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, bool use_ms1_ion_mobility)
	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_target, const RangeMobility &range_im)
	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, RangeMobility im_range, OpenSwath_Scores &scores)
	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, RangeMobility &range_im, const OpenMS::DIAScoring &diascoring, OpenSwath_Scores &scores)
	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...

SpectrumSequence	fetchSpectrumSwath (std::vector< OpenSwath::SwathMap > swath_maps, double RT, int nr_spectra_to_add, const RangeMobility &im_range)
	Prepares a spectrum for DIA analysis (single map) More...

SpectrumSequence	fetchSpectrumSwath (OpenSwath::SpectrumAccessPtr swath_map, double RT, int nr_spectra_to_add, const RangeMobility &im_range)
	Prepares a spectrum for DIA analysis (multiple map) More...

Private Types
enum class	SpectrumAdditionMethod { ADDITION , RESAMPLE }

typedef OpenSwath::LightCompound	CompoundType

typedef OpenSwath::LightTransition	TransitionType

Private Attributes
double	rt_normalization_factor_

double	spacing_for_spectra_resampling_

int	add_up_spectra_

SpectrumAdditionMethod	spectra_addition_method_

double	im_drift_extra_pcnt_

OpenSwath_Scores_Usage	su_

bool	use_ms1_ion_mobility_
	whether to use MS1 ion mobility extraction in DIA scores More...

const std::string	ION_MOBILITY_DESCRIPTION = "Ion Mobility"

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

Member Enumeration Documentation

◆ SpectrumAdditionMethod

enum SpectrumAdditionMethod

strongprivate

Enumerator
ADDITION
RESAMPLE

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,
		RangeMobility &	range_im,
		const OpenMS::DIAScoring &	diascoring,
		OpenSwath_Scores &	scores
	)

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
transition	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
range_im	drift time lower and upper bounds
diascoring	DIA Scoring object to use for scoring
scores	The object to store the result

◆ 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_target,
		const RangeMobility &	range_im
	)

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
	compound	The compound corresponding to the library transitions
	scores	The object to store the result
	mzerror_ppm	m/z and mass error (in ppm) for all transitions
[in]	drift_target	target drift value
[in]	range_im	drift time lower and upper bounds

◆ 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
compound	The compound 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,
		RangeMobility	im_range,
		OpenSwath_Scores &	scores
	)

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
compound	the compound sequence
im_range	drift time lower and upper bounds
scores	The object to store the result

◆ fetchSpectrumSwath() [1/2]

SpectrumSequence fetchSpectrumSwath	(	OpenSwath::SpectrumAccessPtr	swath_map,
		double	RT,
		int	nr_spectra_to_add,
		const RangeMobility &	im_range
	)

Prepares a spectrum for DIA analysis (multiple map)

This function will fetch a SpectrumSequence to be used in DIA analysis. If nr_spectra_to_add == 1, then a vector of length 1 will be returned. Spectra are prepared differently based on the condition Case #1: Non SONAR data and "simple" addition selected - Array of length "nr_spectra_to_add" returned corresponding with "nr_spectra_to_add" spectra Case #2: Non SONAR data and "resampling addition selected - Array of length 1 of the resampled spectrum returned Case #3: SONAR data - Array of length 1 containing the added/resampled spectrum returned

For case #2 and #3 result is all spectra summed up (add) with 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. Spectra are also filtered and summed across drift time to transform an ion mobility spectrum into a non ion mobility spectrum

For case #1 this processing is done downstream in DIA scores to speed up computation time, furthermore drift time filtering is done downstream (these parameters are ignored)

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
[in]	im_range	mobility range, only used if resampling spectrum addition chosen

Returns: Vector of spectra to be used

◆ fetchSpectrumSwath() [2/2]

SpectrumSequence fetchSpectrumSwath	(	std::vector< OpenSwath::SwathMap >	swath_maps,
		double	RT,
		int	nr_spectra_to_add,
		const RangeMobility &	im_range
	)

Prepares a spectrum for DIA analysis (single map)

This function will fetch a vector of spectrum pointers to be used in DIA analysis. If nr_spectra_to_add == 1, then a vector of length 1 will be returned

Case #1: Non SONAR data and "simple" addition selected - Array of length "nr_spectra_to_add" returned corresponding with "nr_spectra_to_add" spectra
Case #2: Non SONAR data and "resampling addition selected - Array of length 1 of the resampled spectrum returned
Case #3: SONAR data - Array of length 1 containing the added/resampled spectrum returned

For case #2 and #3 result is all spectra summed up (add) with 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.

For case #1 this processing is done downstream in DIA scores to speed up computation time

Parameters

[in]	swath_maps	The map containing the spectra
[in]	RT	The target retention time
[in]	nr_spectra_to_add	How many spectra to add up
[in]	im_range	Drift time lower and upper bounds

Returns: Vector of spectra to be used

◆ 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,
		bool	use_ms1_ion_mobility
	)

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
drift_extra	Extend the extraction window to gain a larger field of view beyond drift_upper - drift_lower (in percent)
su	Which scores to actually compute
spectrum_addition_method	Method to use for spectrum addition (valid: "simple", "resample")
use_ms1_ion_mobility	Use MS1 ion mobility extraction in DIA scores

Member Data Documentation

◆ add_up_spectra_

int add_up_spectra_

private

◆ im_drift_extra_pcnt_

double im_drift_extra_pcnt_

private

◆ ION_MOBILITY_DESCRIPTION

const std::string ION_MOBILITY_DESCRIPTION = "Ion Mobility"

private

◆ rt_normalization_factor_

double rt_normalization_factor_

private

◆ spacing_for_spectra_resampling_

double spacing_for_spectra_resampling_

private

◆ spectra_addition_method_

SpectrumAdditionMethod spectra_addition_method_

private

◆ su_

OpenSwath_Scores_Usage su_

private

◆ use_ms1_ion_mobility_

bool use_ms1_ion_mobility_

private

whether to use MS1 ion mobility extraction in DIA scores

Public Member Functions

Private Types

Private Attributes

Detailed Description

Member Typedef Documentation

◆ CompoundType

◆ TransitionType

Member Enumeration Documentation

◆ SpectrumAdditionMethod

Constructor & Destructor Documentation

◆ OpenSwathScoring()

◆ ~OpenSwathScoring()

Member Function Documentation

◆ calculateChromatographicIdScores()

◆ calculateChromatographicScores()

◆ calculateDIAIdScores()

◆ calculateDIAScores()

◆ calculateLibraryScores()

◆ calculatePrecursorDIAScores()

◆ fetchSpectrumSwath() [1/2]

◆ fetchSpectrumSwath() [2/2]

◆ getNormalized_library_intensities_()

◆ initialize()

Member Data Documentation

◆ add_up_spectra_

◆ im_drift_extra_pcnt_

◆ ION_MOBILITY_DESCRIPTION

◆ rt_normalization_factor_

◆ spacing_for_spectra_resampling_

◆ spectra_addition_method_

◆ su_

◆ use_ms1_ion_mobility_