Represents the set of candidates (SpectrumMatches) identified for a single precursor spectrum. More...

#include <OpenMS/METADATA/PeptideIdentification.h>

Inheritance diagram for PeptideIdentification:

Collaboration diagram for PeptideIdentification:

Public Types
typedef PeptideHit	HitType
	Hit type definition. More...

Constructors, destructor, operators
String	id_
	Identifier by which ProteinIdentification and PeptideIdentification are matched. More...

std::vector< PeptideHit >	hits_
	A list containing the peptide hits. More...

String	score_type_
	The score type (Mascot, Sequest, e-value, p-value) More...

bool	higher_score_better_
	The score orientation. More...

double	mz_

double	rt_

	PeptideIdentification ()
	default constructor More...

virtual	~PeptideIdentification () noexcept
	destructor More...

	PeptideIdentification (const PeptideIdentification &)=default
	copy constructor More...

	PeptideIdentification (PeptideIdentification &&) noexcept=default
	Move constructor. More...

PeptideIdentification &	operator= (const PeptideIdentification &)=default
	Assignment operator. More...

PeptideIdentification &	operator= (PeptideIdentification &&)=default
	Move assignment operator. More...

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

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

double	getRT () const
	returns the RT of the MS2 spectrum where the identification occurred More...

void	setRT (double rt)
	sets the RT of the MS2 spectrum where the identification occurred More...

bool	hasRT () const
	shortcut for isnan(getRT()) More...

double	getMZ () const
	returns the MZ of the MS2 spectrum More...

void	setMZ (double mz)
	sets the MZ of the MS2 spectrum More...

bool	hasMZ () const
	shortcut for isnan(getRT()) More...

const std::vector< PeptideHit > &	getHits () const
	returns the peptide hits as const More...

std::vector< PeptideHit > &	getHits ()
	returns the peptide hits More...

void	insertHit (const PeptideHit &hit)
	Appends a peptide hit. More...

void	insertHit (PeptideHit &&hit)
	Appends a peptide hit. More...

void	setHits (const std::vector< PeptideHit > &hits)
	Sets the peptide hits. More...

void	setHits (std::vector< PeptideHit > &&hits)

double	getSignificanceThreshold () const
	returns the peptide significance threshold value (stored as a meta value) More...

void	setSignificanceThreshold (double value)
	setting of the peptide significance threshold value (stored as a meta value) More...

const String &	getScoreType () const
	returns the peptide score type More...

void	setScoreType (const String &type)
	sets the peptide score type More...

bool	isHigherScoreBetter () const
	returns the peptide score orientation More...

void	setHigherScoreBetter (bool value)
	sets the peptide score orientation More...

const String &	getIdentifier () const
	Returns the identifier which links this PI to its corresponding ProteinIdentification. More...

void	setIdentifier (const String &id)
	sets the identifier which links this PI to its corresponding ProteinIdentification More...

String	getBaseName () const
	returns the base name which links to underlying peak map More...

void	setBaseName (const String &base_name)
	sets the base name which links to underlying peak map More...

const String	getExperimentLabel () const
	returns the experiment label for this identification More...

void	setExperimentLabel (const String &type)
	sets the experiment label for this identification More...

String	getSpectrumReference () const

void	setSpectrumReference (const String &ref)

void	assignRanks ()
	Sorts the hits by score and assigns ranks according to the scores. More...

void	sort ()
	Sorts the hits by score. More...

void	sortByRank ()
	Sorts the hits by rank. More...

bool	empty () const
	Returns if this PeptideIdentification result is empty. More...

static std::function< bool(const PeptideHit &, const PeptideHit &)>	getScoreComparator (bool higher_score_better)

static std::vector< PeptideHit >	getReferencingHits (const std::vector< PeptideHit > &, const std::set< String > &accession)
	returns all peptide hits which reference to a given protein accession (i.e. filter by protein accession) More...

static std::multimap< String, std::pair< Size, Size > >	buildUIDsFromAllPepIDs (const ConsensusMap &cmap)
	Builds MultiMap over all PI's via their UID (as obtained from buildUIDFromPepID()), which is mapped to a index of PI therein, i.e. cm[p.first].getPeptideIdentifications()[p.second];. More...

static String	buildUIDFromPepID (const PeptideIdentification &pep_id, const std::map< String, StringList > &identifier_to_msrunpath)
	Builds UID from PeptideIdentification The UID can be formed in two ways. Either it is composed of the map_index and the spectrum-reference or of the ms_run_path and the spectrum_references, if the path is unique. The parts of the UID are separated by '\|'. More...

Additional Inherited Members
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)
	function to copy all meta values from one object to this one More...

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...

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 the set of candidates (SpectrumMatches) identified for a single precursor spectrum.

Typically encapsulates the results of searching one specific MS/MS spectrum against a sequence database or spectral library. It primarily holds a list of PeptideHit objects, each representing a potential match to the spectrum.

Crucially, a PeptideIdentification is typically associated with a parent ProteinIdentification object. This parent object contains global information about the entire identification run, such as the search parameters, database used, and the overall set of identified proteins. The link between a PeptideIdentification and its parent ProteinIdentification is established via a shared identifier string (see getIdentifier() and setIdentifier()). Multiple PeptideIdentification instances (one per spectrum analyzed) can belong to the same ProteinIdentification run.

Each PeptideIdentification stores the precursor ion's retention time (RT) and mass-to-charge ratio (m/z) corresponding to the spectrum that was identified. This information (retrieved via getRT() and getMZ()) is essential for mapping these identifications back to experimental data, such as peaks in an MSExperiment, features in a FeatureMap, or consensus features in a ConsensusMap. The IDMapper class is often used for this purpose.

The class also stores information about the scoring system used (getScoreType(), isHigherScoreBetter()) and an optional significance threshold (getSignificanceThreshold()) for the peptide hits. The significance threshold is stored as a meta value with the key Constants::UserParam::SIGNIFICANCE_THRESHOLD.

PeptideIdentification inherits from MetaInfoInterface, allowing arbitrary metadata (key-value pairs) to be attached.

Deprecated:: Use SpectrumIdentification instead. PeptideIdentification may be removed in a future OpenMS version.

See also: PeptideHit, ProteinIdentification, IDMapper, MetaInfoInterface

<>

Member Typedef Documentation

◆ HitType

typedef PeptideHit HitType

Hit type definition.

Constructor & Destructor Documentation

◆ PeptideIdentification() [1/3]

PeptideIdentification ( )

default constructor

◆ ~PeptideIdentification()

virtual ~PeptideIdentification ( )

virtualnoexcept

destructor

◆ PeptideIdentification() [2/3]

PeptideIdentification ( const PeptideIdentification & )

default

copy constructor

◆ PeptideIdentification() [3/3]

PeptideIdentification ( PeptideIdentification && )

defaultnoexcept

Move constructor.

Member Function Documentation

◆ assignRanks()

void assignRanks ( )

Sorts the hits by score and assigns ranks according to the scores.

◆ buildUIDFromPepID()

static String buildUIDFromPepID	(	const PeptideIdentification &	pep_id,
		const std::map< String, StringList > &	identifier_to_msrunpath
	)

static

Builds UID from PeptideIdentification The UID can be formed in two ways. Either it is composed of the map_index and the spectrum-reference or of the ms_run_path and the spectrum_references, if the path is unique. The parts of the UID are separated by '|'.

Exceptions

Exception::MissingInformation	if Spectrum reference missing at PeptideIdentification
Exception::MissingInformation	if Multiple files in a run, but no map_index in PeptideIdentification found

Parameters

pep_id	PeptideIdentification for which the UID is computed
identifier_to_msrunpath	Mapping required to build UID. Can be obtained from ProteinIdentification::Mapping::identifier_to_msrunpath which can be created from the corresponding ProtID's

Returns: Returns the UID for PeptideIdentification

◆ buildUIDsFromAllPepIDs()

static std::multimap<String, std::pair<Size, Size> > buildUIDsFromAllPepIDs ( const ConsensusMap & cmap )

static

Builds MultiMap over all PI's via their UID (as obtained from buildUIDFromPepID()), which is mapped to a index of PI therein, i.e. cm[p.first].getPeptideIdentifications()[p.second];.

Parameters

cmap	All PI's of the CMap are enumerated and their UID -> pair mapping is computed

Returns: Returns the MultiMap

◆ empty()

bool empty ( ) const

Returns if this PeptideIdentification result is empty.

◆ getBaseName()

String getBaseName ( ) const

returns the base name which links to underlying peak map

◆ getExperimentLabel()

const String getExperimentLabel ( ) const

returns the experiment label for this identification

◆ getHits() [1/2]

std::vector<PeptideHit>& getHits ( )

returns the peptide hits

◆ getHits() [2/2]

const std::vector<PeptideHit>& getHits ( ) const

returns the peptide hits as const

Referenced by IDFilter::annotateBestPerPeptideWithData(), IDMapper::mapPrecursorsToIdentifications(), OPXLHelper::PeptideIDScoreComparator::operator()(), and FeatureFinderIdentificationAlgorithm::PeptideCompare::operator()().

◆ getIdentifier()

const String& getIdentifier ( ) const

Returns the identifier which links this PI to its corresponding ProteinIdentification.

Referenced by ProteinIdentification::Mapping::getPrimaryMSRunPath().

◆ getMZ()

double getMZ ( ) const

returns the MZ of the MS2 spectrum

Referenced by DimMZ::map(), IDMapper::mapPrecursorsToIdentifications(), and IdentificationDataConverter::PepIDCompare::operator()().

◆ getReferencingHits()

static std::vector<PeptideHit> getReferencingHits	(	const std::vector< PeptideHit > &	,
		const std::set< String > &	accession
	)

static

returns all peptide hits which reference to a given protein accession (i.e. filter by protein accession)

◆ getRT()

double getRT ( ) const

returns the RT of the MS2 spectrum where the identification occurred

Referenced by DimRT::map(), IDMapper::mapPrecursorsToIdentifications(), IdentificationDataConverter::PepIDCompare::operator()(), and FeatureFinderIdentificationAlgorithm::PeptideCompare::operator()().

◆ getScoreComparator()

static std::function<bool(const PeptideHit&, const PeptideHit&)> getScoreComparator ( bool higher_score_better )

static

◆ getScoreType()

const String& getScoreType ( ) const

returns the peptide score type

◆ getSignificanceThreshold()

double getSignificanceThreshold ( ) const

returns the peptide significance threshold value (stored as a meta value)

◆ getSpectrumReference()

String getSpectrumReference ( ) const

returns the spectrum reference for this identification. Currently it should almost always be the full native vendor ID.

◆ hasMZ()

bool hasMZ ( ) const

shortcut for isnan(getRT())

Referenced by IdentificationDataConverter::PepIDCompare::operator()().

◆ hasRT()

bool hasRT ( ) const

shortcut for isnan(getRT())

Referenced by IdentificationDataConverter::PepIDCompare::operator()().

◆ insertHit() [1/2]

void insertHit ( const PeptideHit & hit )

Appends a peptide hit.

◆ insertHit() [2/2]

void insertHit ( PeptideHit && hit )

Appends a peptide hit.

◆ isHigherScoreBetter()

bool isHigherScoreBetter ( ) const

returns the peptide score orientation

Referenced by IDFilter::annotateBestPerPeptideWithData().

◆ operator!=()

bool operator!= ( const PeptideIdentification & rhs ) const

Inequality operator.

◆ operator=() [1/2]

PeptideIdentification& operator= ( const PeptideIdentification & )

default

Assignment operator.

◆ operator=() [2/2]

PeptideIdentification& operator= ( PeptideIdentification && )

default

Move assignment operator.

◆ operator==()

bool operator== ( const PeptideIdentification & rhs ) const

Equality operator.

◆ setBaseName()

void setBaseName ( const String & base_name )

sets the base name which links to underlying peak map

◆ setExperimentLabel()

void setExperimentLabel ( const String & type )

sets the experiment label for this identification

◆ setHigherScoreBetter()

void setHigherScoreBetter ( bool value )

sets the peptide score orientation

◆ setHits() [1/2]

void setHits ( const std::vector< PeptideHit > & hits )

Sets the peptide hits.

◆ setHits() [2/2]

void setHits ( std::vector< PeptideHit > && hits )

◆ setIdentifier()

void setIdentifier ( const String & id )

sets the identifier which links this PI to its corresponding ProteinIdentification

◆ setMZ()

void setMZ ( double mz )

sets the MZ of the MS2 spectrum

◆ setRT()

void setRT ( double rt )

sets the RT of the MS2 spectrum where the identification occurred

◆ setScoreType()

void setScoreType ( const String & type )

sets the peptide score type

◆ setSignificanceThreshold()

void setSignificanceThreshold ( double value )

setting of the peptide significance threshold value (stored as a meta value)

◆ setSpectrumReference()

void setSpectrumReference ( const String & ref )

sets the spectrum reference for this identification. Currently it should almost always be the full native vendor ID.

◆ sort()

void sort ( )

Sorts the hits by score.

Sorting takes the score orientation (higher_score_better_) into account, i.e. after sorting, the best-scoring hit is the first.

Referenced by IDFilter::annotateBestPerPeptideWithData().

◆ sortByRank()

void sortByRank ( )

Sorts the hits by rank.

Sorting hits by rank attribute, i.e. after sorting, the hits will be in ascending order of rank.

Member Data Documentation

◆ higher_score_better_

bool higher_score_better_

protected

The score orientation.

◆ hits_

std::vector<PeptideHit> hits_

protected

A list containing the peptide hits.

◆ id_

String id_

protected

Identifier by which ProteinIdentification and PeptideIdentification are matched.

◆ mz_

double mz_

protected

◆ rt_

double rt_

protected

◆ score_type_

String score_type_

protected

The score type (Mascot, Sequest, e-value, p-value)

Public Types

Constructors, destructor, operators

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ HitType

Constructor & Destructor Documentation

◆ PeptideIdentification() [1/3]

◆ ~PeptideIdentification()

◆ PeptideIdentification() [2/3]

◆ PeptideIdentification() [3/3]

Member Function Documentation

◆ assignRanks()

◆ buildUIDFromPepID()

◆ buildUIDsFromAllPepIDs()

◆ empty()

◆ getBaseName()

◆ getExperimentLabel()

◆ getHits() [1/2]

◆ getHits() [2/2]

◆ getIdentifier()

◆ getMZ()

◆ getReferencingHits()

◆ getRT()

◆ getScoreComparator()

◆ getScoreType()

◆ getSignificanceThreshold()

◆ getSpectrumReference()

◆ hasMZ()

◆ hasRT()

◆ insertHit() [1/2]

◆ insertHit() [2/2]

◆ isHigherScoreBetter()

◆ operator!=()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ setBaseName()

◆ setExperimentLabel()

◆ setHigherScoreBetter()

◆ setHits() [1/2]

◆ setHits() [2/2]

◆ setIdentifier()

◆ setMZ()

◆ setRT()

◆ setScoreType()

◆ setSignificanceThreshold()

◆ setSpectrumReference()

◆ sort()

◆ sortByRank()

Member Data Documentation

◆ higher_score_better_

◆ hits_

◆ id_

◆ mz_

◆ rt_

◆ score_type_