MetaboTargetedTargetDecoy Class Reference

Resolve overlapping fragments and missing decoys for experimental specific decoy generation in targeted/pseudo targeted metabolomics. More...

#include <OpenMS/ANALYSIS/TARGETED/MetaboTargetedTargetDecoy.h>

Classes
class	MetaboTargetDecoyMassMapping
	MetaboTargetDecoyMassMapping introduces a mapping of target and decoy masses and their respective compound reference using an identifier. More...

Static Public Member Functions
static std::vector< MetaboTargetDecoyMassMapping >	constructTargetDecoyMassMapping (const TargetedExperiment &t_exp)
	Constructs a mass mapping of targets and decoys using the unique m_id identifier. More...
static void	resolveOverlappingTargetDecoyMassesByDecoyMassShift (TargetedExperiment &t_exp, std::vector< MetaboTargetedTargetDecoy::MetaboTargetDecoyMassMapping > &mappings, const double &mass_to_add, const double &mz_tol, const String &mz_tol_unit)
	Resolves overlapping target and decoy transition masses by adding a specifiable mass (e.g. CH2) to the overlapping decoy fragment. More...
static void	generateMissingDecoysByMassShift (TargetedExperiment &t_exp, std::vector< MetaboTargetedTargetDecoy::MetaboTargetDecoyMassMapping > &mappings, const double &mass_to_add)
	Generate a decoy for targets where fragmentation tree re-rooting was not possible, by adding a specifiable mass to the target fragments. More...

Static Protected Member Functions
static std::map< String, std::vector< OpenMS::ReactionMonitoringTransition > >	constructTransitionsMap_ (const TargetedExperiment &t_exp)
	Generate a TransitionMap based on Compound_Ref and ReactionMonitoringTransitions. More...

Detailed Description

Resolve overlapping fragments and missing decoys for experimental specific decoy generation in targeted/pseudo targeted metabolomics.

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Class Documentation

OpenMS::MetaboTargetedTargetDecoy::MetaboTargetDecoyMassMapping

class OpenMS::MetaboTargetedTargetDecoy::MetaboTargetDecoyMassMapping

MetaboTargetDecoyMassMapping introduces a mapping of target and decoy masses and their respective compound reference using an identifier.

Collaboration diagram for MetaboTargetedTargetDecoy::MetaboTargetDecoyMassMapping:

Class Members
String	decoy_compound_ref	identifier which allows to reference back to the target (e.g. target_transitions_id)
vector< double >	decoy_product_masses	masses of target transitions
String	identifier
String	target_compound_ref	unique identifier (e.g. m_id)
vector< double >	target_product_masses	identifier which allows to reference back to the decoy (e.g. decoy_transitions_id)

Member Function Documentation

constructTargetDecoyMassMapping()

static std::vector<MetaboTargetDecoyMassMapping> constructTargetDecoyMassMapping ( const TargetedExperiment &  t_exp )

static

Constructs a mass mapping of targets and decoys using the unique m_id identifier.

Parameters

t_exp

TransitionExperiment holds compound and transition information used for the mapping.

constructTransitionsMap_()

static std::map<String, std::vector<OpenMS::ReactionMonitoringTransition> > constructTransitionsMap_ ( const TargetedExperiment &  t_exp )

staticprotected

Generate a TransitionMap based on Compound_Ref and ReactionMonitoringTransitions.

Parameters

t_exp

TransitionExperiment holds compound and transition information

generateMissingDecoysByMassShift()

static void generateMissingDecoysByMassShift ( TargetedExperiment &  t_exp, std::vector< MetaboTargetedTargetDecoy::MetaboTargetDecoyMassMapping > &  mappings, const double &  mass_to_add  )

static

Generate a decoy for targets where fragmentation tree re-rooting was not possible, by adding a specifiable mass to the target fragments.

Parameters

t_exp	TransitionExperiment holds compound and transition information
mappings	map of identifier to target and decoy masses
mass_to_add	the maximum number of transitions required per assay

resolveOverlappingTargetDecoyMassesByDecoyMassShift()

static void resolveOverlappingTargetDecoyMassesByDecoyMassShift ( TargetedExperiment &  t_exp, std::vector< MetaboTargetedTargetDecoy::MetaboTargetDecoyMassMapping > &  mappings, const double &  mass_to_add, const double &  mz_tol, const String &  mz_tol_unit  )

static

Resolves overlapping target and decoy transition masses by adding a specifiable mass (e.g. CH2) to the overlapping decoy fragment.

Parameters

t_exp	TransitionExperiment holds compound and transition information
mappings	map of identifier to target and decoy masses
mass_to_add	(e.g. CH2)
mz_tol	m/z tolerarance for target and decoy transition masses to be considered overlapping
mz_tol_unit	m/z tolerance unit ("ppm" or "Da")