Scoring of an spectrum at the peak apex of an chromatographic elution peak. More...

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

Inheritance diagram for DIAScoring:

Collaboration diagram for DIAScoring:

Public Member Functions
Constructors and Destructor
	DIAScoring ()
	Default constructor. More...

	~DIAScoring () override
	Destructor. 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...

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...

Private Types
typedef OpenSwath::SpectrumPtr	SpectrumPtrType
	Type definitions. More...

typedef OpenSwath::LightTransition	TransitionType
	Transition interface (Transition, Peptide, Protein) More...

DIA Scores
double	dia_extract_window_

double	dia_byseries_intensity_min_

double	dia_byseries_ppm_diff_

double	dia_nr_isotopes_

double	dia_nr_charges_

double	peak_before_mono_max_ppm_diff_

bool	dia_extraction_ppm_

bool	dia_centroided_

TheoreticalSpectrumGenerator *	generator

void	dia_isotope_scores (const std::vector< TransitionType > &transitions, SpectrumSequence &spectrum, OpenSwath::IMRMFeature *mrmfeature, const RangeMobility &im_range, double &isotope_corr, double &isotope_overlap) const
	Isotope scores, see class description. More...

void	dia_massdiff_score (const std::vector< TransitionType > &transitions, const SpectrumSequence &spectrum, const std::vector< double > &normalized_library_intensity, const RangeMobility &im_range, double &ppm_score, double &ppm_score_weighted, std::vector< double > &diff_ppm) const
	Massdiff scores, see class description. More...

bool	dia_ms1_massdiff_score (double precursor_mz, const SpectrumSequence &spectrum, const RangeMobility &im_range, double &ppm_score) const

void	dia_ms1_isotope_scores_averagine (double precursor_mz, const SpectrumSequence &spectrum, int charge_state, RangeMobility &im_range, double &isotope_corr, double &isotope_overlap) const
	Precursor isotope scores for precursors (peptides and metabolites) More...

void	dia_ms1_isotope_scores (double precursor_mz, const std::vector< SpectrumPtrType > &spectrum, RangeMobility &im_range, double &isotope_corr, double &isotope_overlap, const EmpiricalFormula &sum_formula) const

void	dia_by_ion_score (const SpectrumSequence &spectrum, AASequence &sequence, int charge, const RangeMobility &im_range, double &bseries_score, double &yseries_score) const
	b/y ion scores More...

void	score_with_isotopes (SpectrumSequence &spectrum, const std::vector< TransitionType > &transitions, const RangeMobility &im_range, double &dotprod, double &manhattan) const
	Dotproduct / Manhattan score with theoretical spectrum. More...

	DIAScoring (const DIAScoring &rhs)
	Copy constructor (algorithm class) More...

DIAScoring &	operator= (const DIAScoring &rhs)
	Assignment operator (algorithm class) More...

void	updateMembers_ () override
	Synchronize members with param class. More...

void	diaIsotopeScoresSub_ (const std::vector< TransitionType > &transitions, const SpectrumSequence &spectrum, std::map< std::string, double > &intensities, const RangeMobility &im_range, double &isotope_corr, double &isotope_overlap) const
	Subfunction of dia_isotope_scores. More...

void	getFirstIsotopeRelativeIntensities_ (const std::vector< TransitionType > &transitions, OpenSwath::IMRMFeature *mrmfeature, std::map< std::string, double > &intensities) const

void	largePeaksBeforeFirstIsotope_ (const SpectrumSequence &spectrum, double mono_mz, double mono_int, int &nr_occurrences, double &max_ratio, const RangeMobility &im_range) const
	Determine whether the current m/z value is a monoisotopic peak. More...

double	scoreIsotopePattern_ (const std::vector< double > &isotopes_int, double product_mz, int putative_fragment_charge) const
	Compare an experimental isotope pattern to a theoretical one. More...

double	scoreIsotopePattern_ (const std::vector< double > &isotopes_int, const EmpiricalFormula &sum_formula) const
	Compare an experimental isotope pattern to a theoretical one. More...

double	scoreIsotopePattern_ (const std::vector< double > &isotopes_int, const IsotopeDistribution &isotope_dist) const
	Compare an experimental isotope pattern to a theoretical one. More...

void	getIsotopeIntysFromExpSpec_ (double precursor_mz, const SpectrumSequence &spectrum, int charge_state, const RangeMobility &im_range, std::vector< double > &isotopes_int) const

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

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

Scoring of an spectrum at the peak apex of an chromatographic elution peak.

In DIA (data independent acquisition) / SWATH analysis, at each chromatographic point a full MS2 spectrum is recorded. This class allows to compute a number of scores based on the full MS2 spectrum available. The scores are the following:

isotope scores:
- isotope_corr: computes the correlation of each fragment ion with the theoretical isotope distribution. This is the pearson correlation to the theoretical isotope pattern weighted by the relative intensity of the transition (more is better).
- isotope_overlap: checks whether a signal at position (mz - 1) / charge exists and how strong it is. This would be an indication that the current peak is an isotopic signal of another peak. This simply counts how often a peak was observed that is higher than the current peak, thus number is then weighted by the relative intensity of the transition (thus less is better here).
massdiff score: computes the difference in ppm of the experimental signal to the expected signal (thus less is better).
- Equation: sum(ppm_difference) / # transitions
- Notes:
  - Divide by the total number of transitions and is thus quite punishing if a transition is missing
  - Also outputs a list of all the ppm differences, if signal is not found output -1.0
b/y ion score: checks for the presence of b/y ions of the peptide in question
theoretical spectrum: a dotproduct and a manhattan score with a theoretical spectrum

This class expects spectra objects that implement the OpenSWATH Spectrum interface. Transitions are expected to be in the light transition format (defined in OPENSWATHALGO/DATAACCESS/TransitionExperiment.h).

Parameters of this class are:

Name	Type	Default	Restrictions	Description
dia_extraction_window	float	0.05	min: 0.0	DIA extraction window in Th or ppm.
dia_extraction_unit	string	Th	Th, ppm	DIA extraction window unit
dia_centroided	string	false	true, false	Use centroided DIA data.
dia_byseries_intensity_min	float	300.0	min: 0.0	DIA b/y series minimum intensity to consider.
dia_byseries_ppm_diff	float	10.0	min: 0.0	DIA b/y series minimal difference in ppm to consider.
dia_nr_isotopes	int	4	min: 0	DIA number of isotopes to consider.
dia_nr_charges	int	4	min: 0	DIA number of charges to consider.
peak_before_mono_max_ppm_diff	float	20.0	min: 0.0	DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic.

Note:

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

Member Typedef Documentation

◆ SpectrumPtrType

typedef OpenSwath::SpectrumPtr SpectrumPtrType

private

Type definitions.

Spectrum type, see Spectrum interface

◆ TransitionType

typedef OpenSwath::LightTransition TransitionType

private

Transition interface (Transition, Peptide, Protein)

Constructor & Destructor Documentation

◆ DIAScoring() [1/2]

DIAScoring ( )

Default constructor.

◆ ~DIAScoring()

~DIAScoring ( )

override

Destructor.

◆ DIAScoring() [2/2]

DIAScoring ( const DIAScoring & rhs )

private

Copy constructor (algorithm class)

Member Function Documentation

◆ dia_by_ion_score()

void dia_by_ion_score	(	const SpectrumSequence &	spectrum,
		AASequence &	sequence,
		int	charge,
		const RangeMobility &	im_range,
		double &	bseries_score,
		double &	yseries_score
	)		const

b/y ion scores

◆ dia_isotope_scores()

void dia_isotope_scores	(	const std::vector< TransitionType > &	transitions,
		SpectrumSequence &	spectrum,
		OpenSwath::IMRMFeature *	mrmfeature,
		const RangeMobility &	im_range,
		double &	isotope_corr,
		double &	isotope_overlap
	)		const

Isotope scores, see class description.

◆ dia_massdiff_score()

void dia_massdiff_score	(	const std::vector< TransitionType > &	transitions,
		const SpectrumSequence &	spectrum,
		const std::vector< double > &	normalized_library_intensity,
		const RangeMobility &	im_range,
		double &	ppm_score,
		double &	ppm_score_weighted,
		std::vector< double > &	diff_ppm
	)		const

Massdiff scores, see class description.

◆ dia_ms1_isotope_scores()

void dia_ms1_isotope_scores	(	double	precursor_mz,
		const std::vector< SpectrumPtrType > &	spectrum,
		RangeMobility &	im_range,
		double &	isotope_corr,
		double &	isotope_overlap,
		const EmpiricalFormula &	sum_formula
	)		const

◆ dia_ms1_isotope_scores_averagine()

void dia_ms1_isotope_scores_averagine	(	double	precursor_mz,
		const SpectrumSequence &	spectrum,
		int	charge_state,
		RangeMobility &	im_range,
		double &	isotope_corr,
		double &	isotope_overlap
	)		const

Precursor isotope scores for precursors (peptides and metabolites)

◆ dia_ms1_massdiff_score()

bool dia_ms1_massdiff_score	(	double	precursor_mz,
		const SpectrumSequence &	spectrum,
		const RangeMobility &	im_range,
		double &	ppm_score
	)		const

Precursor massdifference score

Parameters

precursor_mz	Exact m/z of the precursor to be evaluated
spectrum	MS1 spectrum to be evaluated
im_range	Ion mobility range to keep (filter data); can be empty
ppm_score	Resulting score

Returns: False if no signal was found (and no sensible score calculated), true otherwise

◆ diaIsotopeScoresSub_()

void diaIsotopeScoresSub_	(	const std::vector< TransitionType > &	transitions,
		const SpectrumSequence &	spectrum,
		std::map< std::string, double > &	intensities,
		const RangeMobility &	im_range,
		double &	isotope_corr,
		double &	isotope_overlap
	)		const

private

Subfunction of dia_isotope_scores.

◆ getFirstIsotopeRelativeIntensities_()

void getFirstIsotopeRelativeIntensities_	(	const std::vector< TransitionType > &	transitions,
		OpenSwath::IMRMFeature *	mrmfeature,
		std::map< std::string, double > &	intensities
	)		const

private

retrieves intensities from MRMFeature computes a vector of relative intensities for each feature (output to intensities)

◆ getIsotopeIntysFromExpSpec_()

void getIsotopeIntysFromExpSpec_	(	double	precursor_mz,
		const SpectrumSequence &	spectrum,
		int	charge_state,
		const RangeMobility &	im_range,
		std::vector< double > &	isotopes_int
	)		const

private

Get the intensities of isotopes around precursor_mz in experimental spectrum and fill isotopes_int.

◆ largePeaksBeforeFirstIsotope_()

void largePeaksBeforeFirstIsotope_	(	const SpectrumSequence &	spectrum,
		double	mono_mz,
		double	mono_int,
		int &	nr_occurrences,
		double &	max_ratio,
		const RangeMobility &	im_range
	)		const

private

Determine whether the current m/z value is a monoisotopic peak.

This function will try to determine whether the current peak is a monoisotopic peak or not. It will do so by searching for an intense peak at a lower m/z that could explain the current peak as part of a isotope pattern.

Parameters

spectrum	The spectrum (MS1 or MS2)
mono_mz	The m/z value where a monoisotopic is expected
mono_int	The intensity of the monoisotopic peak (peak at mono_mz)
nr_occurrences	Will contain the count of how often a peak is found at lower m/z than mono_mz with an intensity higher than mono_int. Multiple charge states are tested, see class parameter dia_nr_charges_
max_ratio	Will contain the maximum ratio of a peaks intensity compared to the monoisotopic peak intensity how often a peak is found at lower m/z than mono_mz with an intensity higher than mono_int. Multiple charge states are tested, see class parameter dia_nr_charges_
im_range	Ion mobility subrange to consider (used as filter); can be empty (i.e. no IM filtering)

◆ operator=()

DIAScoring& operator= ( const DIAScoring & rhs )

private

Assignment operator (algorithm class)

◆ score_with_isotopes()

void score_with_isotopes	(	SpectrumSequence &	spectrum,
		const std::vector< TransitionType > &	transitions,
		const RangeMobility &	im_range,
		double &	dotprod,
		double &	manhattan
	)		const

Dotproduct / Manhattan score with theoretical spectrum.

◆ scoreIsotopePattern_() [1/3]

double scoreIsotopePattern_	(	const std::vector< double > &	isotopes_int,
		const EmpiricalFormula &	sum_formula
	)		const

private

Compare an experimental isotope pattern to a theoretical one.

This function will take an array of isotope intensities and compare them (by order only; no m/z matching) to the theoretically expected ones for the given sum_formula. The returned value is a Pearson correlation between the experimental and theoretical pattern.

◆ scoreIsotopePattern_() [2/3]

double scoreIsotopePattern_	(	const std::vector< double > &	isotopes_int,
		const IsotopeDistribution &	isotope_dist
	)		const

private

Compare an experimental isotope pattern to a theoretical one.

This function will take an array of isotope intensities and compare them (by order only; no m/z matching) to the theoretically expected ones given by isotope_dist. The returned value is a Pearson correlation between the experimental and theoretical pattern.

◆ scoreIsotopePattern_() [3/3]

double scoreIsotopePattern_	(	const std::vector< double > &	isotopes_int,
		double	product_mz,
		int	putative_fragment_charge
	)		const

private

Compare an experimental isotope pattern to a theoretical one.

This function will take an array of isotope intensities isotopes_int and compare them (by order only; no m/z matching) to the theoretically expected ones for the given product_mz using an averagine model. The returned value is a Pearson correlation between the experimental and theoretical pattern.

◆ updateMembers_()

void updateMembers_ ( )

overrideprivatevirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ dia_byseries_intensity_min_

double dia_byseries_intensity_min_

private

◆ dia_byseries_ppm_diff_

double dia_byseries_ppm_diff_

private

◆ dia_centroided_

bool dia_centroided_

private

◆ dia_extract_window_

double dia_extract_window_

private

◆ dia_extraction_ppm_

bool dia_extraction_ppm_

private

◆ dia_nr_charges_

double dia_nr_charges_

private

◆ dia_nr_isotopes_

double dia_nr_isotopes_

private

◆ generator

TheoreticalSpectrumGenerator* generator

private

◆ peak_before_mono_max_ppm_diff_

double peak_before_mono_max_ppm_diff_

private

Public Member Functions

Private Types

DIA Scores

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ SpectrumPtrType

◆ TransitionType

Constructor & Destructor Documentation

◆ DIAScoring() [1/2]

◆ ~DIAScoring()

◆ DIAScoring() [2/2]

Member Function Documentation

◆ dia_by_ion_score()

◆ dia_isotope_scores()

◆ dia_massdiff_score()

◆ dia_ms1_isotope_scores()

◆ dia_ms1_isotope_scores_averagine()

◆ dia_ms1_massdiff_score()

◆ diaIsotopeScoresSub_()

◆ getFirstIsotopeRelativeIntensities_()

◆ getIsotopeIntysFromExpSpec_()

◆ largePeaksBeforeFirstIsotope_()

◆ operator=()

◆ score_with_isotopes()

◆ scoreIsotopePattern_() [1/3]

◆ scoreIsotopePattern_() [2/3]

◆ scoreIsotopePattern_() [3/3]

◆ updateMembers_()

Member Data Documentation

◆ dia_byseries_intensity_min_

◆ dia_byseries_ppm_diff_

◆ dia_centroided_

◆ dia_extract_window_

◆ dia_extraction_ppm_

◆ dia_nr_charges_

◆ dia_nr_isotopes_

◆ generator

◆ peak_before_mono_max_ppm_diff_