| 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< 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.

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
| ) |  |

static protected

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