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	CompoundSpectrumPair
	CompoundSpectrumPair stores a pair of CompoundInfo and MSSpectrum. 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< CompoundSpectrumPair > &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...

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...

Detailed Description

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

Class Documentation

◆ OpenMS::MetaboTargetedAssay::CompoundSpectrumPair

struct OpenMS::MetaboTargetedAssay::CompoundSpectrumPair

CompoundSpectrumPair stores a pair of CompoundInfo and MSSpectrum.

Collaboration diagram for MetaboTargetedAssay::CompoundSpectrumPair:

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Class Members
pair< CompoundInfo, MSSpectrum >	compoundspectrumpair

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< CompoundSpectrumPair > &	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.

◆ intensityLess_()

static bool intensityLess_	(	Peak1D	a,
		Peak1D	b
	)

staticprotected

Compare two peaks based on their intensity.

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

Classes

Static Public Member Functions

Public Attributes

Static Protected Member Functions