MetaboTargetedAssay Class Reference

This class provides methods for the extraction of targeted assays for metabolomics. More...

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

Collaboration diagram for MetaboTargetedAssay:

Classes
struct	CompoundTargetDecoyPair
	CompoundTargetDecoyPair stores a pair of CompoundInfo and MSSpectrum (target, decoy) More...

Static Public Member Functions
static std::vector< MetaboTargetedAssay >	extractMetaboTargetedAssay (const MSExperiment &spectra, const FeatureMapping::FeatureToMs2Indices &feature_ms2_index, const double &precursor_rt_tol, const double &precursor_mz_distance, const double &cosine_sim_threshold, const double &transition_threshold, const double &min_fragment_mz, const double &max_fragment_mz, const bool &method_consensus_spectrum, const bool &exclude_ms2_precursor, const unsigned int &file_counter)
	Extract a vector of MetaboTargetedAssays without using fragment annotation. More...
static std::vector< MetaboTargetedAssay >	extractMetaboTargetedAssayFragmentAnnotation (const std::vector< CompoundTargetDecoyPair > &v_cmp_spec, const double &transition_threshold, const double &min_fragment_mz, const double &max_fragment_mz, const bool &use_exact_mass, const bool &exclude_ms2_precursor, const unsigned int &file_counter)
	Extract a vector of MetaboTargetedAssays using fragment annotation. More...
static std::vector< MetaboTargetedAssay::CompoundTargetDecoyPair >	pairCompoundWithAnnotatedSpectra (const std::vector< SiriusMSFile::CompoundInfo > &v_cmpinfo, const std::vector< SiriusFragmentAnnotation::SiriusTargetDecoySpectra > &annotated_spectra)
	Pair compound information (SiriusMSFile) with the annotated target and decoy spectrum from SIRIUS/Passatutto based on the MID (unique identifier) More...

Public Attributes
double	precursor_int
	MetaboTargetedAssay is able to store a precursor and its metadata as well as a reference to a compound. More...
double	transition_quality_score
String	compound_name
String	compound_adduct
TargetedExperiment::Compound	potential_cmp
std::vector< ReactionMonitoringTransition >	potential_rmts

Static Protected Member Functions
static bool	intensityLess_ (Peak1D a, Peak1D b)
	Compare two peaks based on their intensity. More...
static int	getChargeFromAdduct_ (const String &adduct)
	Gets charge from an Adduct ([M+H]+) More...

Detailed Description

This class provides methods for the extraction of targeted assays for metabolomics.

Member Function Documentation

extractMetaboTargetedAssay()

static std::vector<MetaboTargetedAssay> extractMetaboTargetedAssay ( const MSExperiment &  spectra, const FeatureMapping::FeatureToMs2Indices &  feature_ms2_index, const double &  precursor_rt_tol, const double &  precursor_mz_distance, const double &  cosine_sim_threshold, const double &  transition_threshold, const double &  min_fragment_mz, const double &  max_fragment_mz, const bool &  method_consensus_spectrum, const bool &  exclude_ms2_precursor, const unsigned int &  file_counter  )

static

Extract a vector of MetaboTargetedAssays without using fragment annotation.

Returns

Vector of MetaboTargetedAssay

Parameters

spectra	Input of MSExperiment with spectra information
feature_ms2_spectra_map	FeatureMapping class with associated MS2 spectra
precursor_rt_tol	Retention time tolerance of the precursor
precursor_mz_distance	Max m/z distance of the precursor entries of two spectra to be merged
cosine_sim_threshold	Cosine similarty threshold for the usage of SpectraMerger
transition_threshold	Intensity threshold for MS2 peak used in MetaboTargetedAssay
min_fragment_mz	Minimum m/z a fragment ion has to have to be considered as a transition
max_fragment_mz	Maximum m/z a fragment ion has to have to be considered as a transition
method_consensus_spectrum	Boolean to use consensus spectrum method
exclude_ms2_precursor	Boolean to exclude MS2 precursor from MetaboTargetedAssay
file_counter	Count if multiple files are used.

extractMetaboTargetedAssayFragmentAnnotation()

static std::vector<MetaboTargetedAssay> extractMetaboTargetedAssayFragmentAnnotation ( const std::vector< CompoundTargetDecoyPair > &  v_cmp_spec, const double &  transition_threshold, const double &  min_fragment_mz, const double &  max_fragment_mz, const bool &  use_exact_mass, const bool &  exclude_ms2_precursor, const unsigned int &  file_counter  )

static

Extract a vector of MetaboTargetedAssays using fragment annotation.

Returns

Vector of MetaboTargetedAssay

Parameters

v_cmp_spec	Vector of CompoundInfo with associated fragment annotated MSspectrum
transition_threshold	Intensity threshold for MS2 peak used in MetaboTargetedAssay
min_fragment_mz	Minimum m/z a fragment ion has to have to be considered as a transition
max_fragment_mz	Maximum m/z a fragment ion has to have to be considered as a transition
use_exact_mass	Boolean if exact mass should be used as peak mass for annotated fragments
exclude_ms2_precursor	Boolean to exclude MS2 precursor from MetaboTargetedAssay
file_counter	Count if multiple files are used.

getChargeFromAdduct_()

static int getChargeFromAdduct_ ( const String &  adduct )

staticprotected

Gets charge from an Adduct ([M+H]+)

intensityLess_()

static bool intensityLess_ ( Peak1D  a, Peak1D  b  )

staticprotected

Compare two peaks based on their intensity.

pairCompoundWithAnnotatedSpectra()

static std::vector< MetaboTargetedAssay::CompoundTargetDecoyPair > pairCompoundWithAnnotatedSpectra ( const std::vector< SiriusMSFile::CompoundInfo > &  v_cmpinfo, const std::vector< SiriusFragmentAnnotation::SiriusTargetDecoySpectra > &  annotated_spectra  )

static

Pair compound information (SiriusMSFile) with the annotated target and decoy spectrum from SIRIUS/Passatutto based on the MID (unique identifier)

Returns

Vector of MetaboTargetedAssay::CompoundTargetDecoyPair

Parameters

v_cmpinfo	Vector of SiriusMSFile::CompoundInfo
annotated_spectra	Vector of SiriusTargetDecoySpectra

Member Data Documentation

compound_adduct

String compound_adduct

compound_name

String compound_name

potential_cmp

TargetedExperiment::Compound potential_cmp

potential_rmts

std::vector<ReactionMonitoringTransition> potential_rmts

precursor_int

double precursor_int

MetaboTargetedAssay is able to store a precursor and its metadata as well as a reference to a compound.

transition_quality_score

double transition_quality_score