residues get created and added if getModifiedResidue is called. More...

class	Ribonucleotide
	Representation of a ribonucleotide (modified or unmodified) More...

class	RibonucleotideDB
	Database of ribonucleotides (modified and unmodified) More...

class	RNaseDB
	Database for enzymes that digest RNA (RNases) More...

class	RNaseDigestion
	Class for the enzymatic digestion of RNAs. More...

class	SimpleTSGXLMS
	Generates theoretical spectra for cross-linked peptides. More...

class	SpectrumAnnotator
	Annotates spectra from identifications and theoretical spectra or identifications from spectra and theoretical spectra matching with various options. More...

class	TheoreticalSpectrumGenerator
	Generates theoretical spectra for peptides with various options. More...

Typedefs
using	ModificationTag = std::variant< CvAccession, NamedMod, MassDelta, FormulaTag, GlycanComposition, InfoTag, PositionConstraint >
	Variant type representing any modification tag content.

using	SequenceSection = std::variant< SequenceElement, AmbiguousRegion, ModifiedRange >
	Variant type representing a section of the sequence.

using	GlobalModEntry = std::variant< IsotopeReplacement, GlobalModification >
	Variant type for global modification entries.

using	ChargeState = std::variant< int, std::vector< AdductIon > >
	Charge state specification.

Enumerations
enum class	AASequenceConversionPolicy { FAIL_ON_LOSS , DROP_UNLOCALISED , BEST_EFFORT }
	Conversion policy for transforming Peptidoform to AASequence. More...

enum class	ConversionIssueType { UNRESOLVED_MOD , UNLOCALISED_MOD , LABILE_MOD , GLOBAL_MOD , AMBIGUOUS_MOD , AMBIGUOUS_REGION , MODIFIED_RANGE , CROSS_LINK , MULTIPLE_CHAINS , ALTERNATIVE_MODS , UNSUPPORTED_FEATURE }
	Issue type for AASequence conversion problems. More...

enum class	ProFormaWriteMode { LOSSLESS , CANONICAL }
	Write mode for ProForma string serialization. More...

enum class	CvDatabase { UNIMOD , MOD , RESID , XLMOD , GNO }
	Controlled vocabulary database prefix for modification accessions. More...

enum class	ProFormaErrorCode { UNEXPECTED_CHARACTER , UNCLOSED_BRACKET , UNMATCHED_BRACKET , INVALID_CV_PREFIX , INVALID_CV_ACCESSION , INVALID_AMINO_ACID , INVALID_MASS_VALUE , INVALID_FORMULA , UNKNOWN_MONOSACCHARIDE , DANGLING_CROSSLINK_LABEL , EMPTY_SEQUENCE , INVALID_CHARGE , INVALID_OCCURRENCE_SPECIFIER , UNEXPECTED_END_OF_INPUT , INTERNAL_ERROR }
	Error codes for programmatic handling of ProForma parse errors. More...

Detailed Description

Class Documentation

◆ OpenMS::ConversionIssue

struct OpenMS::ConversionIssue

Description of a conversion issue from Peptidoform to AASequence.

Records problems encountered when attempting to convert a ProForma Peptidoform to an OpenMS AASequence representation.

Collaboration diagram for ConversionIssue:

[legend]

Class Members
String	description	Human-readable description.
size_t	position	Position in sequence (SIZE_MAX if not position-specific)
ConversionIssueType	type	The type of issue.

◆ OpenMS::CvAccession

struct OpenMS::CvAccession

Controlled vocabulary accession for a modification.

Represents a modification specified by a CV accession number, e.g., UNIMOD:35 for Oxidation. The accession string contains only the identifier portion (e.g., "35" for UNIMOD:35).

Collaboration diagram for CvAccession:

[legend]

Class Members
String	accession	The accession identifier (e.g., "35" for UNIMOD:35, full string for GNO)
CvDatabase	database	The source database (UNIMOD, MOD, RESID, XLMOD, or GNO)

◆ OpenMS::NamedMod

struct OpenMS::NamedMod

Named modification with optional CV prefix hint.

Represents a modification specified by name, optionally with a CV prefix hint to disambiguate which database to search (e.g., "U:Oxidation" for UniMod, "M:Oxidation" for PSI-MOD).

Collaboration diagram for NamedMod:

[legend]

Class Members
optional< CvDatabase >	cv_hint	Optional CV prefix hint (U, M, R, X, G)
String	name	The modification name (e.g., "Oxidation", "Phospho")

◆ OpenMS::FormulaTag

struct OpenMS::FormulaTag

Chemical formula with optional charge.

Represents a modification specified by chemical formula. The optional charge is specified via the :z+N suffix in ProForma (e.g., Formula:C12H20O2:z+2).

Collaboration diagram for FormulaTag:

[legend]

Class Members
optional< int >	charge	Optional charge from :z+N suffix.
String	formula_string	The chemical formula string (e.g., "C12H20O2")

◆ OpenMS::GlycanComposition

struct OpenMS::GlycanComposition

Glycan composition specification.

Represents a glycan modification as a composition of monosaccharides. Each component can be either a named monosaccharide (e.g., "Hex", "HexNAc") or a custom formula specification.

Example: Glycan:HexNAc1Hex2 -> [(HexNAc, 1), (Hex, 2)]

Collaboration diagram for GlycanComposition:

[legend]

Class Members
typedef variant< String, FormulaTag >	Monosaccharide	A monosaccharide component: either a name (String) or a custom formula (FormulaTag)

Class Members
vector< pair< Monosaccharide, int > >	components	List of (monosaccharide, count) pairs.

◆ OpenMS::InfoTag

struct OpenMS::InfoTag

Info tag for arbitrary text annotations.

Represents an INFO: tag in ProForma that carries arbitrary text metadata about a modification or site. Example: INFO:provenance_data

Collaboration diagram for InfoTag:

[legend]

Class Members
String	text	The info text content.

◆ OpenMS::PositionConstraint

struct OpenMS::PositionConstraint

Position constraint specifying allowed residues for a modification.

Represents a Position: tag in ProForma that constrains where a modification can be localized. This is typically used as an alternative to a modification to indicate its possible sites.

Example: [Oxidation|Position:M] means Oxidation can only occur at M residues

Collaboration diagram for PositionConstraint:

[legend]

Class Members
bool	c_term = false	True if modification can be at C-terminus.
bool	n_term = false	True if modification can be at N-terminus.
vector< char >	residues	List of allowed amino acid residues.

◆ OpenMS::Modification

struct OpenMS::Modification

A modification with one or more alternative tags.

In ProForma, a modification can have multiple alternatives separated by |, representing uncertainty about the exact modification. Each alternative consists of a tag and an optional label.

Example: K[Phospho|+79.97] has two alternatives

The resolved_mod field is populated by resolveModifications() and points to the ResidueModification in ModificationsDB (for the first/primary alternative).

Collaboration diagram for Modification:

[legend]

Class Members
vector< pair< ModificationTag, optional< Label > > >	alternatives	Each alternative is a (tag, optional_label) pair.
const ResidueModification *	resolved_mod = nullptr	Resolved modification pointer (populated by resolveModifications) Points to the ResidueModification for the first alternative, if found

◆ OpenMS::SequenceElement

struct OpenMS::SequenceElement

A single amino acid with its modifications.

Represents one position in the peptide sequence: the amino acid residue and zero or more modifications attached to it.

Collaboration diagram for SequenceElement:

[legend]

Class Members
char	amino_acid	Single-letter amino acid code (A-Z)
vector< Modification >	modifications	Modifications at this position.

◆ OpenMS::AmbiguousRegion

struct OpenMS::AmbiguousRegion

Ambiguous amino acid region.

Represents a region where the amino acid sequence is uncertain. ProForma notation: (?DQ) means either D or Q at this position.

Collaboration diagram for AmbiguousRegion:

[legend]

Class Members
vector< SequenceElement >	elements	The ambiguous amino acid possibilities.

◆ OpenMS::ModifiedRange

struct OpenMS::ModifiedRange

Modified sequence range with shared modifications.

Represents a subsequence where one or more modifications apply to the entire range, but the exact position is uncertain.

ProForma notation: (EOSFORMS)[+19.0523] means +19.0523 applies somewhere in EOSFORMS

Collaboration diagram for ModifiedRange:

[legend]

Class Members
vector< SequenceElement >	elements	The amino acids in the range.
vector< Modification >	modifications	Modifications applying to the entire range.

◆ OpenMS::UnlocalisedMod

struct OpenMS::UnlocalisedMod

Unlocalised modification with optional occurrence count.

Represents a modification that is known to exist on the peptide but whose exact position is unknown. The occurrence specifies how many instances of this modification are present.

ProForma notation: [Phospho]?PEPTIDE or [Phospho]^2?PEPTIDE

Collaboration diagram for UnlocalisedMod:

[legend]

Class Members
vector< Modification >	modifications	The unlocalised modification(s)
optional< int >	occurrence	Optional occurrence count from ^N suffix.

◆ OpenMS::LabileModification

struct OpenMS::LabileModification

Labile modification that may be lost during fragmentation.

Labile modifications are typically lost during ionization or fragmentation and thus may not be observed in MS/MS spectra.

ProForma notation: {Glycan:Hex}PEPTIDE

Collaboration diagram for LabileModification:

[legend]

Class Members
Modification	modification	The labile modification.

◆ OpenMS::GlobalModification

struct OpenMS::GlobalModification

Global modification applied to specific locations.

A global modification applies the same modification to all occurrences of specified residues or termini throughout the peptide.

ProForma notation: <[TMT6plex]@K,N-term>

Collaboration diagram for GlobalModification:

[legend]

Class Members
vector< String >	locations	Target locations ("K", "N-term", "C-term:K", etc.)
Modification	modification	The modification to apply.

◆ OpenMS::IsotopeReplacement

struct OpenMS::IsotopeReplacement

Isotope replacement for stable isotope labeling.

Represents global replacement of an element with a specific isotope, used for stable isotope labeling experiments.

ProForma notation: <13C> or <15N> or <D>

Collaboration diagram for IsotopeReplacement:

[legend]

Class Members
String	isotope	The isotope specification (e.g., "13C", "15N", "D")

◆ OpenMS::AdductIon

struct OpenMS::AdductIon

Adduct ion specification for charge state.

Represents an adduct ion contributing to the charge state of a peptidoform ion. Multiple adducts can combine to give the total charge.

ProForma notation: Na:z+1 in /[Na:z+1,H:z+1]

Collaboration diagram for AdductIon:

[legend]

Class Members
int	charge	The charge contribution of this adduct.
String	formula	The adduct formula (e.g., "Na", "H", "K")
optional< int >	occurrence	Optional occurrence count from ^N suffix.

◆ OpenMS::Peptidoform

struct OpenMS::Peptidoform

A single peptidoform (one peptide chain)

Represents a complete peptide chain including:

Optional name identifier (from v2.1 extension)
Global modifications (<13C>, <[TMT6plex]@K>)
Unlocalised modifications ([Phospho]?)
Labile modifications ({Glycan:Hex})
N-terminal modifications ([Acetyl]-)
The amino acid sequence with modifications
C-terminal modifications (-[Amidated])

Collaboration diagram for Peptidoform:

[legend]

Class Members
vector< Modification >	c_term_mods	C-terminal modifications: -[Amidated].
optional< ChargeState >	charge	Optional per-chain charge (for chimeric spectra)
vector< GlobalModEntry >	global_mods	Global modifications: `<13C>`, `<[TMT6plex]@K>`
vector< LabileModification >	labile_mods	Labile modifications: {Glycan:Hex}.
vector< Modification >	n_term_mods	N-terminal modifications: [Acetyl]-.
optional< String >	name	Optional name from (>name) v2.1 extension.
vector< SequenceSection >	sequence	The sequence with modifications.
vector< UnlocalisedMod >	unlocalised_mods	Unlocalised modifications: [Phospho]?

◆ OpenMS::PeptidoformIon

struct OpenMS::PeptidoformIon

A peptidoform ion (one or more chains with optional charge)

Represents one or more peptide chains that form a single ion species. Multiple chains can be present in cross-linked or multi-chain entities.

ProForma notation: chains are separated by //

Collaboration diagram for PeptidoformIon:

[legend]

Class Members
vector< Peptidoform >	chains	One or more peptide chains (separated by // or + in ProForma)
optional< ChargeState >	charge	Optional charge state specification.
bool	is_chimeric = false	True if chains are chimeric (+ separator), false if cross-linked (//)
optional< String >	name	Optional name from (>>name) v2.1 extension.

◆ OpenMS::CrossLinkGroup

struct OpenMS::CrossLinkGroup

Cross-link group connecting sites across chains.

Groups together all sites that share a cross-link label. Each site is identified by its chain index and position within that chain.

Derived during parsing from matching #XL labels.

Collaboration diagram for CrossLinkGroup:

[legend]

Class Members
String	label	The cross-link label (e.g., `XL1`)
vector< pair< size_t, size_t > >	sites	(chain_index, site_index) pairs

Typedef Documentation

◆ ChargeState

using ChargeState = std::variant< int, std::vector<AdductIon> >

Charge state specification.

The charge state can be specified as either:

A simple integer charge (/2, /+2, /-1)
A list of adduct ions (/[Na:z+1,H:z+1])

◆ GlobalModEntry

using GlobalModEntry = std::variant< IsotopeReplacement, GlobalModification >

Variant type for global modification entries.

A GlobalModEntry can be either:

IsotopeReplacement: Global isotope substitution (<13C>)
GlobalModification: Position-specific global mod (<[TMT6plex]@K>)

◆ ModificationTag

using ModificationTag = std::variant< CvAccession, NamedMod, MassDelta, FormulaTag, GlycanComposition, InfoTag, PositionConstraint >

Variant type representing any modification tag content.

A ModificationTag can be one of:

CvAccession: CV database accession (e.g., UNIMOD:35)
NamedMod: Named modification with optional CV hint (e.g., Oxidation, U:Oxidation)
MassDelta: Mass difference with optional source (e.g., +15.9949, Obs:+79.978)
FormulaTag: Chemical formula (e.g., Formula:C12H20O2)
GlycanComposition: Glycan composition (e.g., Glycan:HexNAc1Hex2)
InfoTag: Info annotation (e.g., INFO:comment)
PositionConstraint: Allowed residue positions (e.g., Position:MKC)

◆ SequenceSection

using SequenceSection = std::variant< SequenceElement, AmbiguousRegion, ModifiedRange >

Variant type representing a section of the sequence.

A SequenceSection can be:

SequenceElement: A single amino acid with its modifications
AmbiguousRegion: Uncertain amino acid identity (?XY)
ModifiedRange: Subsequence with range-wide modifications (XYZ)[mod]

Enumeration Type Documentation

◆ AASequenceConversionPolicy

enum class AASequenceConversionPolicy

strong

Conversion policy for transforming Peptidoform to AASequence.

Controls how the conversion handles modifications that cannot be directly represented in AASequence (e.g., unlocalised, labile, or ambiguous modifications).

Enumerator
FAIL_ON_LOSS	Fail if any modification cannot be fully represented.
DROP_UNLOCALISED	Drop unlocalised, labile, and global modifications.
BEST_EFFORT	Try to convert as much as possible, skip unsupported.

◆ ConversionIssueType

enum class ConversionIssueType

strong

Issue type for AASequence conversion problems.

Enumerator
UNRESOLVED_MOD	Modification could not be found in ModificationsDB.
UNLOCALISED_MOD	Modification has no specific position.
LABILE_MOD	Labile modification (lost during fragmentation)
GLOBAL_MOD	Global modification (applies to multiple sites)
AMBIGUOUS_MOD	Ambiguously localized modification.
AMBIGUOUS_REGION	Ambiguous amino acid region.
MODIFIED_RANGE	Modified range (position uncertain)
CROSS_LINK	Cross-link between chains.
MULTIPLE_CHAINS	Multiple peptide chains.
ALTERNATIVE_MODS	Multiple alternative modifications (\|)
UNSUPPORTED_FEATURE	Other unsupported ProForma feature.

◆ CvDatabase

enum class CvDatabase

strong

Controlled vocabulary database prefix for modification accessions.

Identifies the source database for a modification accession in ProForma notation. Examples: UNIMOD:35, MOD:00046, XLMOD:02001, GNO:G59626AS

Enumerator
UNIMOD	UniMod database (https://www.unimod.org/)
MOD	PSI-MOD ontology (https://www.ebi.ac.uk/ols/ontologies/mod)
RESID	RESID database.
XLMOD	Cross-linking modifications ontology.
GNO	Glycan naming ontology.

◆ ProFormaErrorCode

enum class ProFormaErrorCode

strong

Error codes for programmatic handling of ProForma parse errors.

These error codes provide machine-readable categorization of parsing failures, enabling downstream code to handle specific error types appropriately.

Enumerator
UNEXPECTED_CHARACTER	Unexpected character encountered during parsing.
UNCLOSED_BRACKET	Opening bracket without matching close bracket.
UNMATCHED_BRACKET	Closing bracket without matching open bracket.
INVALID_CV_PREFIX	Invalid controlled vocabulary prefix (e.g., not UNIMOD, MOD, etc.)
INVALID_CV_ACCESSION	Invalid CV accession number format.
INVALID_AMINO_ACID	Invalid amino acid one-letter code.
INVALID_MASS_VALUE	Invalid mass value format or value.
INVALID_FORMULA	Invalid chemical formula.
UNKNOWN_MONOSACCHARIDE	Unknown monosaccharide abbreviation.
DANGLING_CROSSLINK_LABEL	Crosslink label without a matching partner.
EMPTY_SEQUENCE	Empty sequence provided.
INVALID_CHARGE	Invalid charge state specification.
INVALID_OCCURRENCE_SPECIFIER	Invalid occurrence specifier (e.g., ^2)
UNEXPECTED_END_OF_INPUT	Unexpected end of input string.
INTERNAL_ERROR	Internal parser error (should not occur)

◆ ProFormaWriteMode

enum class ProFormaWriteMode

strong

Write mode for ProForma string serialization.

Controls whether the output preserves original formatting (LOSSLESS) or produces a normalized, deterministic output (CANONICAL).

Enumerator
LOSSLESS	Preserve original spelling/formatting where possible (e.g., mass delta text)
CANONICAL	Normalized output: uppercase CV prefixes, sorted mods, 4 decimal places for masses.

Classes

Typedefs

Enumerations

Detailed Description

Class Documentation

◆ OpenMS::ConversionIssue

◆ OpenMS::CvAccession

◆ OpenMS::NamedMod

◆ OpenMS::FormulaTag

◆ OpenMS::GlycanComposition

◆ OpenMS::InfoTag

◆ OpenMS::PositionConstraint

◆ OpenMS::Modification

◆ OpenMS::SequenceElement

◆ OpenMS::AmbiguousRegion

◆ OpenMS::ModifiedRange

◆ OpenMS::UnlocalisedMod

◆ OpenMS::LabileModification

◆ OpenMS::GlobalModification

◆ OpenMS::IsotopeReplacement

◆ OpenMS::AdductIon

◆ OpenMS::Peptidoform

◆ OpenMS::PeptidoformIon

◆ OpenMS::CrossLinkGroup

Typedef Documentation

◆ ChargeState

◆ GlobalModEntry

◆ ModificationTag

◆ SequenceSection

Enumeration Type Documentation

◆ AASequenceConversionPolicy

◆ ConversionIssueType

◆ CvDatabase

◆ ProFormaErrorCode

◆ ProFormaWriteMode