MRMIonSeries Class Reference

Generate theoretical fragment ion series for use in MRMAssay and MRMDecoy. More...

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

Public Types
typedef boost::unordered_map< String, double >	IonSeries

Public Member Functions
std::pair< String, double >	getIon (IonSeries ionseries, String ionid)
	Selects ion from IonSeries according to annotation string. More...
std::pair< String, double >	annotateIon (IonSeries ionseries, double ProductMZ, double mz_threshold)
	Selects ion from IonSeries according to product m/z. More...
void	annotateTransitionCV (ReactionMonitoringTransition &tr, String annotation)
	Annotates transition with CV terms. More...
void	annotateTransition (ReactionMonitoringTransition &tr, const TargetedExperiment::Peptide peptide, const double mz_threshold, bool enable_reannotation, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_losses, int round_decPow=-4)
	Annotates transition. More...
IonSeries	getIonSeries (AASequence sequence, size_t precursor_charge, std::vector< String > fragment_types, std::vector< size_t > fragment_charges, bool enable_losses, int round_decPow=-4)
	Computed theoretical fragment ion series. More...
	MRMIonSeries ()
	Constructor. More...
	~MRMIonSeries ()
	Destructor. More...

Private Member Functions
CVTermList	annotationToCVTermList_ (String annotation)
void	annotationToCV_ (ReactionMonitoringTransition &tr)

Detailed Description

Generate theoretical fragment ion series for use in MRMAssay and MRMDecoy.

Will generate theoretical fragment ionseries based on AASequence and parameters. Neutral losses are supported according to a model similar to the one in SpectraST. ReactionMonitoringTransition objects can be annotated with the corresponding CV terms.

Member Typedef Documentation

typedef boost::unordered_map<String, double> IonSeries

Constructor & Destructor Documentation

MRMIonSeries

(

)

Constructor.

~MRMIonSeries

(

)

Destructor.

Member Function Documentation

std::pair<String, double> annotateIon	(	IonSeries	ionseries,
		double	ProductMZ,
		double	mz_threshold
	)

Selects ion from IonSeries according to product m/z.

Parameters

ionseries	the IonSeries from which to choose
ProductMz	the product m/z of the queried fragment ion
mz_threshold	the m/z threshold for annotation of the fragment ion std::pair<String, double> the annotation and product m/z of the queried fragment ion

void annotateTransition	(	ReactionMonitoringTransition &	tr,
		const TargetedExperiment::Peptide	peptide,
		const double	mz_threshold,
		bool	enable_reannotation,
		std::vector< String >	fragment_types,
		std::vector< size_t >	fragment_charges,
		bool	enable_losses,
		int	round_decPow = -4
	)

Annotates transition.

Parameters

tr	the transition to annotate
peptide	the corresponding peptide
mz_threshold	the m/z threshold for annotation of the fragment ion
enable_reannotation	whether the original (e.g. SpectraST) annotation should be used or reannotation should be conducted
fragment_types	the fragment ion types for reannotation
fragment_charges	the fragment ion charges for reannotation
enable_losses	whether neutral losses should be considered
round_decPow	round product m/z values to decimal power (default: -4)

void annotateTransitionCV	(	ReactionMonitoringTransition &	tr,
		String	annotation
	)

Annotates transition with CV terms.

Parameters

tr	the transition to annotate
annotation	the fragment ion annotation.

void annotationToCV_ ( ReactionMonitoringTransition &  tr )

private

CVTermList annotationToCVTermList_ ( String  annotation )

private

std::pair<String, double> getIon	(	IonSeries	ionseries,
		String	ionid
	)

Selects ion from IonSeries according to annotation string.

Parameters

ionseries	the IonSeries from which to choose
ionid	the annotation string of the query fragment ion std::pair<String, double> the annotation and product m/z of the queried fragment ion

IonSeries getIonSeries	(	AASequence	sequence,
		size_t	precursor_charge,
		std::vector< String >	fragment_types,
		std::vector< size_t >	fragment_charges,
		bool	enable_losses,
		int	round_decPow = -4
	)

Computed theoretical fragment ion series.

Parameters

sequence	the peptide amino acid sequence
precursor_charge	the charge of the peptide precursor
fragment_types	the fragment ion types for reannotation
fragment_charges	the fragment ion charges for reannotation
enable_losses	whether neutral losses should be considered
round_decPow	round product m/z values to decimal power (default: -4) IonSeries the theoretical fragment ion series