Represents a single spectrum match (candidate) for a specific tandem mass spectrum (MS/MS). More...

#include <OpenMS/METADATA/PeptideHit.h>

Inheritance diagram for PeptideHit:

Collaboration diagram for PeptideHit:

Classes
struct	PeakAnnotation
	Contains annotations of a peak. More...

class	PepXMLAnalysisResult
	Analysis Result (containing search engine / prophet results) More...

class	RankLess
	Lesser predicate for scores of hits. More...

class	ScoreLess
	Lesser predicate for scores of hits. More...

class	ScoreMore
	Greater predicate for scores of hits. More...

class	SequenceLessComparator
	Lesser predicate for (modified) sequence of hits. More...

Public Types
enum class	TargetDecoyType { TARGET , DECOY , TARGET_DECOY , UNKNOWN }
	Enum for target/decoy annotation. More...

Public Member Functions
Constructors and Assignment
	PeptideHit ()
	Default constructor. More...

	PeptideHit (double score, UInt rank, Int charge, const AASequence &sequence)
	Values constructor that copies sequence. More...

	PeptideHit (double score, UInt rank, Int charge, AASequence &&sequence)
	Values constructor that moves sequence R-value. More...

	PeptideHit (const PeptideHit &source)
	Copy constructor. More...

	PeptideHit (PeptideHit &&) noexcept
	Move constructor. More...

virtual	~PeptideHit ()
	Destructor. More...

PeptideHit &	operator= (const PeptideHit &source)
	Assignment operator. More...

PeptideHit &	operator= (PeptideHit &&) noexcept
	Move assignment operator. More...

bool	operator== (const PeptideHit &rhs) const
	Equality operator. More...

bool	operator!= (const PeptideHit &rhs) const
	Inequality operator. More...

Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()
	Constructor. More...

	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor. More...

	MetaInfoInterface (MetaInfoInterface &&) noexcept
	Move constructor. More...

	~MetaInfoInterface ()
	Destructor. More...

MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator. More...

MetaInfoInterface &	operator= (MetaInfoInterface &&) noexcept
	Move assignment operator. More...

void	swap (MetaInfoInterface &rhs)
	Swap contents. More...

bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator. More...

bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator. More...

const DataValue &	getMetaValue (const String &name) const
	Returns the value corresponding to a string, or DataValue::EMPTY if not found. More...

DataValue	getMetaValue (const String &name, const DataValue &default_value) const
	Returns the value corresponding to a string, or a default value (e.g.: DataValue::EMPTY) if not found More...

const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to the index, or DataValue::EMPTY if not found. More...

DataValue	getMetaValue (UInt index, const DataValue &default_value) const
	Returns the value corresponding to the index, or a default value (e.g.: DataValue::EMPTY) if not found More...

bool	metaValueExists (const String &name) const
	Returns whether an entry with the given name exists. More...

bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists. More...

void	setMetaValue (const String &name, const DataValue &value)
	Sets the DataValue corresponding to a name. More...

void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index. More...

void	removeMetaValue (const String &name)
	Removes the DataValue corresponding to `name` if it exists. More...

void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to `index` if it exists. More...

void	addMetaValues (const MetaInfoInterface &from)

void	getKeys (std::vector< String > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...

void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...

bool	isMetaEmpty () const
	Returns if the MetaInfo is empty. More...

void	clearMetaInfo ()
	Removes all meta values. More...

Accessors
AASequence	sequence_

double	score_ {}
	the score of the peptide hit More...

Int	charge_ {}
	the charge of the peptide More...

std::vector< PeptideEvidence >	peptide_evidences_
	information on the potential peptides observed through this PSM. More...

std::vector< PeptideHit::PeakAnnotation >	fragment_annotations_
	annotations of fragments in the corresponding spectrum More...

const AASequence &	getSequence () const
	returns the peptide sequence More...

AASequence &	getSequence ()
	returns the mutable peptide sequence More...

void	setSequence (const AASequence &sequence)
	sets the peptide sequence More...

void	setSequence (AASequence &&sequence)
	sets the peptide sequence More...

Int	getCharge () const
	returns the charge of the peptide More...

void	setCharge (Int charge)
	sets the charge of the peptide More...

const std::vector< PeptideEvidence > &	getPeptideEvidences () const
	returns information on peptides (potentially) identified by this PSM More...

void	setPeptideEvidences (const std::vector< PeptideEvidence > &peptide_evidences)
	set information on peptides (potentially) identified by this PSM More...

void	setPeptideEvidences (std::vector< PeptideEvidence > &&peptide_evidences)

void	addPeptideEvidence (const PeptideEvidence &peptide_evidence)
	adds information on a peptide that is (potentially) identified by this PSM More...

double	getScore () const
	returns the PSM score More...

void	setScore (double score)
	sets the PSM score More...

void	setAnalysisResults (const std::vector< PepXMLAnalysisResult > &aresult)
	set information on (search engine) sub scores associated with this PSM (only used by pepXML) More...

void	addAnalysisResults (const PepXMLAnalysisResult &aresult)
	add information on (search engine) sub scores associated with this PSM (only used by pepXML) More...

std::vector< PepXMLAnalysisResult >	getAnalysisResults () const
	returns information on (search engine) sub scores associated with this PSM (only used by pepXML) More...

UInt	getRank () const
	returns the PSM rank More...

void	setRank (UInt newrank)
	sets the PSM rank (0 = top hit) More...

std::vector< PeptideHit::PeakAnnotation > &	getPeakAnnotations ()
	returns the fragment annotations More...

const std::vector< PeptideHit::PeakAnnotation > &	getPeakAnnotations () const

void	setPeakAnnotations (std::vector< PeptideHit::PeakAnnotation > frag_annotations)
	sets the fragment annotations More...

bool	isDecoy () const
	Returns true if this hit is annotated as mapping to decoy sequences only. Returns false for TargetDecoyType::TARGET and TargetDecoyType::TARGET_DECOY. Note: an unknown/unannotated state (TargetDecoyType::UNKNOWN) will yield false. More...

void	setTargetDecoyType (TargetDecoyType type)
	Sets the target/decoy type for this peptide hit. More...

TargetDecoyType	getTargetDecoyType () const
	Returns the target/decoy type for this peptide hit. More...

std::set< String >	extractProteinAccessionsSet () const
	extracts the set of non-empty protein accessions from peptide evidences More...

size_t	getNumberOfAnalysisResultsFromMetaValues_ () const
	Get the number of analysis results stored as meta values (only for pepXML results) More...

std::vector< PepXMLAnalysisResult >	extractAnalysisResultsFromMetaValues_ () const
	Extract analysis results from meta values (only for pepXML results) More...

Additional Inherited Members
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry. More...

Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist. More...

Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_
	Pointer to the MetaInfo object (0 by default) More...

Detailed Description

Represents a single spectrum match (candidate) for a specific tandem mass spectrum (MS/MS).

Stores the primary information about a potential match, including:

The sequence (potentially with modifications) using AASequence.
The primary score assigned by the identification algorithm (e.g., search engine).
The rank of this hit compared to other hits for the same spectrum (stored as a meta value with key "rank").
The precursor charge state assumed for this match.
Evidence linking the peptide sequence to specific protein sequences (PeptideEvidence).
Optional annotations mapping fragment ions in the MS/MS spectrum to interpretations (PeakAnnotation).
Optional secondary scores from post-processing tools (PepXMLAnalysisResult).

Objects are typically contained within a PeptideIdentification object, which represents all hits found for a single spectrum. Inherits from MetaInfoInterface, allowing arbitrary metadata (key-value pairs) to be attached.

Deprecated:: Use SpectrumMatch instead. PeptideHit may be removed in a future OpenMS version.

See also: PeptideIdentification, AASequence, PeptideEvidence, PeakAnnotation, PepXMLAnalysisResult, MetaInfoInterface

Member Enumeration Documentation

◆ TargetDecoyType

enum TargetDecoyType

strong

Enum for target/decoy annotation.

Enumerator
TARGET	Only matches target proteins.
DECOY	Only matches decoy proteins.
TARGET_DECOY	Matches BOTH target and decoy proteins.
UNKNOWN	Target/decoy status is unknown (meta value not set)

Constructor & Destructor Documentation

◆ PeptideHit() [1/5]

PeptideHit ( )

Default constructor.

◆ PeptideHit() [2/5]

PeptideHit	(	double	score,
		UInt	rank,
		Int	charge,
		const AASequence &	sequence
	)

Values constructor that copies sequence.

◆ PeptideHit() [3/5]

PeptideHit	(	double	score,
		UInt	rank,
		Int	charge,
		AASequence &&	sequence
	)

Values constructor that moves sequence R-value.

◆ PeptideHit() [4/5]

PeptideHit ( const PeptideHit & source )

Copy constructor.

◆ PeptideHit() [5/5]

PeptideHit ( PeptideHit && )

noexcept

Move constructor.

◆ ~PeptideHit()

virtual ~PeptideHit ( )

virtual

Destructor.

Member Function Documentation

◆ addAnalysisResults()

void addAnalysisResults ( const PepXMLAnalysisResult & aresult )

add information on (search engine) sub scores associated with this PSM (only used by pepXML)

◆ addPeptideEvidence()

void addPeptideEvidence ( const PeptideEvidence & peptide_evidence )

adds information on a peptide that is (potentially) identified by this PSM

◆ extractAnalysisResultsFromMetaValues_()

std::vector<PepXMLAnalysisResult> extractAnalysisResultsFromMetaValues_ ( ) const

private

Extract analysis results from meta values (only for pepXML results)

◆ extractProteinAccessionsSet()

std::set<String> extractProteinAccessionsSet ( ) const

extracts the set of non-empty protein accessions from peptide evidences

Referenced by IDFilter::HasMatchingAccessionUnordered< HitType >::operator()(), and IDFilter::HasMatchingAccession< HitType >::operator()().

◆ getAnalysisResults()

std::vector<PepXMLAnalysisResult> getAnalysisResults ( ) const

returns information on (search engine) sub scores associated with this PSM (only used by pepXML)

◆ getCharge()

Int getCharge ( ) const

returns the charge of the peptide

Referenced by NuXLRTPrediction::buildPredictorsAndResponse_(), IDBoostGraph::LabelVisitor::operator()(), and IDScoreGetterSetter::setScoreAndMoveIfTarget_().

◆ getNumberOfAnalysisResultsFromMetaValues_()

size_t getNumberOfAnalysisResultsFromMetaValues_ ( ) const

private

Get the number of analysis results stored as meta values (only for pepXML results)

◆ getPeakAnnotations() [1/2]

std::vector<PeptideHit::PeakAnnotation>& getPeakAnnotations ( )

returns the fragment annotations

◆ getPeakAnnotations() [2/2]

const std::vector<PeptideHit::PeakAnnotation>& getPeakAnnotations ( ) const

◆ getPeptideEvidences()

const std::vector<PeptideEvidence>& getPeptideEvidences ( ) const

returns information on peptides (potentially) identified by this PSM

◆ getRank()

UInt getRank ( ) const

returns the PSM rank

◆ getScore()

double getScore ( ) const

returns the PSM score

Referenced by NuXLLinearRescore::apply(), MapAlignmentAlgorithmIdentification::getRetentionTimes_(), IDBoostGraph::GetPosteriorVisitor::operator()(), IDBoostGraph::GetScoreTgTVisitor::operator()(), and IDScoreGetterSetter::setScoreAndMoveIfTarget_().

◆ getSequence() [1/2]

AASequence& getSequence ( )

returns the mutable peptide sequence

◆ getSequence() [2/2]

const AASequence& getSequence ( ) const

returns the peptide sequence

Referenced by NuXLLinearRescore::apply(), NuXLRTPrediction::buildPredictorsAndResponse_(), NuXLRTPrediction::buildPredictorsAndResponseFromIdentifiedFeatures_(), MapAlignmentAlgorithmIdentification::getRetentionTimes_(), IDBoostGraph::LabelVisitor::operator()(), IDFilter::PeptideDigestionFilter::operator()(), IDBoostGraph::PrintAddressVisitor< CharT >::operator()(), and IDConflictResolverAlgorithm::resolveBetweenFeatures_().

◆ getTargetDecoyType()

TargetDecoyType getTargetDecoyType ( ) const

Returns the target/decoy type for this peptide hit.

This method performs case-insensitive parsing of the "target_decoy" meta value and returns the corresponding enum value. Returns UNKNOWN if the meta value does not exist.

Returns

The target/decoy classification:

TARGET: Only matches target proteins
DECOY: Only matches decoy proteins
TARGET_DECOY: Matches both target and decoy proteins
UNKNOWN: Target/decoy status not set (meta value missing)

◆ isDecoy()

bool isDecoy ( ) const

Returns true if this hit is annotated as mapping to decoy sequences only. Returns false for TargetDecoyType::TARGET and TargetDecoyType::TARGET_DECOY. Note: an unknown/unannotated state (TargetDecoyType::UNKNOWN) will yield false.

◆ operator!=()

bool operator!= ( const PeptideHit & rhs ) const

Inequality operator.

◆ operator=() [1/2]

PeptideHit& operator= ( const PeptideHit & source )

Assignment operator.

◆ operator=() [2/2]

PeptideHit& operator= ( PeptideHit && )

noexcept

Move assignment operator.

◆ operator==()

bool operator== ( const PeptideHit & rhs ) const

Equality operator.

◆ setAnalysisResults()

void setAnalysisResults ( const std::vector< PepXMLAnalysisResult > & aresult )

set information on (search engine) sub scores associated with this PSM (only used by pepXML)

◆ setCharge()

void setCharge ( Int charge )

sets the charge of the peptide

◆ setPeakAnnotations()

void setPeakAnnotations ( std::vector< PeptideHit::PeakAnnotation > frag_annotations )

sets the fragment annotations

◆ setPeptideEvidences() [1/2]

void setPeptideEvidences ( const std::vector< PeptideEvidence > & peptide_evidences )

set information on peptides (potentially) identified by this PSM

◆ setPeptideEvidences() [2/2]

void setPeptideEvidences ( std::vector< PeptideEvidence > && peptide_evidences )

◆ setRank()

void setRank ( UInt newrank )

sets the PSM rank (0 = top hit)

◆ setScore()

void setScore ( double score )

sets the PSM score

Referenced by NuXLLinearRescore::apply(), IDBoostGraph::SetPosteriorVisitor::operator()(), and IDScoreGetterSetter::setScoreAndMoveIfTarget_().

◆ setSequence() [1/2]

void setSequence ( AASequence && sequence )

sets the peptide sequence

◆ setSequence() [2/2]

void setSequence ( const AASequence & sequence )

sets the peptide sequence

◆ setTargetDecoyType()

void setTargetDecoyType ( TargetDecoyType type )

Sets the target/decoy type for this peptide hit.

This method provides a type-safe way to annotate peptide hits with their target/decoy status. Use TARGET_DECOY for peptides that match both target and decoy protein sequences (these are treated as targets in FDR calculations). Note: UNKNOWN should only be used in special cases where the status needs to be explicitly marked as unknown.

Parameters

type	The target/decoy classification: TARGET: Only matches target proteins DECOY: Only matches decoy proteins TARGET_DECOY: Matches both target and decoy proteins UNKNOWN: Target/decoy status is unknown (explicit unknown state)

Member Data Documentation

◆ charge_

Int charge_ {}

protected

the charge of the peptide

◆ fragment_annotations_

std::vector<PeptideHit::PeakAnnotation> fragment_annotations_

protected

annotations of fragments in the corresponding spectrum

◆ peptide_evidences_

std::vector<PeptideEvidence> peptide_evidences_

protected

information on the potential peptides observed through this PSM.

◆ score_

double score_ {}

protected

the score of the peptide hit

◆ sequence_

AASequence sequence_

protected

Classes

Public Types

Public Member Functions

Accessors

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ TargetDecoyType

Constructor & Destructor Documentation

◆ PeptideHit() [1/5]

◆ PeptideHit() [2/5]

◆ PeptideHit() [3/5]

◆ PeptideHit() [4/5]

◆ PeptideHit() [5/5]

◆ ~PeptideHit()

Member Function Documentation

◆ addAnalysisResults()

◆ addPeptideEvidence()

◆ extractAnalysisResultsFromMetaValues_()

◆ extractProteinAccessionsSet()

◆ getAnalysisResults()

◆ getCharge()

◆ getNumberOfAnalysisResultsFromMetaValues_()

◆ getPeakAnnotations() [1/2]

◆ getPeakAnnotations() [2/2]

◆ getPeptideEvidences()

◆ getRank()

◆ getScore()

◆ getSequence() [1/2]

◆ getSequence() [2/2]

◆ getTargetDecoyType()

◆ isDecoy()

◆ operator!=()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ setAnalysisResults()

◆ setCharge()

◆ setPeakAnnotations()

◆ setPeptideEvidences() [1/2]

◆ setPeptideEvidences() [2/2]

◆ setRank()

◆ setScore()

◆ setSequence() [1/2]

◆ setSequence() [2/2]

◆ setTargetDecoyType()

Member Data Documentation

◆ charge_

◆ fragment_annotations_

◆ peptide_evidences_

◆ score_

◆ sequence_