The MRMFeatureFinder finds and scores peaks of transitions that coelute. More...

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

Inheritance diagram for MRMFeatureFinderScoring:

Public Types


typedef MSSpectrum < ChromatogramPeak >	RichPeakChromatogram
	Type definitions.
typedef OpenSwath::LightTransition	TransitionType
typedef OpenSwath::LightTargetedExperiment	TargetedExpType
typedef OpenSwath::LightPeptide	PeptideType
typedef OpenSwath::LightProtein	ProteinType
typedef OpenSwath::LightModification	ModificationType
typedef MRMTransitionGroup < MSSpectrum< ChromatogramPeak > , TransitionType >	MRMTransitionGroupType
typedef std::map< String, MRMTransitionGroupType >	TransitionGroupMapType
Public Member Functions
	MRMFeatureFinderScoring ()
	Constructor.
	~MRMFeatureFinderScoring ()
	Destructor.
void	pickExperiment (OpenSwath::SpectrumAccessPtr input, FeatureMap< Feature > &output, OpenSwath::LightTargetedExperiment &transition_exp, TransformationDescription trafo, OpenSwath::SpectrumAccessPtr swath_map, TransitionGroupMapType &transition_group_map)
void	mapExperimentToTransitionList (OpenSwath::SpectrumAccessPtr input, OpenSwath::LightTargetedExperiment &transition_exp, TransitionGroupMapType &transition_group_map, TransformationDescription trafo, double rt_extraction_window)
void	setStrictFlag (bool f)
Private Member Functions
template<typename SpectrumT , typename TransitionT >
void	scorePeakgroups_ (MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, TransformationDescription &trafo, OpenSwath::SpectrumAccessPtr swath_map, FeatureMap< Feature > &output)
	Score all peak groups.
OpenSwath::SpectrumPtr	getAddedSpectra_ (OpenSwath::SpectrumAccessPtr swath_map, double RT, int nr_spectra_to_add)
	Returns the addition of "nr_spectra_to_add" spectra around the given RT.
template<typename SpectrumT , typename TransitionT >
void	calculateSwathScores_ (MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, MRMFeature &mrmfeature_, OpenSwath::SpectrumAccessPtr swath_map, std::vector< double > &normalized_library_intensity, OpenSwath_Scores scores)
void	updateMembers_ ()
	Synchronize members with param class.
Private Attributes
DoubleReal	rt_extraction_window_
DoubleReal	quantification_cutoff_
bool	use_coelution_score_
bool	use_shape_score_
bool	use_rt_score_
bool	use_library_score_
bool	use_elution_model_score_
bool	use_intensity_score_
bool	use_total_xic_score_
bool	use_nr_peaks_score_
bool	use_sn_score_
int	stop_report_after_feature_
int	add_up_spectra_
DoubleReal	spacing_for_spectra_resampling_
bool	write_convex_hull_
bool	strict_
DoubleReal	rt_normalization_factor_
std::map< OpenMS::String, double >	PeptideRTMap_
std::map< OpenMS::String, const PeptideType * >	PeptideRefMap_
std::map< OpenMS::String, const ProteinType * >	ProteinRefMap_
OpenSwath::MRMScoring	mrmscore_
OpenMS::DIAScoring	diascoring_
OpenMS::EmgScoring	emgscoring_

Detailed Description

The MRMFeatureFinder finds and scores peaks of transitions that coelute.

It does so using an internal peakpicker for each chromatogram and then creating consensus / meta-peaks (MRMFeatures) that contain the information of all corresponding chromatograms at the peak-position. It then goes on to score those MRMFeatures using different criteria described in the MRMScoring class.

Member Typedef Documentation

typedef OpenSwath::LightModification ModificationType

typedef MRMTransitionGroup<MSSpectrum <ChromatogramPeak>, TransitionType> MRMTransitionGroupType

typedef OpenSwath::LightPeptide PeptideType

typedef OpenSwath::LightProtein ProteinType

typedef MSSpectrum<ChromatogramPeak> RichPeakChromatogram

Type definitions.

typedef OpenSwath::LightTargetedExperiment TargetedExpType

typedef std::map<String, MRMTransitionGroupType> TransitionGroupMapType

typedef OpenSwath::LightTransition TransitionType

Constructor & Destructor Documentation

MRMFeatureFinderScoring ( )

Constructor.

~MRMFeatureFinderScoring ( )

Destructor.

Member Function Documentation

void calculateSwathScores_	(	MRMTransitionGroup< SpectrumT, TransitionT > &	transition_group,
		MRMFeature &	mrmfeature_,
		OpenSwath::SpectrumAccessPtr	swath_map,
		std::vector< double > &	normalized_library_intensity,
		OpenSwath_Scores	scores
	)			`[inline, private]`

References MRMFeature::addScore(), OpenSwath_Scores::calculate_swath_lda_prescore(), OpenSwathDataAccessHelper::convertPeptideToAASequence(), Peak2D::getRT(), MRMTransitionGroup< SpectrumType, TransitionType >::getTransitions(), OpenSwath_Scores::isotope_correlation, OpenSwath_Scores::isotope_overlap, OpenSwath_Scores::massdev_score, Feature::setOverallQuality(), MRMTransitionGroup< SpectrumType, TransitionType >::size(), OpenSwath::SpectrumPtr, and OpenSwath_Scores::yseries_score.

OpenSwath::SpectrumPtr getAddedSpectra_	(	OpenSwath::SpectrumAccessPtr	swath_map,
		double	RT,
		int	nr_spectra_to_add
	)			`[inline, private]`

Returns the addition of "nr_spectra_to_add" spectra around the given RT.

References SpectrumAddition::addUpSpectra(), and OpenSwath::SpectrumPtr.

void mapExperimentToTransitionList	(	OpenSwath::SpectrumAccessPtr	input,
		OpenSwath::LightTargetedExperiment &	transition_exp,
		TransitionGroupMapType &	transition_group_map,
		TransformationDescription	trafo,
		double	rt_extraction_window
	)

void pickExperiment	(	OpenSwath::SpectrumAccessPtr	input,
		FeatureMap< Feature > &	output,
		OpenSwath::LightTargetedExperiment &	transition_exp,
		TransformationDescription	trafo,
		OpenSwath::SpectrumAccessPtr	swath_map,
		TransitionGroupMapType &	transition_group_map
	)			`[inline]`

References MRMTransitionGroup< SpectrumType, TransitionType >::getChromatograms(), LightTargetedExperiment::getPeptides(), FeatureMap< FeatureT >::getProteinIdentifications(), LightTargetedExperiment::getProteins(), MRMTransitionGroup< SpectrumType, TransitionType >::getTransitions(), LightTargetedExperiment::getTransitions(), LightProtein::id, LightPeptide::id, MRMTransitionGroupPicker::pickTransitionGroup(), LightPeptide::rt, run_identifier, LightProtein::sequence, ProteinHit::setAccession(), ProteinIdentification::setHits(), ProteinIdentification::setIdentifier(), DefaultParamHandler::setParameters(), and ProteinHit::setSequence().

void scorePeakgroups_	(	MRMTransitionGroup< SpectrumT, TransitionT > &	transition_group,
		TransformationDescription &	trafo,
		OpenSwath::SpectrumAccessPtr	swath_map,
		FeatureMap< Feature > &	output
	)			`[inline, private]`