DIAScoring Class Reference

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.
	~DIAScoring () override
	Destructor.
Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const std::string &name)
	Constructor with name that is displayed in error messages.
	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.
virtual	~DefaultParamHandler ()
	Destructor.
DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator.
virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator.
void	setParameters (const Param &param)
	Sets the parameters.
const Param &	getParameters () const
	Non-mutable access to the parameters.
const Param &	getDefaults () const
	Non-mutable access to the default parameters.
const std::string &	getName () const
	Non-mutable access to the name.
void	setName (const std::string &name)
	Mutable access to the name.
const std::vector< std::string > &	getSubsections () const
	Non-mutable access to the registered subsections.

Private Types
typedef OpenSwath::SpectrumPtr	SpectrumPtrType
	Type definitions.
typedef OpenSwath::LightTransition	TransitionType
	Transition interface (Transition, Peptide, Protein)

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
	Compute the isotope-pattern correlation and isotope-overlap scores for a transition group (see class description).
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
	Compute fragment-ion mass-error scores in ppm against the theoretical product m/z of each transition.
bool	dia_ms1_massdiff_score (double precursor_mz, const SpectrumSequence &spectrum, const RangeMobility &im_range, double &ppm_score) const
	Compute the precursor-mass-error score on an MS1 spectrum.
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-pattern scores using an averagine model.
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
	Precursor isotope-pattern scores using an explicit sum formula.
void	dia_by_ion_score (const SpectrumSequence &spectrum, AASequence &sequence, int charge, const RangeMobility &im_range, double &bseries_score, double &yseries_score) const
	Count the b- and y-fragment ions of a peptide that have evidence in a DIA spectrum.
void	score_with_isotopes (SpectrumSequence &spectrum, const std::vector< TransitionType > &transitions, const RangeMobility &im_range, double &dotprod, double &manhattan) const
	Dot-product and Manhattan-distance scores between the spectrum and the transition group's theoretical isotope pattern.
double	getDIAExtractionWindow () const
	Return the DIA extraction window.
bool	isDIAExtractionPPM () const
	Return whether the DIA extraction window is interpreted in ppm.
	DIAScoring (const DIAScoring &rhs)
	Copy constructor (algorithm class)
DIAScoring &	operator= (const DIAScoring &rhs)
	Assignment operator (algorithm class)
void	updateMembers_ () override
	Synchronize members with param class.
void	diaIsotopeScoresSub_ (const std::vector< TransitionType > &transitions, const SpectrumSequence &spectrum, OpenSwath::IMRMFeature *mrmfeature, const RangeMobility &im_range, double &isotope_corr, double &isotope_overlap) const
	Subfunction of dia_isotope_scores.
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.
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.
double	scoreIsotopePattern_ (const std::vector< double > &isotopes_int, const EmpiricalFormula &sum_formula) const
	Compare an experimental isotope pattern to a theoretical one.
double	scoreIsotopePattern_ (const std::vector< double > &isotopes_int, const IsotopeDistribution &isotope_dist) const
	Compare an experimental isotope pattern to a theoretical one.
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 std::string &key_prefix="")
	Writes all parameters to meta values.
Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.
Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters.
Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes!
std::vector< std::string >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes!
std::string	error_name_
	Name that is displayed in error messages during the parameter checking.
bool	check_defaults_
	If this member is set to false no checking if parameters in done;.
bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;.

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

Count the b- and y-fragment ions of a peptide that have evidence in a DIA spectrum.

For every b/y ion of sequence at the given charge, a peak is considered a match if its ppm error is below "dia_byseries_ppm_diff" and its intensity is above "dia_byseries_intensity_min". The returned scores are the number of matching b- and y-ions.

Parameters

[in]	spectrum	DIA MS2 spectrum sequence.
[in]	sequence	Peptide sequence.
[in]	charge	Fragment-ion charge state. Must be > 0; passing a non-positive value is a programming error (checked in debug builds).
[in]	im_range	Ion-mobility range filter; pass an empty range to disable IM filtering.
[out]	bseries_score	Number of matching b-ions.
[out]	yseries_score	Number of matching y-ions.

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

Compute the isotope-pattern correlation and isotope-overlap scores for a transition group (see class description).

Delegates to the internal diaIsotopeScoresSub_ after zero-initialising the two output arguments. mrmfeature is consulted for per-transition apex intensities used to weight the correlation.

Parameters

[in]	transitions	Transitions whose fragment-ion isotope patterns are scored.
[in]	spectrum	DIA MS2 spectrum sequence (one or more spectra around the apex) the patterns are read from.
[in]	mrmfeature	MRM feature providing per-transition apex intensities used to weight the correlation.
[in]	im_range	Ion-mobility range filter; pass an empty range to disable IM filtering.
[out]	isotope_corr	Intensity-weighted Pearson correlation against the averagine isotope distribution (higher = better).
[out]	isotope_overlap	Intensity-weighted count of peaks at lower m/z than each transition's monoisotope (lower = better).

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

Compute fragment-ion mass-error scores in ppm against the theoretical product m/z of each transition.

For every transition, integrates the spectrum in a window around the theoretical product m/z (window width and ppm-vs-Th controlled by parameter "dia_extraction_window" and "dia_extraction_unit") and records the signed ppm error between the measured and theoretical m/z. Transitions where no signal was found contribute -1.0 to diff_ppm and are excluded from the averages.

Parameters

[in]	transitions	Transitions whose theoretical product m/z values are the targets.
[in]	spectrum	DIA MS2 spectrum sequence.
[in]	normalized_library_intensity	Per-transition library intensities (parallel to transitions) used to weight ppm_score_weighted.
[in]	im_range	Ion-mobility range filter; pass an empty range to disable IM filtering.
[out]	ppm_score	Mean of the absolute ppm errors over observed transitions (0 if none observed).
[out]	ppm_score_weighted	Sum of |ppm| * normalized_library_intensity over observed transitions.
[out]	diff_ppm	Per-transition signed ppm error; -1.0 entries mark transitions with no signal in the extraction window.

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

Precursor isotope-pattern scores using an explicit sum formula.

Builds the theoretical pattern from sum_formula (and uses its charge), then places it at precursor_mz (the actual precursor m/z, which may differ slightly from what sum_formula would predict — e.g. when adducts are present).

Parameters

[in]	precursor_mz	Exact m/z of the precursor to be evaluated.
[in]	spectrum	MS1 spectrum sequence.
[in,out]	im_range	Ion-mobility range filter; may be narrowed during the call.
[out]	isotope_corr	Pearson correlation against the formula-derived isotope distribution.
[out]	isotope_overlap	Count of peaks at lower m/z that could explain precursor_mz as part of a larger isotope envelope.
[in]	sum_formula	Neutral sum formula of the precursor compound; its getCharge() is used for the isotope spacing.

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-pattern scores using an averagine model.

Drives the same scoring as dia_ms1_isotope_scores but builds the theoretical isotope pattern via an averagine model parameterised by precursor_mz and charge_state (suitable for peptides where no exact sum formula is available).

Parameters

[in]	precursor_mz	Exact m/z of the precursor to be evaluated.
[in]	spectrum	MS1 spectrum sequence.
[in]	charge_state	Precursor charge state used to space the averagine isotope envelope.
[in,out]	im_range	Ion-mobility range filter; may be narrowed during the call.
[out]	isotope_corr	Pearson correlation against the averagine isotope distribution.
[out]	isotope_overlap	Count of peaks at lower m/z that could explain precursor_mz as part of a larger isotope envelope.

dia_ms1_massdiff_score()

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

Compute the precursor-mass-error score on an MS1 spectrum.

Integrates the spectrum in a window around precursor_mz and reports the absolute ppm difference between the measured and theoretical m/z.

Parameters

[in]	precursor_mz	Exact m/z of the precursor to be evaluated.
[in]	spectrum	MS1 spectrum sequence.
[in]	im_range	Ion-mobility range filter; pass an empty range to disable IM filtering.
[out]	ppm_score	On success, the absolute ppm error of the measured peak. On failure (no signal found), set to the absolute ppm width of the extraction window as a worst-case bound — not -1.

Returns

true if a signal was integrated successfully, false if no peak was found inside the extraction window (in which case ppm_score still carries the worst-case bound described above).

diaIsotopeScoresSub_()

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

private

Subfunction of dia_isotope_scores.

getDIAExtractionWindow()

double getDIAExtractionWindow ( ) const

inline

Return the DIA extraction window.

The value is expressed in Thomson or ppm, depending on isDIAExtractionPPM().

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.

isDIAExtractionPPM()

bool isDIAExtractionPPM ( ) const

inline

Return whether the DIA extraction window is interpreted in ppm.

Returns false when the extraction window is interpreted in Thomson.

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

[in]	spectrum	The spectrum (MS1 or MS2)
[in]	mono_mz	The m/z value where a monoisotopic is expected
[in]	mono_int	The intensity of the monoisotopic peak (peak at mono_mz)
[out]	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_
[out]	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_
[in]	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

Dot-product and Manhattan-distance scores between the spectrum and the transition group's theoretical isotope pattern.

Parameters

[in]	spectrum	DIA MS2 spectrum sequence.
[in]	transitions	Transition group whose theoretical pattern is scored against spectrum.
[in]	im_range	Ion-mobility range filter; pass an empty range to disable IM filtering.
[out]	dotprod	Dot product of the two intensity vectors (higher = better).
[out]	manhattan	Manhattan distance of the two intensity vectors (lower = better).

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