A class that calls the scoring routines. More...

#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScoring.h>

Collaboration diagram for OpenSwathScoring:

Public Member Functions
	OpenSwathScoring ()
	Constructor. More...

	~OpenSwathScoring ()
	Destructor. More...

void	initialize (double rt_normalization_factor, int add_up_spectra, double spacing_for_spectra_resampling, const double drift_extra, const OpenSwath_Scores_Usage &su, const std::string &spectrum_addition_method)
	Initialize the scoring object. More...

void	calculateChromatographicScores (OpenSwath::IMRMFeature *imrmfeature, const std::vector< std::string > &native_ids, const std::vector< std::string > &precursor_ids, const std::vector< double > &normalized_library_intensity, std::vector< OpenSwath::ISignalToNoisePtr > &signal_noise_estimators, OpenSwath_Scores &scores) const
	Score a single peakgroup in a chromatogram using only chromatographic properties. More...

void	calculateChromatographicIdScores (OpenSwath::IMRMFeature *imrmfeature, const std::vector< std::string > &native_ids_identification, const std::vector< std::string > &native_ids_detection, std::vector< OpenSwath::ISignalToNoisePtr > &signal_noise_estimators, OpenSwath_Ind_Scores &scores) const
	Score identification transitions against detection transitions of a single peakgroup in a chromatogram using only chromatographic properties. More...

void	calculateLibraryScores (OpenSwath::IMRMFeature *imrmfeature, const std::vector< TransitionType > &transitions, const CompoundType &compound, const double normalized_feature_rt, OpenSwath_Scores &scores)
	Score a single chromatographic feature against a spectral library. More...

void	calculateDIAScores (OpenSwath::IMRMFeature *imrmfeature, const std::vector< TransitionType > &transitions, const std::vector< OpenSwath::SwathMap > &swath_maps, const OpenSwath::SpectrumAccessPtr &ms1_map, const OpenMS::DIAScoring &diascoring, const CompoundType &compound, OpenSwath_Scores &scores, std::vector< double > &mzerror_ppm, const double drift_lower, const double drift_upper, const double drift_target)
	Score a single chromatographic feature using DIA / SWATH scores. More...

void	calculatePrecursorDIAScores (const OpenSwath::SpectrumAccessPtr &ms1_map, const OpenMS::DIAScoring &diascoring, double precursor_mz, double rt, const CompoundType &compound, OpenSwath_Scores &scores, double drift_lower, double drift_upper)
	Score a single chromatographic feature using the precursor map. More...

void	calculateDIAIdScores (OpenSwath::IMRMFeature *imrmfeature, const TransitionType &transition, const std::vector< OpenSwath::SwathMap > &swath_maps, const OpenMS::DIAScoring &diascoring, OpenSwath_Scores &scores, double drift_lower, double drift_upper)
	Score a single chromatographic feature using DIA / SWATH scores. More...

void	getNormalized_library_intensities_ (const std::vector< TransitionType > &transitions, std::vector< double > &normalized_library_intensity)
	Computing the normalized library intensities from the transition objects. More...

OpenSwath::SpectrumPtr	fetchSpectrumSwath (std::vector< OpenSwath::SwathMap > swath_maps, double RT, int nr_spectra_to_add, const double drift_lower, const double drift_upper)
	Prepares a spectrum for DIA analysis (multiple map) More...

OpenSwath::SpectrumPtr	fetchSpectrumSwath (OpenSwath::SpectrumAccessPtr swath_map, double RT, int nr_spectra_to_add, const double drift_lower, const double drift_upper)
	Prepares a spectrum for DIA analysis (single map) More...

Protected Member Functions
OpenSwath::SpectrumPtr	getAddedSpectra_ (const OpenSwath::SpectrumAccessPtr &swath_map, double RT, int nr_spectra_to_add, const double drift_lower, const double drift_upper)
	Returns an averaged spectrum. More...

Private Types
typedef OpenSwath::LightCompound	CompoundType

typedef OpenSwath::LightTransition	TransitionType

Private Attributes
double	rt_normalization_factor_

double	spacing_for_spectra_resampling_

int	add_up_spectra_

std::string	spectra_addition_method_

double	im_drift_extra_pcnt_

OpenSwath_Scores_Usage	su_

Detailed Description

A class that calls the scoring routines.

Use this class to invoke the individual OpenSWATH scoring routines.

Member Typedef Documentation

◆ CompoundType

typedef OpenSwath::LightCompound CompoundType

private

◆ TransitionType

typedef OpenSwath::LightTransition TransitionType

private

Constructor & Destructor Documentation

◆ OpenSwathScoring()

OpenSwathScoring ( )

Constructor.

◆ ~OpenSwathScoring()

~OpenSwathScoring ( )

Destructor.

Member Function Documentation

◆ calculateChromatographicIdScores()

void calculateChromatographicIdScores	(	OpenSwath::IMRMFeature *	imrmfeature,
		const std::vector< std::string > &	native_ids_identification,
		const std::vector< std::string > &	native_ids_detection,
		std::vector< OpenSwath::ISignalToNoisePtr > &	signal_noise_estimators,
		OpenSwath_Ind_Scores &	scores
	)		const

Score identification transitions against detection transitions of a single peakgroup in a chromatogram using only chromatographic properties.

This function only uses the chromatographic properties (coelution, signal to noise, etc.) of a peakgroup in a chromatogram to compute scores. The scores are computed by scoring identification against detection transitions.

The scores are returned in the OpenSwath_Scores object. Only those scores specified in the OpenSwath_Scores_Usage object are computed.

Parameters

imrmfeature	The feature to be scored
native_ids_identification	The list of identification native ids (giving a canonical ordering of the transitions)
native_ids_detection	The list of detection native ids (giving a canonical ordering of the transitions)
signal_noise_estimators	The signal-to-noise estimators for each transition
scores	The object to store the result

◆ calculateChromatographicScores()

void calculateChromatographicScores	(	OpenSwath::IMRMFeature *	imrmfeature,
		const std::vector< std::string > &	native_ids,
		const std::vector< std::string > &	precursor_ids,
		const std::vector< double > &	normalized_library_intensity,
		std::vector< OpenSwath::ISignalToNoisePtr > &	signal_noise_estimators,
		OpenSwath_Scores &	scores
	)		const

Score a single peakgroup in a chromatogram using only chromatographic properties.

This function only uses the chromatographic properties (coelution, signal to noise, etc.) of a peakgroup in a chromatogram to compute scores. If more information is available, also consider using the library based scoring and the full-spectrum based scoring.

The scores are returned in the OpenSwath_Scores object. Only those scores specified in the OpenSwath_Scores_Usage object are computed.

Parameters

imrmfeature	The feature to be scored
native_ids	The list of native ids (giving a canonical ordering of the transitions)
precursor_ids	The list of precursor ids
normalized_library_intensity	The weights to be used for each transition (e.g. normalized library intensities)
signal_noise_estimators	The signal-to-noise estimators for each transition
scores	The object to store the result

◆ calculateDIAIdScores()

void calculateDIAIdScores	(	OpenSwath::IMRMFeature *	imrmfeature,
		const TransitionType &	transition,
		const std::vector< OpenSwath::SwathMap > &	swath_maps,
		const OpenMS::DIAScoring &	diascoring,
		OpenSwath_Scores &	scores,
		double	drift_lower,
		double	drift_upper
	)

Score a single chromatographic feature using DIA / SWATH scores.

The scores are returned in the OpenSwath_Scores object.

Parameters

imrmfeature	The feature to be scored
transitions	The library transition to score the feature against
swath_maps	The SWATH-MS (DIA) maps from which to retrieve full MS/MS spectra at the chromatographic peak apices
diascoring	DIA Scoring object to use for scoring
scores	The object to store the result
drift_lower	Drift time lower extraction boundary
drift_upper	Drift time upper extraction boundary

◆ calculateDIAScores()

void calculateDIAScores	(	OpenSwath::IMRMFeature *	imrmfeature,
		const std::vector< TransitionType > &	transitions,
		const std::vector< OpenSwath::SwathMap > &	swath_maps,
		const OpenSwath::SpectrumAccessPtr &	ms1_map,
		const OpenMS::DIAScoring &	diascoring,
		const CompoundType &	compound,
		OpenSwath_Scores &	scores,
		std::vector< double > &	mzerror_ppm,
		const double	drift_lower,
		const double	drift_upper,
		const double	drift_target
	)

Score a single chromatographic feature using DIA / SWATH scores.

The scores are returned in the OpenSwath_Scores object.

Parameters

imrmfeature	The feature to be scored
transitions	The library transition to score the feature against
swath_maps	The SWATH-MS (DIA) maps from which to retrieve full MS/MS spectra at the chromatographic peak apices
ms1_map	The corresponding MS1 (precursor ion map) from which the precursor spectra can be retrieved (optional, may be NULL)
diascoring	DIA Scoring object to use for scoring
pep	The peptide corresponding to the library transitions
scores	The object to store the result
mzerror_ppm	m/z and mass error (in ppm) for all transitions
drift_lower	Drift time lower extraction boundary
drift_upper	Drift time upper extraction boundary

◆ calculateLibraryScores()

void calculateLibraryScores	(	OpenSwath::IMRMFeature *	imrmfeature,
		const std::vector< TransitionType > &	transitions,
		const CompoundType &	compound,
		const double	normalized_feature_rt,
		OpenSwath_Scores &	scores
	)

Score a single chromatographic feature against a spectral library.

The spectral library is provided in a set of transition objects and a peptide object. Both contain information about the expected elution time on the chromatography and the relative intensity of the transitions.

The scores are returned in the OpenSwath_Scores object.

Parameters

imrmfeature	The feature to be scored
transitions	The library transition to score the feature against
pep	The peptide corresponding to the library transitions
normalized_feature_rt	The retention time of the feature in normalized space
scores	The object to store the result

◆ calculatePrecursorDIAScores()

void calculatePrecursorDIAScores	(	const OpenSwath::SpectrumAccessPtr &	ms1_map,
		const OpenMS::DIAScoring &	diascoring,
		double	precursor_mz,
		double	rt,
		const CompoundType &	compound,
		OpenSwath_Scores &	scores,
		double	drift_lower,
		double	drift_upper
	)

Score a single chromatographic feature using the precursor map.

The scores are returned in the OpenSwath_Scores object.

Parameters

ms1_map	The MS1 (precursor ion map) from which the precursor spectra can be retrieved
diascoring	DIA Scoring object to use for scoring
precursor_mz	The m/z ratio of the precursor
rt	The compound retention time
scores	The object to store the result
drift_lower	Drift time lower extraction boundary
drift_upper	Drift time upper extraction boundary

◆ fetchSpectrumSwath() [1/2]

OpenSwath::SpectrumPtr fetchSpectrumSwath	(	OpenSwath::SpectrumAccessPtr	swath_map,
		double	RT,
		int	nr_spectra_to_add,
		const double	drift_lower,
		const double	drift_upper
	)

Prepares a spectrum for DIA analysis (single map)

This function will sum up (add) the intensities of multiple spectra a single swath map (assuming these are regular SWATH / DIA maps) around the given retention time and return an "averaged" spectrum which may contain less noise.

Parameters

[in]	swath_map	The map containing the spectra
[in]	RT	The target retention time
[in]	nr_spectra_to_add	How many spectra to add up
	drift_lower	Drift time lower extraction boundary
	drift_upper	Drift time upper extraction boundary

Returns: Added up spectrum

◆ fetchSpectrumSwath() [2/2]

OpenSwath::SpectrumPtr fetchSpectrumSwath	(	std::vector< OpenSwath::SwathMap >	swath_maps,
		double	RT,
		int	nr_spectra_to_add,
		const double	drift_lower,
		const double	drift_upper
	)

Prepares a spectrum for DIA analysis (multiple map)

This function will sum up (add) the intensities of multiple spectra from multiple swath maps (assuming these are SONAR maps of shifted precursor isolation windows) around the given retention time and return an "averaged" spectrum which may contain less noise.

Parameters

[in]	swath_maps	The map(s) containing the spectra
[in]	RT	The target retention time
[in]	nr_spectra_to_add	How many spectra to add up
	drift_lower	Drift time lower extraction boundary
	drift_upper	Drift time upper extraction boundary

Returns: Added up spectrum

◆ getAddedSpectra_()

OpenSwath::SpectrumPtr getAddedSpectra_	(	const OpenSwath::SpectrumAccessPtr &	swath_map,
		double	RT,
		int	nr_spectra_to_add,
		const double	drift_lower,
		const double	drift_upper
	)

protected

Returns an averaged spectrum.

This function will sum up (add) the intensities of multiple spectra around the given retention time and return an "averaged" spectrum which may contain less noise.

Parameters

[in]	swath_map	The map containing the spectra
[in]	RT	The target retention time
[in]	nr_spectra_to_add	How many spectra to add up
	drift_lower	Drift time lower extraction boundary
	drift_upper	Drift time upper extraction boundary

Returns: Added up spectrum

◆ getNormalized_library_intensities_()

void getNormalized_library_intensities_	(	const std::vector< TransitionType > &	transitions,
		std::vector< double > &	normalized_library_intensity
	)

Computing the normalized library intensities from the transition objects.

The intensities are normalized such that the sum to one.

Parameters

[in]	transitions	The library transition to score the feature against
[out]	normalized_library_intensity	The resulting normalized library intensities

◆ initialize()

void initialize	(	double	rt_normalization_factor,
		int	add_up_spectra,
		double	spacing_for_spectra_resampling,
		const double	drift_extra,
		const OpenSwath_Scores_Usage &	su,
		const std::string &	spectrum_addition_method
	)

Initialize the scoring object.

Sets the parameters for the scoring.

Parameters

rt_normalization_factor	Specifies the range of the normalized retention time space
add_up_spectra	How many spectra to add up (default 1)
spacing_for_spectra_resampling	Spacing factor for spectra addition
su	Which scores to actually compute
spectrum_addition_method	Method to use for spectrum addition (valid: "simple", "resample")

Member Data Documentation

◆ add_up_spectra_

int add_up_spectra_

private

◆ im_drift_extra_pcnt_

double im_drift_extra_pcnt_

private

◆ rt_normalization_factor_

double rt_normalization_factor_

private

◆ spacing_for_spectra_resampling_

double spacing_for_spectra_resampling_

private

◆ spectra_addition_method_

std::string spectra_addition_method_

private

◆ su_

OpenSwath_Scores_Usage su_

private

Public Member Functions

Protected Member Functions

Private Types

Private Attributes

Detailed Description

Member Typedef Documentation

◆ CompoundType

◆ TransitionType

Constructor & Destructor Documentation

◆ OpenSwathScoring()

◆ ~OpenSwathScoring()

Member Function Documentation

◆ calculateChromatographicIdScores()

◆ calculateChromatographicScores()

◆ calculateDIAIdScores()

◆ calculateDIAScores()

◆ calculateLibraryScores()

◆ calculatePrecursorDIAScores()

◆ fetchSpectrumSwath() [1/2]

◆ fetchSpectrumSwath() [2/2]

◆ getAddedSpectra_()

◆ getNormalized_library_intensities_()

◆ initialize()

Member Data Documentation

◆ add_up_spectra_

◆ im_drift_extra_pcnt_

◆ rt_normalization_factor_

◆ spacing_for_spectra_resampling_

◆ spectra_addition_method_

◆ su_