OpenMS
MRMScoring Class Reference

This class implements different scores for peaks found in SRM/MRM. More...

#include <OpenMS/ANALYSIS/OPENSWATH/MRMScoring.h>

Collaboration diagram for MRMScoring:
[legend]

Public Types

typedef OpenSwath::Scoring::XCorrArrayType XCorrArrayType
 Type definitions. More...
 
typedef OpenMS::Matrix< XCorrArrayTypeXCorrMatrixType
 Cross Correlation matrix. More...
 
typedef OpenSwath::SpectrumPtr SpectrumType
 
typedef OpenSwath::LightTransition TransitionType
 
typedef OpenSwath::LightCompound PeptideType
 
typedef OpenSwath::LightProtein ProteinType
 
typedef boost::shared_ptr< OpenSwath::IFeatureFeatureType
 

Public Member Functions

Accessors
const XCorrMatrixTypegetXCorrMatrix () const
 non-mutable access to the cross-correlation matrix More...
 
const XCorrMatrixTypegetXCorrContrastMatrix () const
 non-mutable access to the cross-correlation contrast matrix More...
 
const XCorrMatrixTypegetXCorrPrecursorContrastMatrix () const
 non-mutable access to the cross-correlation precursor contrast matrix More...
 
const XCorrMatrixTypegetXCorrPrecursorCombinedMatrix () const
 non-mutable access to the cross-correlation precursor contrast matrix More...
 

Private Attributes

Members
XCorrMatrixType xcorr_matrix_
 the precomputed cross correlation matrix More...
 
OpenMS::Matrix< int > xcorr_matrix_max_peak_
 contains max Peaks from xcorr_matrix_ More...
 
OpenMS::Matrix< double > xcorr_matrix_max_peak_sec_
 
XCorrMatrixType xcorr_contrast_matrix_
 the precomputed contrast cross correlation More...
 
OpenMS::Matrix< double > xcorr_contrast_matrix_max_peak_sec_
 contains max Peaks from xcorr_contrast_matrix_ More...
 
XCorrMatrixType xcorr_precursor_matrix_
 the precomputed cross correlation matrix of the MS1 trace More...
 
XCorrMatrixType xcorr_precursor_contrast_matrix_
 the precomputed cross correlation against the MS1 trace More...
 
XCorrMatrixType xcorr_precursor_combined_matrix_
 the precomputed cross correlation with the MS1 trace More...
 
OpenMS::Matrix< double > mi_matrix_
 the precomputed mutual information matrix More...
 
OpenMS::Matrix< double > mi_contrast_matrix_
 the precomputed contrast mutual information matrix More...
 
OpenMS::Matrix< double > mi_precursor_matrix_
 the precomputed mutual information matrix of the MS1 trace More...
 
OpenMS::Matrix< double > mi_precursor_contrast_matrix_
 the precomputed contrast mutual information matrix against the MS1 trace More...
 
OpenMS::Matrix< double > mi_precursor_combined_matrix_
 the precomputed contrast mutual information matrix with the MS1 trace More...
 

Scores

void initializeXCorrMatrix (const std::vector< std::vector< double > > &data)
 Initialize the scoring object and building the cross-correlation matrix. More...
 
void initializeXCorrMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &native_ids)
 Initialize the scoring object and building the cross-correlation matrix. More...
 
void initializeXCorrContrastMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &native_ids_set1, const std::vector< std::string > &native_ids_set2)
 Initialize the scoring object and building the cross-correlation matrix of chromatograms of set1 (e.g. identification transitions) vs set2 (e.g. detection transitions) More...
 
void initializeXCorrPrecursorMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids)
 Initialize the scoring object and building the cross-correlation matrix. More...
 
void initializeXCorrPrecursorContrastMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids, const std::vector< std::string > &native_ids)
 Initialize the scoring object and building the cross-correlation matrix of chromatograms of precursor isotopes vs transitions. More...
 
void initializeXCorrPrecursorContrastMatrix (const std::vector< std::vector< double > > &data_precursor, const std::vector< std::vector< double > > &data_fragments)
 Initialize the scoring object and building the cross-correlation matrix of chromatograms of precursor isotopes vs transitions. More...
 
void initializeXCorrPrecursorCombinedMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids, const std::vector< std::string > &native_ids)
 Initialize the scoring object and building the cross-correlation matrix of chromatograms of precursor isotopes and transitions. More...
 
double calcXcorrCoelutionScore ()
 Calculate the cross-correlation coelution score. More...
 
double calcXcorrCoelutionWeightedScore (const std::vector< double > &normalized_library_intensity)
 Calculate the weighted cross-correlation coelution score. More...
 
std::vector< double > calcSeparateXcorrContrastCoelutionScore ()
 calculate the separate cross-correlation contrast score More...
 
double calcXcorrPrecursorCoelutionScore ()
 calculate the precursor cross-correlation contrast score More...
 
double calcXcorrPrecursorContrastCoelutionScore ()
 Calculate the precursor cross-correlation contrast score against the transitions. More...
 
double calcXcorrPrecursorContrastSumFragCoelutionScore ()
 
double calcXcorrPrecursorCombinedCoelutionScore ()
 calculate the precursor cross-correlation coelution score including the transitions More...
 
double calcXcorrShapeScore ()
 Calculate the cross-correlation shape score. More...
 
double calcXcorrShapeWeightedScore (const std::vector< double > &normalized_library_intensity)
 Calculate the weighted cross-correlation shape score. More...
 
double calcXcorrContrastShapeScore ()
 calculate the cross-correlation contrast shape score More...
 
std::vector< double > calcSeparateXcorrContrastShapeScore ()
 calculate the separate cross-correlation contrast shape score More...
 
double calcXcorrPrecursorShapeScore ()
 calculate the precursor cross-correlation shape score More...
 
double calcXcorrPrecursorContrastShapeScore ()
 calculate the precursor cross-correlation shape score against the transitions More...
 
double calcXcorrPrecursorContrastSumFragShapeScore ()
 
double calcXcorrPrecursorCombinedShapeScore ()
 calculate the precursor cross-correlation shape score including the transitions More...
 
const OpenMS::Matrix< double > & getMIMatrix () const
 non-mutable access to the MI matrix More...
 
const OpenMS::Matrix< double > & getMIContrastMatrix () const
 non-mutable access to the MI contrast matrix More...
 
const OpenMS::Matrix< double > & getMIPrecursorContrastMatrix () const
 non-mutable access to the MI precursor contrast matrix More...
 
const OpenMS::Matrix< double > & getMIPrecursorCombinedMatrix () const
 non-mutable access to the MI precursor combined matrix More...
 
void initializeMIMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &native_ids)
 Initialize the scoring object and building the MI matrix. More...
 
void initializeMIContrastMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &native_ids_set1, const std::vector< std::string > &native_ids_set2)
 Initialize the scoring object and building the MI matrix of chromatograms of set1 (e.g. identification transitions) vs set2 (e.g. detection transitions) More...
 
void initializeMIPrecursorMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids)
 Initialize the scoring object and building the MI matrix. More...
 
void initializeMIPrecursorContrastMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids, const std::vector< std::string > &native_ids)
 Initialize the mutual information vector against the MS1 trace. More...
 
void initializeMIPrecursorCombinedMatrix (OpenSwath::IMRMFeature *mrmfeature, const std::vector< std::string > &precursor_ids, const std::vector< std::string > &native_ids)
 Initialize the mutual information vector with the MS1 trace. More...
 
double calcMIScore ()
 
double calcMIWeightedScore (const std::vector< double > &normalized_library_intensity)
 
double calcMIPrecursorScore ()
 
double calcMIPrecursorContrastScore ()
 
double calcMIPrecursorCombinedScore ()
 
std::vector< double > calcSeparateMIContrastScore ()
 
static void calcLibraryScore (OpenSwath::IMRMFeature *mrmfeature, const std::vector< TransitionType > &transitions, double &correlation, double &norm_manhattan, double &manhattan, double &dotprod, double &spectral_angle, double &rmsd)
 calculate the library correlation score More...
 
static double calcRTScore (const PeptideType &peptide, double normalized_experimental_rt)
 calculate the retention time correlation score More...
 
static double calcSNScore (OpenSwath::IMRMFeature *mrmfeature, std::vector< OpenSwath::ISignalToNoisePtr > &signal_noise_estimators)
 calculate the Signal to Noise ratio More...
 
static std::vector< double > calcSeparateSNScore (OpenSwath::IMRMFeature *mrmfeature, std::vector< OpenSwath::ISignalToNoisePtr > &signal_noise_estimators)
 

Detailed Description

This class implements different scores for peaks found in SRM/MRM.

It uses scores based on different parameters of the peaks from the individual transitions and stores them individually. The idea and the scores are based on the following paper: Reiter L, Rinner O, Picotti P, Huettenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R. mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods. 2011 May;8(5):430-5. Epub 2011 Mar 20.

The currently implemented scores include:

  • xcorr_coelution: Cross-correlation of the different transitions
  • xcorr_shape: Cross-correlation shape score (whether the maximal Cross-correlation coincides with the maximal intensity)
  • library_rmsd: normalized RMSD of the measured intensities to the expected intensities
  • library_correlation: correlation of the measured intensities to the expected intensities
  • rt_score: deviation from the expected retention time
  • elution_fit_score: how well the elution profile fits a theoretical elution profile

Member Typedef Documentation

◆ FeatureType

typedef boost::shared_ptr<OpenSwath::IFeature> FeatureType

◆ PeptideType

◆ ProteinType

◆ SpectrumType

◆ TransitionType

◆ XCorrArrayType

Type definitions.

Cross Correlation array

◆ XCorrMatrixType

Cross Correlation matrix.

Member Function Documentation

◆ calcLibraryScore()

static void calcLibraryScore ( OpenSwath::IMRMFeature mrmfeature,
const std::vector< TransitionType > &  transitions,
double &  correlation,
double &  norm_manhattan,
double &  manhattan,
double &  dotprod,
double &  spectral_angle,
double &  rmsd 
)
static

calculate the library correlation score

◆ calcMIPrecursorCombinedScore()

double calcMIPrecursorCombinedScore ( )

◆ calcMIPrecursorContrastScore()

double calcMIPrecursorContrastScore ( )

◆ calcMIPrecursorScore()

double calcMIPrecursorScore ( )

◆ calcMIScore()

double calcMIScore ( )

◆ calcMIWeightedScore()

double calcMIWeightedScore ( const std::vector< double > &  normalized_library_intensity)

◆ calcRTScore()

static double calcRTScore ( const PeptideType peptide,
double  normalized_experimental_rt 
)
static

calculate the retention time correlation score

◆ calcSeparateMIContrastScore()

std::vector<double> calcSeparateMIContrastScore ( )

◆ calcSeparateSNScore()

static std::vector<double> calcSeparateSNScore ( OpenSwath::IMRMFeature mrmfeature,
std::vector< OpenSwath::ISignalToNoisePtr > &  signal_noise_estimators 
)
static

◆ calcSeparateXcorrContrastCoelutionScore()

std::vector<double> calcSeparateXcorrContrastCoelutionScore ( )

calculate the separate cross-correlation contrast score

◆ calcSeparateXcorrContrastShapeScore()

std::vector<double> calcSeparateXcorrContrastShapeScore ( )

calculate the separate cross-correlation contrast shape score

◆ calcSNScore()

static double calcSNScore ( OpenSwath::IMRMFeature mrmfeature,
std::vector< OpenSwath::ISignalToNoisePtr > &  signal_noise_estimators 
)
static

calculate the Signal to Noise ratio

◆ calcXcorrCoelutionScore()

double calcXcorrCoelutionScore ( )

Calculate the cross-correlation coelution score.

The score is a distance where zero indicates perfect coelution.

◆ calcXcorrCoelutionWeightedScore()

double calcXcorrCoelutionWeightedScore ( const std::vector< double > &  normalized_library_intensity)

Calculate the weighted cross-correlation coelution score.

The score is a distance where zero indicates perfect coelution. The score is weighted by the transition intensities, non-perfect coelution in low-intensity transitions should thus become less important.

◆ calcXcorrContrastShapeScore()

double calcXcorrContrastShapeScore ( )

calculate the cross-correlation contrast shape score

◆ calcXcorrPrecursorCoelutionScore()

double calcXcorrPrecursorCoelutionScore ( )

calculate the precursor cross-correlation contrast score

◆ calcXcorrPrecursorCombinedCoelutionScore()

double calcXcorrPrecursorCombinedCoelutionScore ( )

calculate the precursor cross-correlation coelution score including the transitions

◆ calcXcorrPrecursorCombinedShapeScore()

double calcXcorrPrecursorCombinedShapeScore ( )

calculate the precursor cross-correlation shape score including the transitions

◆ calcXcorrPrecursorContrastCoelutionScore()

double calcXcorrPrecursorContrastCoelutionScore ( )

Calculate the precursor cross-correlation contrast score against the transitions.

The score is a distance where zero indicates perfect coelution.

◆ calcXcorrPrecursorContrastShapeScore()

double calcXcorrPrecursorContrastShapeScore ( )

calculate the precursor cross-correlation shape score against the transitions

◆ calcXcorrPrecursorContrastSumFragCoelutionScore()

double calcXcorrPrecursorContrastSumFragCoelutionScore ( )
  @brief Calculate the precursor cross-correlation contrast score against the sum of transitions

implemented the same as calcXcorrPrecursorCoelutionScore(), however assertion is different.

  The score is a distance where zero indicates perfect coelution.

◆ calcXcorrPrecursorContrastSumFragShapeScore()

double calcXcorrPrecursorContrastSumFragShapeScore ( )
  @brief Calculate the precursor cross-correlation contrast score against the sum of transitions

implemented the same as calcXcorrPrecursorContrastShapeScore(), however assertion is different.

  The score is a distance where zero indicates perfect coelution.

◆ calcXcorrPrecursorShapeScore()

double calcXcorrPrecursorShapeScore ( )

calculate the precursor cross-correlation shape score

◆ calcXcorrShapeScore()

double calcXcorrShapeScore ( )

Calculate the cross-correlation shape score.

The score is a correlation measure where 1 indicates perfect correlation and 0 means no correlation.

◆ calcXcorrShapeWeightedScore()

double calcXcorrShapeWeightedScore ( const std::vector< double > &  normalized_library_intensity)

Calculate the weighted cross-correlation shape score.

The score is a correlation measure where 1 indicates perfect correlation and 0 means no correlation. The score is weighted by the transition intensities, non-perfect coelution in low-intensity transitions should thus become less important.

◆ getMIContrastMatrix()

const OpenMS::Matrix<double>& getMIContrastMatrix ( ) const

non-mutable access to the MI contrast matrix

◆ getMIMatrix()

const OpenMS::Matrix<double>& getMIMatrix ( ) const

non-mutable access to the MI matrix

◆ getMIPrecursorCombinedMatrix()

const OpenMS::Matrix<double>& getMIPrecursorCombinedMatrix ( ) const

non-mutable access to the MI precursor combined matrix

◆ getMIPrecursorContrastMatrix()

const OpenMS::Matrix<double>& getMIPrecursorContrastMatrix ( ) const

non-mutable access to the MI precursor contrast matrix

◆ getXCorrContrastMatrix()

const XCorrMatrixType& getXCorrContrastMatrix ( ) const

non-mutable access to the cross-correlation contrast matrix

◆ getXCorrMatrix()

const XCorrMatrixType& getXCorrMatrix ( ) const

non-mutable access to the cross-correlation matrix

◆ getXCorrPrecursorCombinedMatrix()

const XCorrMatrixType& getXCorrPrecursorCombinedMatrix ( ) const

non-mutable access to the cross-correlation precursor contrast matrix

◆ getXCorrPrecursorContrastMatrix()

const XCorrMatrixType& getXCorrPrecursorContrastMatrix ( ) const

non-mutable access to the cross-correlation precursor contrast matrix

◆ initializeMIContrastMatrix()

void initializeMIContrastMatrix ( OpenSwath::IMRMFeature mrmfeature,
const std::vector< std::string > &  native_ids_set1,
const std::vector< std::string > &  native_ids_set2 
)

Initialize the scoring object and building the MI matrix of chromatograms of set1 (e.g. identification transitions) vs set2 (e.g. detection transitions)

◆ initializeMIMatrix()

void initializeMIMatrix ( OpenSwath::IMRMFeature mrmfeature,
const std::vector< std::string > &  native_ids 
)

Initialize the scoring object and building the MI matrix.

◆ initializeMIPrecursorCombinedMatrix()

void initializeMIPrecursorCombinedMatrix ( OpenSwath::IMRMFeature mrmfeature,
const std::vector< std::string > &  precursor_ids,
const std::vector< std::string > &  native_ids 
)

Initialize the mutual information vector with the MS1 trace.

◆ initializeMIPrecursorContrastMatrix()

void initializeMIPrecursorContrastMatrix ( OpenSwath::IMRMFeature mrmfeature,
const std::vector< std::string > &  precursor_ids,
const std::vector< std::string > &  native_ids 
)

Initialize the mutual information vector against the MS1 trace.

◆ initializeMIPrecursorMatrix()

void initializeMIPrecursorMatrix ( OpenSwath::IMRMFeature mrmfeature,
const std::vector< std::string > &  precursor_ids 
)

Initialize the scoring object and building the MI matrix.

◆ initializeXCorrContrastMatrix()

void initializeXCorrContrastMatrix ( OpenSwath::IMRMFeature mrmfeature,
const std::vector< std::string > &  native_ids_set1,
const std::vector< std::string > &  native_ids_set2 
)

Initialize the scoring object and building the cross-correlation matrix of chromatograms of set1 (e.g. identification transitions) vs set2 (e.g. detection transitions)

◆ initializeXCorrMatrix() [1/2]

void initializeXCorrMatrix ( const std::vector< std::vector< double > > &  data)

Initialize the scoring object and building the cross-correlation matrix.

◆ initializeXCorrMatrix() [2/2]

void initializeXCorrMatrix ( OpenSwath::IMRMFeature mrmfeature,
const std::vector< std::string > &  native_ids 
)

Initialize the scoring object and building the cross-correlation matrix.

◆ initializeXCorrPrecursorCombinedMatrix()

void initializeXCorrPrecursorCombinedMatrix ( OpenSwath::IMRMFeature mrmfeature,
const std::vector< std::string > &  precursor_ids,
const std::vector< std::string > &  native_ids 
)

Initialize the scoring object and building the cross-correlation matrix of chromatograms of precursor isotopes and transitions.

◆ initializeXCorrPrecursorContrastMatrix() [1/2]

void initializeXCorrPrecursorContrastMatrix ( const std::vector< std::vector< double > > &  data_precursor,
const std::vector< std::vector< double > > &  data_fragments 
)

Initialize the scoring object and building the cross-correlation matrix of chromatograms of precursor isotopes vs transitions.

◆ initializeXCorrPrecursorContrastMatrix() [2/2]

void initializeXCorrPrecursorContrastMatrix ( OpenSwath::IMRMFeature mrmfeature,
const std::vector< std::string > &  precursor_ids,
const std::vector< std::string > &  native_ids 
)

Initialize the scoring object and building the cross-correlation matrix of chromatograms of precursor isotopes vs transitions.

◆ initializeXCorrPrecursorMatrix()

void initializeXCorrPrecursorMatrix ( OpenSwath::IMRMFeature mrmfeature,
const std::vector< std::string > &  precursor_ids 
)

Initialize the scoring object and building the cross-correlation matrix.

Member Data Documentation

◆ mi_contrast_matrix_

OpenMS::Matrix<double> mi_contrast_matrix_
private

the precomputed contrast mutual information matrix

◆ mi_matrix_

OpenMS::Matrix<double> mi_matrix_
private

the precomputed mutual information matrix

◆ mi_precursor_combined_matrix_

OpenMS::Matrix<double> mi_precursor_combined_matrix_
private

the precomputed contrast mutual information matrix with the MS1 trace

◆ mi_precursor_contrast_matrix_

OpenMS::Matrix<double> mi_precursor_contrast_matrix_
private

the precomputed contrast mutual information matrix against the MS1 trace

◆ mi_precursor_matrix_

OpenMS::Matrix<double> mi_precursor_matrix_
private

the precomputed mutual information matrix of the MS1 trace

◆ xcorr_contrast_matrix_

XCorrMatrixType xcorr_contrast_matrix_
private

the precomputed contrast cross correlation

◆ xcorr_contrast_matrix_max_peak_sec_

OpenMS::Matrix<double> xcorr_contrast_matrix_max_peak_sec_
private

contains max Peaks from xcorr_contrast_matrix_

◆ xcorr_matrix_

XCorrMatrixType xcorr_matrix_
private

the precomputed cross correlation matrix

◆ xcorr_matrix_max_peak_

OpenMS::Matrix<int> xcorr_matrix_max_peak_
private

contains max Peaks from xcorr_matrix_

◆ xcorr_matrix_max_peak_sec_

OpenMS::Matrix<double> xcorr_matrix_max_peak_sec_
private

◆ xcorr_precursor_combined_matrix_

XCorrMatrixType xcorr_precursor_combined_matrix_
private

the precomputed cross correlation with the MS1 trace

◆ xcorr_precursor_contrast_matrix_

XCorrMatrixType xcorr_precursor_contrast_matrix_
private

the precomputed cross correlation against the MS1 trace

◆ xcorr_precursor_matrix_

XCorrMatrixType xcorr_precursor_matrix_
private

the precomputed cross correlation matrix of the MS1 trace