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

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

Collaboration diagram for MetaboTargetedAssay:

Classes
class	CompoundSpectrumPair
	CompoundTargetDecoyPair stores a pair of CompoundInfo and MSSpectrum. More...

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

struct	TargetDecoyGroup
	TargetDecoyGroup stores the mz, rt and file number in correspondence to the index of a MetaboTargetedAssay vector. 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 >	pairCompoundWithAnnotatedTDSpectraPairs (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 m_id (unique identifier composed of description_filepath_native_id_k introduced in the SiriusMSConverter) More...

static std::vector< MetaboTargetedAssay::CompoundSpectrumPair >	pairCompoundWithAnnotatedSpectra (const std::vector< SiriusMSFile::CompoundInfo > &v_cmpinfo, const std::vector< MSSpectrum > &annotated_spectra)

static std::unordered_map< UInt64, std::vector< MetaboTargetedAssay > >	buildAmbiguityGroup (const std::vector< MetaboTargetedAssay > &v_mta, const double &ar_mz_tol, const double &ar_rt_tol, const String &ar_mz_tol_unit_res, size_t in_files_size)
	Perform feature linking to build ambiguity groups based on the target and decoy position in the vector of MetaboTargetedAssays. More...

static void	resolveAmbiguityGroup (std::unordered_map< UInt64, std::vector< MetaboTargetedAssay > > &map_mta_filter, const double &total_occurrence_filter, size_t in_files_size)
	Resolve ambiguity groups based on occurrence in samples (e.g. at least in 20% of the samples) and if multiple possible identifications are reported within one ambiguity group use the one with the highest occurrence. More...

Public Attributes
double	precursor_int
	MetaboTargetedAssay is able to store a precursor, metadata as well as compound information. More...

double	transition_quality_score
	transitions quality score (not yet used) More...

double	precursor_mz
	precursor mass-to-charge More...

double	compound_rt
	compound retention time More...

String	molecular_formula
	< (putative) molecular formula More...

int	compound_file
	integer of file it belongs to in a list of files More...

String	compound_name
	compound name More...

String	compound_adduct
	compound adduct More...

TargetedExperiment::Compound	potential_cmp
	compound information stored in a TargetedExperiment More...

std::vector< ReactionMonitoringTransition >	potential_rmts
	vector of transitions belonging to the compound More...

Static Protected Member Functions
static bool	intensityLess_ (const Peak1D &a, const Peak1D &b)
	Compare two peaks based on their intensity. More...

static int	getChargeFromAdduct_ (const String &adduct)
	Gets charge from a singly charged adduct ([M+H]+/[M-H]-) More...

static void	filterBasedOnTotalOccurrence_ (std::vector< MetaboTargetedAssay > &mta, double total_occurrence_filter, size_t in_files_size)
	Filter one ambiguity group based on occurrence in samples (e.g. at least in 20% of the samples) More...

static void	filterBasedOnMolFormAdductOccurrence_ (std::vector< MetaboTargetedAssay > &mta)
	Filter one ambiguity group with multiple possible identifications to use the one with the highest occurrence. More...

static void	sortByPrecursorInt (std::vector< MetaboTargetedAssay > &vec_mta)
	Sort vector of MetaboTargetedAssay by precursor ion intensity. More...

Static Protected Attributes
static constexpr float	noise_threshold_constant_ = 1.1
	Used to calculate the hard noise intensity threshold hard minimal threshold of min_int * noise_threshold_constant_. More...

Detailed Description

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

Class Documentation

◆ OpenMS::MetaboTargetedAssay::TargetDecoyGroup

struct OpenMS::MetaboTargetedAssay::TargetDecoyGroup

TargetDecoyGroup stores the mz, rt and file number in correspondence to the index of a MetaboTargetedAssay vector.

Collaboration diagram for MetaboTargetedAssay::TargetDecoyGroup:

[legend]

Class Members
int	decoy_file_number
int	decoy_index
double	decoy_mz
double	decoy_rt
int	target_file_number
int	target_index
double	target_mz
double	target_rt

Member Function Documentation

◆ buildAmbiguityGroup()

static std::unordered_map< UInt64, std::vector<MetaboTargetedAssay> > buildAmbiguityGroup	(	const std::vector< MetaboTargetedAssay > &	v_mta,
		const double &	ar_mz_tol,
		const double &	ar_rt_tol,
		const String &	ar_mz_tol_unit_res,
		size_t	in_files_size
	)

static

Perform feature linking to build ambiguity groups based on the target and decoy position in the vector of MetaboTargetedAssays.

Returns: Map of pair (mz, rt) and vector of ambiguities for this mz,rt combination (MetaboTargetedAssay)

Parameters

v_mta	Vector of MetaboTargetedAssay
ar_mz_tol	FeatureGroupingAlgorithmQT parameter distance_MZ:max_difference
ar_rt_tol	FeatureGroupingAlgorithmQT parameter distance_RT:max_difference
ar_mz_tol_unit_res	FeatureGroupingAlgorithmQT parameter distance_MZ_unit (ppm, Da)
in_files_size	Number of files which were processed in the vector of MetaboTargetedAssay (e.g. initially 5 different files in the vector<MetaboTargetedAssay>)

◆ 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 similarity 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.

◆ filterBasedOnMolFormAdductOccurrence_()

static void filterBasedOnMolFormAdductOccurrence_ ( std::vector< MetaboTargetedAssay > & mta )

staticprotected

Filter one ambiguity group with multiple possible identifications to use the one with the highest occurrence.

Returns: Vector of MetaboTargetedAssay

◆ filterBasedOnTotalOccurrence_()

static void filterBasedOnTotalOccurrence_	(	std::vector< MetaboTargetedAssay > &	mta,
		double	total_occurrence_filter,
		size_t	in_files_size
	)

staticprotected

Filter one ambiguity group based on occurrence in samples (e.g. at least in 20% of the samples)

Returns: Vector of MetaboTargetedAssay

Parameters

total_occurrence_filter	Value which has to be reached for the ambiguity group to be reported (e.g. in 20 % of the samples)
in_files_size	Number of files which were processed in the vector of MetaboTargetedAssay (e.g. initially 5 different files in the vector<MetaboTargetedAssay>)

◆ getChargeFromAdduct_()

static int getChargeFromAdduct_ ( const String & adduct )

staticprotected

Gets charge from a singly charged adduct ([M+H]+/[M-H]-)

◆ intensityLess_()

static bool intensityLess_	(	const Peak1D &	a,
		const Peak1D &	b
	)

staticprotected

Compare two peaks based on their intensity.

◆ pairCompoundWithAnnotatedSpectra()

static std::vector< MetaboTargetedAssay::CompoundSpectrumPair > pairCompoundWithAnnotatedSpectra	(	const std::vector< SiriusMSFile::CompoundInfo > &	v_cmpinfo,
		const std::vector< MSSpectrum > &	annotated_spectra
	)

static

◆ pairCompoundWithAnnotatedTDSpectraPairs()

static std::vector< MetaboTargetedAssay::CompoundTargetDecoyPair > pairCompoundWithAnnotatedTDSpectraPairs	(	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 m_id (unique identifier composed of description_filepath_native_id_k introduced in the SiriusMSConverter)

Returns: Vector of MetaboTargetedAssay::CompoundTargetDecoyPair

Parameters

v_cmpinfo	Vector of SiriusMSFile::CompoundInfo
annotated_spectra	Vector of SiriusTargetDecoySpectra

◆ resolveAmbiguityGroup()

static void resolveAmbiguityGroup	(	std::unordered_map< UInt64, std::vector< MetaboTargetedAssay > > &	map_mta_filter,
		const double &	total_occurrence_filter,
		size_t	in_files_size
	)

static

Resolve ambiguity groups based on occurrence in samples (e.g. at least in 20% of the samples) and if multiple possible identifications are reported within one ambiguity group use the one with the highest occurrence.

Returns: Map of pair (mz, rt) and vector of ambiguities for this mz,rt combination (MetaboTargetedAssay)

Parameters

total_occurrence_filter	Value which has to be reached for the ambiguity group to be reported (e.g. in 20 % of the samples)
in_files_size	Number of files which were processed in the vector of MetaboTargetedAssay (e.g. initially 5 different files in the vector<MetaboTargetedAssay>)

◆ sortByPrecursorInt()

static void sortByPrecursorInt ( std::vector< MetaboTargetedAssay > & vec_mta )

staticprotected

Sort vector of MetaboTargetedAssay by precursor ion intensity.

Member Data Documentation

◆ compound_adduct

String compound_adduct

compound adduct

◆ compound_file

int compound_file

integer of file it belongs to in a list of files

◆ compound_name

String compound_name

compound name

◆ compound_rt

double compound_rt

compound retention time

◆ molecular_formula

String molecular_formula

< (putative) molecular formula

◆ noise_threshold_constant_

constexpr float noise_threshold_constant_ = 1.1

staticconstexprprotected

Used to calculate the hard noise intensity threshold hard minimal threshold of min_int * noise_threshold_constant_.

◆ potential_cmp

TargetedExperiment::Compound potential_cmp

compound information stored in a TargetedExperiment

◆ potential_rmts

std::vector<ReactionMonitoringTransition> potential_rmts

vector of transitions belonging to the compound

◆ precursor_int

double precursor_int

MetaboTargetedAssay is able to store a precursor, metadata as well as compound information.

precursor intensity

◆ precursor_mz

double precursor_mz

precursor mass-to-charge

◆ transition_quality_score

double transition_quality_score

transitions quality score (not yet used)

Classes

Static Public Member Functions

Public Attributes

Static Protected Member Functions

Static Protected Attributes

Detailed Description

Class Documentation

◆ OpenMS::MetaboTargetedAssay::TargetDecoyGroup

Member Function Documentation

◆ buildAmbiguityGroup()

◆ extractMetaboTargetedAssay()

◆ extractMetaboTargetedAssayFragmentAnnotation()

◆ filterBasedOnMolFormAdductOccurrence_()

◆ filterBasedOnTotalOccurrence_()

◆ getChargeFromAdduct_()

◆ intensityLess_()

◆ pairCompoundWithAnnotatedSpectra()

◆ pairCompoundWithAnnotatedTDSpectraPairs()

◆ resolveAmbiguityGroup()

◆ sortByPrecursorInt()

Member Data Documentation

◆ compound_adduct

◆ compound_file

◆ compound_name

◆ compound_rt

◆ molecular_formula

◆ noise_threshold_constant_

◆ potential_cmp

◆ potential_rmts

◆ precursor_int

◆ precursor_mz

◆ transition_quality_score