OpenMS  2.5.0
Classes | Static Public Member Functions | Public Attributes | Static Protected Member Functions | List of all members
MetaboTargetedAssay Class Reference

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

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

Classes

struct  CompoundSpectrumPair
 CompoundSpectrumPair stores a pair of CompoundInfo and MSSpectrum. More...
 

Static Public Member Functions

static std::vector< MetaboTargetedAssayextractMetaboTargetedAssay (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< MetaboTargetedAssayextractMetaboTargetedAssayFragmentAnnotation (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< ReactionMonitoringTransitionpotential_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.

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
spectraInput of MSExperiment with spectra information
feature_ms2_spectra_mapFeatureMapping class with associated MS2 spectra
precursor_rt_tolRetention time tolerance of the precursor
precursor_mz_distanceMax m/z distance of the precursor entries of two spectra to be merged
cosine_sim_thresholdCosine similarty threshold for the usage of SpectraMerger
transition_thresholdIntensity threshold for MS2 peak used in MetaboTargetedAssay
min_fragment_mzMinimum m/z a fragment ion has to have to be considered as a transition
max_fragment_mzMaximum m/z a fragment ion has to have to be considered as a transition
method_consensus_spectrumBoolean to use consensus spectrum method
exclude_ms2_precursorBoolean to exclude MS2 precursor from MetaboTargetedAssay
file_counterCount 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_specVector of CompoundInfo with associated fragment annotated MSspectrum
transition_thresholdIntensity threshold for MS2 peak used in MetaboTargetedAssay
min_fragment_mzMinimum m/z a fragment ion has to have to be considered as a transition
max_fragment_mzMaximum m/z a fragment ion has to have to be considered as a transition
use_exact_massBoolean if exact mass should be used as peak mass for annotated fragments
exclude_ms2_precursorBoolean to exclude MS2 precursor from MetaboTargetedAssay
file_counterCount 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

◆ 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