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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, doubleIonSeries
 

Public Member Functions

std::pair< String, doublegetIon (IonSeries ionseries, String ionid)
 Selects ion from IonSeries according to annotation string. More...
 
std::pair< String, doubleannotateIon (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

Constructor.

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
ionseriesthe IonSeries from which to choose
ProductMzthe product m/z of the queried fragment ion
mz_thresholdthe 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
trthe transition to annotate
peptidethe corresponding peptide
mz_thresholdthe m/z threshold for annotation of the fragment ion
enable_reannotationwhether the original (e.g. SpectraST) annotation should be used or reannotation should be conducted
fragment_typesthe fragment ion types for reannotation
fragment_chargesthe fragment ion charges for reannotation
enable_losseswhether neutral losses should be considered
round_decPowround product m/z values to decimal power (default: -4)
void annotateTransitionCV ( ReactionMonitoringTransition tr,
String  annotation 
)

Annotates transition with CV terms.

Parameters
trthe transition to annotate
annotationthe 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
ionseriesthe IonSeries from which to choose
ionidthe 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
sequencethe peptide amino acid sequence
precursor_chargethe charge of the peptide precursor
fragment_typesthe fragment ion types for reannotation
fragment_chargesthe fragment ion charges for reannotation
enable_losseswhether neutral losses should be considered
round_decPowround product m/z values to decimal power (default: -4) IonSeries the theoretical fragment ion series

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 12:49:28 using doxygen 1.8.11