Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications. More...

#include <OpenMS/ANALYSIS/ID/IDMapper.h>

Inheritance diagram for IDMapper:

Collaboration diagram for IDMapper:

Classes
struct	SpectraIdentificationState
	Result of a partitioning by identification state with mapPrecursorsToIdentifications(). More...

Public Types
enum	Measure { MEASURE_PPM = 0 , MEASURE_DA }

Public Member Functions
	IDMapper ()
	Default constructor. More...

	IDMapper (const IDMapper &cp)
	Copy C'Tor. More...

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

void	annotate (PeakMap &map, const std::vector< PeptideIdentification > &peptide_ids, const std::vector< ProteinIdentification > &protein_ids, const bool clear_ids=false, const bool map_ms1=false)
	Mapping method for peak maps. More...

void	annotate (PeakMap &map, FeatureMap fmap, const bool clear_ids=false, const bool map_ms1=false)
	Mapping method for peak maps. More...

void	annotate (FeatureMap &map, const std::vector< PeptideIdentification > &ids, const std::vector< ProteinIdentification > &protein_ids, bool use_centroid_rt=false, bool use_centroid_mz=false, const PeakMap &spectra=PeakMap())
	Mapping method for feature maps. More...

void	annotate (ConsensusMap &map, const std::vector< PeptideIdentification > &ids, const std::vector< ProteinIdentification > &protein_ids, bool measure_from_subelements=false, bool annotate_ids_with_subelements=false, const PeakMap &spectra=PeakMap())
	Mapping method for consensus maps. More...

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

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

virtual	~DefaultParamHandler ()
	Destructor. More...

virtual DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Static Public Member Functions
static SpectraIdentificationState	mapPrecursorsToIdentifications (const PeakMap &spectra, const std::vector< PeptideIdentification > &ids, double mz_tol=0.001, double rt_tol=0.001)
	Mapping of peptide identifications to spectra This helper function partitions all spectra into those that had: More...

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")
	Writes all parameters to meta values. More...

Protected Member Functions
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

double	getAbsoluteMZTolerance_ (const double mz) const

bool	isMatch_ (const double rt_distance, const double mz_theoretical, const double mz_observed) const
	check if distance constraint is fulfilled (using `rt_tolerance_`, `mz_tolerance_` and `measure_`) More...

void	checkHits_ (const std::vector< PeptideIdentification > &ids) const
	helper function that checks if all peptide hits are annotated with RT and MZ meta values More...

void	getIDDetails_ (const PeptideIdentification &id, double &rt_pep, DoubleList &mz_values, IntList &charges, bool use_avg_mass=false) const

void	increaseBoundingBox_ (DBoundingBox< 2 > &box)
	increase a bounding box by the given RT and m/z tolerances More...

bool	checkMassType_ (const std::vector< DataProcessing > &processing) const

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
double	rt_tolerance_
	Allowed RT deviation. More...

double	mz_tolerance_
	Allowed m/z deviation. More...

Measure	measure_
	Measure used for m/z. More...

bool	ignore_charge_
	Ignore charge states during matching? More...

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Detailed Description

Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications.

ProteinIdentifications are assigned to the whole map.

The retention time and mass-to-charge ratio of the PeptideIdentification as the respective "MZ" and "RT" members.

m/z-matching on peptide side can be done either with the precursor m/z value of the peptide identification or with the theoretical masses of the peptide hits (see "mz_reference" parameter).

See the documentation of the individual annotate methods for more in-depth information.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
rt_tolerance	float	5.0	min: 0.0	RT tolerance (in seconds) for the matching
mz_tolerance	float	20.0	min: 0.0	m/z tolerance (in ppm or Da) for the matching
mz_measure	string	ppm	ppm, Da	unit of 'mz_tolerance' (ppm or Da)
mz_reference	string	precursor	precursor, peptide	source of m/z values for peptide identifications
ignore_charge	string	false	true, false	For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature.

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Class Documentation

◆ OpenMS::IDMapper::SpectraIdentificationState

struct OpenMS::IDMapper::SpectraIdentificationState

Result of a partitioning by identification state with mapPrecursorsToIdentifications().

Collaboration diagram for IDMapper::SpectraIdentificationState:

[legend]

Class Members
vector< Size >	identified
vector< Size >	no_precursors
vector< Size >	unidentified

Member Enumeration Documentation

◆ Measure

enum Measure

Enumerator
MEASURE_PPM
MEASURE_DA

Constructor & Destructor Documentation

◆ IDMapper() [1/2]

IDMapper ( )

Default constructor.

◆ IDMapper() [2/2]

IDMapper ( const IDMapper & cp )

Copy C'Tor.

Member Function Documentation

◆ annotate() [1/4]

void annotate	(	ConsensusMap &	map,
		const std::vector< PeptideIdentification > &	ids,
		const std::vector< ProteinIdentification > &	protein_ids,
		bool	measure_from_subelements = `false`,
		bool	annotate_ids_with_subelements = `false`,
		const PeakMap &	spectra = `PeakMap()`
	)

Mapping method for consensus maps.

If several consensus features lie inside the allowed deviation, the peptide identifications are mapped to all the consensus features.

Parameters

map	ConsensusMap to receive the identifications
ids	PeptideIdentification for the ConsensusFeatures
protein_ids	ProteinIdentification for the ConsensusMap
measure_from_subelements	Do distance estimate from FeatureHandles instead of Centroid
annotate_ids_with_subelements	Store map index of FeatureHandle in peptide identification?
spectra	Whether precursors not contained in the identifications are annotated with an empty PeptideIdentification object containing the scan index.

Exceptions

Exception::MissingInformation is thrown if the MetaInfoInterface of ids does not contain 'MZ' and 'RT'

◆ annotate() [2/4]

void annotate	(	FeatureMap &	map,
		const std::vector< PeptideIdentification > &	ids,
		const std::vector< ProteinIdentification > &	protein_ids,
		bool	use_centroid_rt = `false`,
		bool	use_centroid_mz = `false`,
		const PeakMap &	spectra = `PeakMap()`
	)

Mapping method for feature maps.

If all features have at least one convex hull, peptide positions are matched against the bounding boxes of the convex hulls by default. If not, the positions of the feature centroids are used. The respective coordinates of the centroids are also used for matching (in place of the corresponding ranges from the bounding boxes) if use_centroid_rt or use_centroid_mz are true.

In any case, tolerance in RT and m/z dimension is applied according to the global parameters rt_tolerance and mz_tolerance. Tolerance is understood as "plus or minus x", so the matching range is actually increased by twice the tolerance value.

If several features (incl. tolerance) overlap the position of a peptide identification, the identification is annotated to all of them.

Parameters

map	FeatureMap to receive the identifications
ids	PeptideIdentification for the ConsensusFeatures
protein_ids	ProteinIdentification for the ConsensusMap
use_centroid_rt	Whether to use the RT value of feature centroids even if convex hulls are present
use_centroid_mz	Whether to use the m/z value of feature centroids even if convex hulls are present
spectra	Whether precursors not contained in the identifications are annotated with an empty PeptideIdentification object containing the scan index.

Exceptions

Exception::MissingInformation is thrown if entries of ids do not contain 'MZ' and 'RT' information.

◆ annotate() [3/4]

void annotate	(	PeakMap &	map,
		const std::vector< PeptideIdentification > &	peptide_ids,
		const std::vector< ProteinIdentification > &	protein_ids,
		const bool	clear_ids = `false`,
		const bool	map_ms1 = `false`
	)

Mapping method for peak maps.

The identifications stored in a PeptideIdentification instance can be added to the corresponding spectrum. Note that a PeptideIdentication is added to ALL spectra which are within the allowed RT and MZ boundaries.

Parameters

map	MSExperiment to receive the identifications
peptide_ids	PeptideIdentification for the MSExperiment
protein_ids	ProteinIdentification for the MSExperiment
clear_ids	Reset peptide and protein identifications of each scan before annotating
map_ms1	Attach Ids to MS1 spectra using RT mapping only (without precursor, without m/z)

Exceptions

Exception::MissingInformation is thrown if entries of peptide_ids do not contain 'MZ' and 'RT' information.

◆ annotate() [4/4]

void annotate	(	PeakMap &	map,
		FeatureMap	fmap,
		const bool	clear_ids = `false`,
		const bool	map_ms1 = `false`
	)

Mapping method for peak maps.

Add peptide identifications stored in a feature map to their corresponding spectrum.

This function converts the feature map to a vector of peptide identifications (all peptide IDs from each feature are taken) and calls the respective annotate() function. RT and m/z are taken from the peptides, or (if missing) from the feature itself.

Parameters

map	MSExperiment to receive the identifications
fmap	FeatureMap with PeptideIdentifications for the MSExperiment
clear_ids	Reset peptide and protein identifications of each scan before annotating
map_ms1	attach Ids to MS1 spectra using RT mapping only (without precursor, without m/z)

◆ checkHits_()

void checkHits_ ( const std::vector< PeptideIdentification > & ids ) const

protected

helper function that checks if all peptide hits are annotated with RT and MZ meta values

◆ checkMassType_()

bool checkMassType_ ( const std::vector< DataProcessing > & processing ) const

protected

try to determine the type of m/z value reported for features, return whether average peptide masses should be used for matching

◆ getAbsoluteMZTolerance_()

double getAbsoluteMZTolerance_ ( const double mz ) const

protected

compute absolute Da tolerance, for a given m/z, when measure is MEASURE_DA, the value is unchanged, for MEASURE_PPM it is computed according to currently allowed ppm tolerance

◆ getIDDetails_()

void getIDDetails_	(	const PeptideIdentification &	id,
		double &	rt_pep,
		DoubleList &	mz_values,
		IntList &	charges,
		bool	use_avg_mass = `false`
	)		const

protected

get RT, m/z and charge value(s) of a PeptideIdentification

multiple m/z values are returned if "mz_reference" is set to "peptide" (one for each PeptideHit)
one m/z value is returned if "mz_reference" is set to "precursor"

◆ increaseBoundingBox_()

void increaseBoundingBox_ ( DBoundingBox< 2 > & box )

protected

increase a bounding box by the given RT and m/z tolerances

◆ isMatch_()

bool isMatch_	(	const double	rt_distance,
		const double	mz_theoretical,
		const double	mz_observed
	)		const

protected

check if distance constraint is fulfilled (using rt_tolerance_, mz_tolerance_ and measure_)

◆ mapPrecursorsToIdentifications()

static SpectraIdentificationState mapPrecursorsToIdentifications	(	const PeakMap &	spectra,
		const std::vector< PeptideIdentification > &	ids,
		double	mz_tol = `0.001`,
		double	rt_tol = `0.001`
	)

inlinestatic

Mapping of peptide identifications to spectra This helper function partitions all spectra into those that had:

no precursor (e.g. MS1 spectra),
at least one identified precursor,
or only unidentified precursor.
Parameters

spectra The mass spectra

ids The peptide identifications @mz_tol Tolerance used to map to precursor m/z @rt_tol Tolerance used to map to spectrum retention time

Note: mz/tol and rt_tol should, in principle, be zero (or close to zero under numeric inaccuracies).

Returns: A struct of vectors holding spectra indices of the partitioning.

References PeptideIdentification::getHits(), PeptideIdentification::getMZ(), SpectrumSettings::getPrecursors(), MSSpectrum::getRT(), PeptideIdentification::getRT(), IDMapper::SpectraIdentificationState::identified, IDMapper::SpectraIdentificationState::no_precursors, MSExperiment::size(), and IDMapper::SpectraIdentificationState::unidentified.

◆ operator=()

IDMapper& operator= ( const IDMapper & rhs )

Assignment.

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ ignore_charge_

bool ignore_charge_

protected

Ignore charge states during matching?

◆ measure_

Measure measure_

protected

Measure used for m/z.

◆ mz_tolerance_

double mz_tolerance_

protected

Allowed m/z deviation.

◆ rt_tolerance_

double rt_tolerance_

protected

Allowed RT deviation.

spectra	The mass spectra
ids	The peptide identifications @mz_tol Tolerance used to map to precursor m/z @rt_tol Tolerance used to map to spectrum retention time

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Class Documentation

◆ OpenMS::IDMapper::SpectraIdentificationState

Member Enumeration Documentation

◆ Measure

Constructor & Destructor Documentation

◆ IDMapper() [1/2]

◆ IDMapper() [2/2]

Member Function Documentation

◆ annotate() [1/4]

◆ annotate() [2/4]

◆ annotate() [3/4]

◆ annotate() [4/4]

◆ checkHits_()

◆ checkMassType_()

◆ getAbsoluteMZTolerance_()

◆ getIDDetails_()

◆ increaseBoundingBox_()

◆ isMatch_()

◆ mapPrecursorsToIdentifications()

◆ operator=()

◆ updateMembers_()

Member Data Documentation

◆ ignore_charge_

◆ measure_

◆ mz_tolerance_

◆ rt_tolerance_