OpenMS
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< MetaboTargetDecoyMassMappingconstructTargetDecoyMassMapping (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.


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:
[legend]
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_expTransitionExperiment 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_expTransitionExperiment 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_expTransitionExperiment holds compound and transition information
mappingsmap of identifier to target and decoy masses
mass_to_addthe 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_expTransitionExperiment holds compound and transition information
mappingsmap of identifier to target and decoy masses
mass_to_add(e.g. CH2)
mz_tolm/z tolerarance for target and decoy transition masses to be considered overlapping
mz_tol_unitm/z tolerance unit ("ppm" or "Da")