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
	An MRM ion series which maps: "ion_type" -> "fragment m/z". More...

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

Private Member Functions
TargetedExperiment::Interpretation	annotationToCVTermList_ (const 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.

MRMIonSeries uses internally an annotation format that is compatible with SpectraST, which is derived from Roepstoff and Fohlman (1984, PMID: 6525415). An annotation tag starts with ion type (a, b, c, x, y, z) followed by the ordinal (number of amino acids). The caret symbol follows "^" with a positive integer indicating the fragment ion charge. If no caret symbol is present, a charge of 1 is assumed. In case of neutral loss, a negative symbol "-" followed by the integer mass (e.g. 17 for ammonia) OR the molecular composition, compatible with EmpiricalFormula (e.g. N1H3 for ammonia) is allowed.

Valid examples: y3, y3^1, y3^1-18, y3^1-H2O, y3-H2O

Limitations: Special SpectraST multi-assignments, immonium, precursors are not supported.

Member Typedef Documentation

IonSeries

typedef boost::unordered_map<String, double> IonSeries

An MRM ion series which maps: "ion_type" -> "fragment m/z".

Constructor & Destructor Documentation

MRMIonSeries()

MRMIonSeries

(

)

Constructor.

~MRMIonSeries()

~MRMIonSeries

(

)

Destructor.

Member Function Documentation

annotateIon()

std::pair<String, double> annotateIon	(	const IonSeries &	ionseries,
		const double	ProductMZ,
		const 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 @value std::pair<String, double> the annotation and product m/z of the queried fragment ion

annotateTransition()

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

Annotates transition.

Parameters

tr	the transition to annotate
peptide	the corresponding peptide
precursor_mz_threshold	the m/z threshold for annotation of the precursor ion
product_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_specific_losses	whether specific neutral losses should be considered
enable_unspecific_losses	whether unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) should be considered
round_decPow	round precursor and product m/z values to decimal power (default: -4)

annotateTransitionCV()

void annotateTransitionCV	(	ReactionMonitoringTransition &	tr,
		const String &	annotation
	)

Annotates transition with CV terms.

Parameters

tr	the transition to annotate
annotation	the fragment ion annotation.

annotationToCV_()

void annotationToCV_ ( ReactionMonitoringTransition &  tr )

private

annotationToCVTermList_()

TargetedExperiment::Interpretation annotationToCVTermList_ ( const String &  annotation )

private

getIon()

std::pair<String, double> getIon	(	IonSeries &	ionseries,
		const 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 @value std::pair<String, double> the annotation and product m/z of the queried fragment ion

getIonSeries()

IonSeries getIonSeries	(	const AASequence &	sequence,
		size_t	precursor_charge,
		const std::vector< String > &	fragment_types,
		const std::vector< size_t > &	fragment_charges,
		const bool	enable_specific_losses,
		const bool	enable_unspecific_losses,
		const 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_specific_losses	whether specific neutral losses should be considered
enable_unspecific_losses	whether unspecific neutral losses (H2O1, H3N1, C1H2N2, C1H2N1O1) should be considered
round_decPow	round product m/z values to decimal power (default: -4) @value IonSeries the theoretical fragment ion series