| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Private Types | Private Attributes | List of all members
OpenSwathScoring Class Reference

A class that calls the scoring routines. More...

`#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScoring.h>`

## Public Member Functions

| OpenSwathScoring ()
| Constructor. More...
| ~OpenSwathScoring ()
| Destructor. More...
void | initialize (double rt_normalization_factor, int add_up_spectra, double spacing_for_spectra_resampling, const double drift_extra, const OpenSwath_Scores_Usage &su, const std::string &spectrum_addition_method)
| Initialize the scoring object. More...
void | calculateChromatographicScores (OpenSwath::IMRMFeature *imrmfeature, const std::vector< std::string > &native_ids, const std::vector< std::string > &precursor_ids, const std::vector< double > &normalized_library_intensity, std::vector< OpenSwath::ISignalToNoisePtr > &signal_noise_estimators, OpenSwath_Scores &scores)
| Score a single peakgroup in a chromatogram using only chromatographic properties. More...
void | calculateChromatographicIdScores (OpenSwath::IMRMFeature *imrmfeature, const std::vector< std::string > &native_ids_identification, const std::vector< std::string > &native_ids_detection, std::vector< OpenSwath::ISignalToNoisePtr > &signal_noise_estimators, OpenSwath_Ind_Scores &scores)
| Score identification transitions against detection transitions of a single peakgroup in a chromatogram using only chromatographic properties. More...
void | calculateLibraryScores (OpenSwath::IMRMFeature *imrmfeature, const std::vector< TransitionType > &transitions, const CompoundType &compound, const double normalized_feature_rt, OpenSwath_Scores &scores)
| Score a single chromatographic feature against a spectral library. More...
void | calculateDIAScores (OpenSwath::IMRMFeature *imrmfeature, const std::vector< TransitionType > &transitions, const std::vector< OpenSwath::SwathMap > &swath_maps, OpenSwath::SpectrumAccessPtr ms1_map, OpenMS::DIAScoring &diascoring, const CompoundType &compound, OpenSwath_Scores &scores, std::vector< double > &mzerror_ppm, const double drift_lower, const double drift_upper, const double drift_target)
| Score a single chromatographic feature using DIA / SWATH scores. More...
void | calculatePrecursorDIAScores (OpenSwath::SpectrumAccessPtr ms1_map, OpenMS::DIAScoring &diascoring, double precursor_mz, double rt, const CompoundType &compound, OpenSwath_Scores &scores, double drift_lower, double drift_upper)
| Score a single chromatographic feature using the precursor map. More...
void | calculateDIAIdScores (OpenSwath::IMRMFeature *imrmfeature, const TransitionType &transition, const std::vector< OpenSwath::SwathMap > swath_maps, OpenMS::DIAScoring &diascoring, OpenSwath_Scores &scores, double drift_lower, double drift_upper)
| Score a single chromatographic feature using DIA / SWATH scores. More...
void | getNormalized_library_intensities_ (const std::vector< TransitionType > &transitions, std::vector< double > &normalized_library_intensity)
| Computing the normalized library intensities from the transition objects. More...
OpenSwath::SpectrumPtr | fetchSpectrumSwath (std::vector< OpenSwath::SwathMap > swath_maps, double RT, int nr_spectra_to_add, const double drift_lower, const double drift_upper)
| Prepares a spectrum for DIA analysis (multiple map) More...
OpenSwath::SpectrumPtr | fetchSpectrumSwath (OpenSwath::SpectrumAccessPtr swath_map, double RT, int nr_spectra_to_add, const double drift_lower, const double drift_upper)
| Prepares a spectrum for DIA analysis (single map) More...

## Protected Member Functions

OpenSwath::SpectrumPtr | getAddedSpectra_ (OpenSwath::SpectrumAccessPtr swath_map, double RT, int nr_spectra_to_add, const double drift_lower, const double drift_upper)
| Returns an averaged spectrum. More...

## Private Types

typedef OpenSwath::LightCompound | CompoundType
typedef OpenSwath::LightTransition | TransitionType

## Private Attributes

double | rt_normalization_factor_
double | spacing_for_spectra_resampling_
int | add_up_spectra_
std::string | spectra_addition_method_
double | im_drift_extra_pcnt_
OpenSwath_Scores_Usage | su_

## Detailed Description

A class that calls the scoring routines.

Use this class to invoke the individual OpenSWATH scoring routines.

## Member Typedef Documentation

## ◆ CompoundType

typedef OpenSwath::LightCompound CompoundType

private

## ◆ TransitionType

typedef OpenSwath::LightTransition TransitionType

private

## Constructor & Destructor Documentation

## ◆ OpenSwathScoring()

OpenSwathScoring | ( |  | ) |

Constructor.

## ◆ ~OpenSwathScoring()

~OpenSwathScoring | ( |  | ) |

Destructor.

## Member Function Documentation

## ◆ calculateChromatographicIdScores()

void calculateChromatographicIdScores | ( | OpenSwath::IMRMFeature * | imrmfeature,
|  | const std::vector< std::string > & | native_ids_identification,
|  | const std::vector< std::string > & | native_ids_detection,
|  | std::vector< OpenSwath::ISignalToNoisePtr > & | signal_noise_estimators,
|  | OpenSwath_Ind_Scores & | scores
| ) |  |

Score identification transitions against detection transitions of a single peakgroup in a chromatogram using only chromatographic properties.

This function only uses the chromatographic properties (coelution, signal to noise, etc.) of a peakgroup in a chromatogram to compute scores. The scores are computed by scoring identification against detection transitions.

The scores are returned in the OpenSwath_Scores object. Only those scores specified in the OpenSwath_Scores_Usage object are computed.

Parameters

  imrmfeature | The feature to be scored
  native_ids_identification | The list of identification native ids (giving a canonical ordering of the transitions)
  native_ids_detection | The list of detection native ids (giving a canonical ordering of the transitions)
  signal_noise_estimators | The signal-to-noise estimators for each transition
  scores | The object to store the result

## ◆ calculateChromatographicScores()

void calculateChromatographicScores | ( | OpenSwath::IMRMFeature * | imrmfeature,
|  | const std::vector< std::string > & | native_ids,
|  | const std::vector< std::string > & | precursor_ids,
|  | const std::vector< double > & | normalized_library_intensity,
|  | std::vector< OpenSwath::ISignalToNoisePtr > & | signal_noise_estimators,
|  | OpenSwath_Scores & | scores
| ) |  |

Score a single peakgroup in a chromatogram using only chromatographic properties.

This function only uses the chromatographic properties (coelution, signal to noise, etc.) of a peakgroup in a chromatogram to compute scores. If more information is available, also consider using the library based scoring and the full-spectrum based scoring.

The scores are returned in the OpenSwath_Scores object. Only those scores specified in the OpenSwath_Scores_Usage object are computed.

Parameters

  imrmfeature | The feature to be scored
  native_ids | The list of native ids (giving a canonical ordering of the transitions)
  precursor_ids | The list of precursor ids
  normalized_library_intensity | The weights to be used for each transition (e.g. normalized library intensities)
  signal_noise_estimators | The signal-to-noise estimators for each transition
  scores | The object to store the result

## ◆ calculateDIAIdScores()

void calculateDIAIdScores | ( | OpenSwath::IMRMFeature * | imrmfeature,
|  | const TransitionType & | transition,
|  | const std::vector< OpenSwath::SwathMap > | swath_maps,
|  | OpenMS::DIAScoring & | diascoring,
|  | OpenSwath_Scores & | scores,
|  | double | drift_lower,
|  | double | drift_upper
| ) |  |

Score a single chromatographic feature using DIA / SWATH scores.

The scores are returned in the OpenSwath_Scores object.

Parameters

  imrmfeature | The feature to be scored
  transitions | The library transition to score the feature against
  swath_maps | The SWATH-MS (DIA) maps from which to retrieve full MS/MS spectra at the chromatographic peak apices
  diascoring | DIA Scoring object to use for scoring
  scores | The object to store the result
  drift_lower | Drift time lower extraction boundary
  drift_upper | Drift time upper extraction boundary

## ◆ calculateDIAScores()

void calculateDIAScores | ( | OpenSwath::IMRMFeature * | imrmfeature,
|  | const std::vector< TransitionType > & | transitions,
|  | const std::vector< OpenSwath::SwathMap > & | swath_maps,
|  | OpenSwath::SpectrumAccessPtr | ms1_map,
|  | OpenMS::DIAScoring & | diascoring,
|  | const CompoundType & | compound,
|  | OpenSwath_Scores & | scores,
|  | std::vector< double > & | mzerror_ppm,
|  | const double | drift_lower,
|  | const double | drift_upper,
|  | const double | drift_target
| ) |  |

Score a single chromatographic feature using DIA / SWATH scores.

The scores are returned in the OpenSwath_Scores object.

Parameters

  imrmfeature | The feature to be scored
  transitions | The library transition to score the feature against
  swath_maps | The SWATH-MS (DIA) maps from which to retrieve full MS/MS spectra at the chromatographic peak apices
  ms1_map | The corresponding MS1 (precursor ion map) from which the precursor spectra can be retrieved (optional, may be NULL)
  diascoring | DIA Scoring object to use for scoring
  pep | The peptide corresponding to the library transitions
  scores | The object to store the result
  mzerror_ppm | m/z and mass error (in ppm) for all transitions
  drift_lower | Drift time lower extraction boundary
  drift_upper | Drift time upper extraction boundary

## ◆ calculateLibraryScores()

void calculateLibraryScores | ( | OpenSwath::IMRMFeature * | imrmfeature,
|  | const std::vector< TransitionType > & | transitions,
|  | const CompoundType & | compound,
|  | const double | normalized_feature_rt,
|  | OpenSwath_Scores & | scores
| ) |  |

Score a single chromatographic feature against a spectral library.

The spectral library is provided in a set of transition objects and a peptide object. Both contain information about the expected elution time on the chromatography and the relative intensity of the transitions.

The scores are returned in the OpenSwath_Scores object.

Parameters

  imrmfeature | The feature to be scored
  transitions | The library transition to score the feature against
  pep | The peptide corresponding to the library transitions
  normalized_feature_rt | The retention time of the feature in normalized space
  scores | The object to store the result

## ◆ calculatePrecursorDIAScores()

void calculatePrecursorDIAScores | ( | OpenSwath::SpectrumAccessPtr | ms1_map,
|  | OpenMS::DIAScoring & | diascoring,
|  | double | precursor_mz,
|  | double | rt,
|  | const CompoundType & | compound,
|  | OpenSwath_Scores & | scores,
|  | double | drift_lower,
|  | double | drift_upper
| ) |  |

Score a single chromatographic feature using the precursor map.

The scores are returned in the OpenSwath_Scores object.

Parameters

  ms1_map | The MS1 (precursor ion map) from which the precursor spectra can be retrieved
  diascoring | DIA Scoring object to use for scoring
  precursor_mz | The m/z ratio of the precursor
  rt | The compound retention time
  scores | The object to store the result
  drift_lower | Drift time lower extraction boundary
  drift_upper | Drift time upper extraction boundary

## ◆ fetchSpectrumSwath() [1/2]

OpenSwath::SpectrumPtr fetchSpectrumSwath | ( | std::vector< OpenSwath::SwathMap > | swath_maps,
|  | double | RT,
|  | int | nr_spectra_to_add,
|  | const double | drift_lower,
|  | const double | drift_upper
| ) |  |

Prepares a spectrum for DIA analysis (multiple map)

This function will sum up (add) the intensities of multiple spectra from multiple swath maps (assuming these are SONAR maps of shifted precursor isolation windows) around the given retention time and return an "averaged" spectrum which may contain less noise.

Parameters

  [in] | swath_maps | The map(s) containing the spectra
  [in] | RT | The target retention time
  [in] | nr_spectra_to_add | How many spectra to add up
  | drift_lower | Drift time lower extraction boundary
  | drift_upper | Drift time upper extraction boundary

Returns
  Added up spectrum

## ◆ fetchSpectrumSwath() [2/2]

OpenSwath::SpectrumPtr fetchSpectrumSwath | ( | OpenSwath::SpectrumAccessPtr | swath_map,
|  | double | RT,
|  | int | nr_spectra_to_add,
|  | const double | drift_lower,
|  | const double | drift_upper
| ) |  |

Prepares a spectrum for DIA analysis (single map)

This function will sum up (add) the intensities of multiple spectra a single swath map (assuming these are regular SWATH / DIA maps) around the given retention time and return an "averaged" spectrum which may contain less noise.

Parameters

  [in] | swath_map | The map containing the spectra
  [in] | RT | The target retention time
  [in] | nr_spectra_to_add | How many spectra to add up
  | drift_lower | Drift time lower extraction boundary
  | drift_upper | Drift time upper extraction boundary

Returns
  Added up spectrum

## ◆ getAddedSpectra_()

OpenSwath::SpectrumPtr getAddedSpectra_ | ( | OpenSwath::SpectrumAccessPtr | swath_map,
|  | double | RT,
|  | int | nr_spectra_to_add,
|  | const double | drift_lower,
|  | const double | drift_upper
| ) |  |

protected

Returns an averaged spectrum.

This function will sum up (add) the intensities of multiple spectra around the given retention time and return an "averaged" spectrum which may contain less noise.

Parameters

  [in] | swath_map | The map containing the spectra
  [in] | RT | The target retention time
  [in] | nr_spectra_to_add | How many spectra to add up
  | drift_lower | Drift time lower extraction boundary
  | drift_upper | Drift time upper extraction boundary

Returns
  Added up spectrum

## ◆ getNormalized_library_intensities_()

void getNormalized_library_intensities_ | ( | const std::vector< TransitionType > & | transitions,
|  | std::vector< double > & | normalized_library_intensity
| ) |  |

Computing the normalized library intensities from the transition objects.

The intensities are normalized such that the sum to one.

Parameters

  [in] | transitions | The library transition to score the feature against
  [out] | normalized_library_intensity | The resulting normalized library intensities

## ◆ initialize()

void initialize | ( | double | rt_normalization_factor,
|  | int | add_up_spectra,
|  | double | spacing_for_spectra_resampling,
|  | const double | drift_extra,
|  | const OpenSwath_Scores_Usage & | su,
|  | const std::string & | spectrum_addition_method
| ) |  |

Initialize the scoring object.

Sets the parameters for the scoring.

Parameters

  rt_normalization_factor | Specifies the range of the normalized retention time space
  add_up_spectra | How many spectra to add up (default 1)
  spacing_for_spectra_resampling | Spacing factor for spectra addition
  su | Which scores to actually compute
  spectrum_addition_method | Method to use for spectrum addition (valid: "simple", "resample")

## Member Data Documentation

## ◆ add_up_spectra_

int add_up_spectra_

private

## ◆ im_drift_extra_pcnt_

double im_drift_extra_pcnt_

private

## ◆ rt_normalization_factor_

double rt_normalization_factor_

private

## ◆ spacing_for_spectra_resampling_

double spacing_for_spectra_resampling_

private

## ◆ spectra_addition_method_

std::string spectra_addition_method_

private

## ◆ su_

OpenSwath_Scores_Usage su_

private