HyperScore Struct Reference

An implementation of the X!Tandem HyperScore PSM scoring function. More...

#include <OpenMS/ANALYSIS/ID/HyperScore.h>

Classes
struct	PSMDetail
	compute the (ln transformed) X!Tandem HyperScore overload that returns some additional information on the match More...

Public Types
typedef std::pair< Size, double >	IndexScorePair

Static Public Member Functions
static double	compute (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &exp_spectrum, const PeakSpectrum &theo_spectrum)
	compute the (ln transformed) X!Tandem HyperScore
static double	computeWithDetail (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &exp_spectrum, const PeakSpectrum &theo_spectrum, PSMDetail &d)
static double	computeMassAccuracy (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &exp_spectrum, const PeakSpectrum &theo_spectrum, double mass_error_sd_ppm, PSMDetail &detail)
	HyperScore with mass-accuracy-weighted fragment evidence.
static double	compute (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &exp_spectrum, const DataArrays::IntegerDataArray &exp_charges, const PeakSpectrum &theo_spectrum, const DataArrays::IntegerDataArray &theo_charges)
static double	compute (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &exp_spectrum, const DataArrays::IntegerDataArray &exp_charges, const PeakSpectrum &theo_spectrum, const DataArrays::IntegerDataArray &theo_charges, std::vector< double > &intensity_sum)

Static Private Member Functions
static double	logfactorial_ (const int x, int base=2)
	helper to compute the log factorial

Detailed Description

An implementation of the X!Tandem HyperScore PSM scoring function.

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Class Documentation

OpenMS::HyperScore::PSMDetail

struct OpenMS::HyperScore::PSMDetail

compute the (ln transformed) X!Tandem HyperScore overload that returns some additional information on the match

Class Members
size_t	matched_prefix_ions = 0	N-terminal ions (a, b, c)
size_t	matched_suffix_ions = 0	C-terminal ions (x, y, z)
double	mean_error = 0.0

Member Typedef Documentation

IndexScorePair

typedef std::pair<Size, double> IndexScorePair

Member Function Documentation

compute() [1/3]

static double compute ( double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, const PeakSpectrum &  exp_spectrum, const DataArrays::IntegerDataArray &  exp_charges, const PeakSpectrum &  theo_spectrum, const DataArrays::IntegerDataArray &  theo_charges  )

static

compute() [2/3]

static double compute ( double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, const PeakSpectrum &  exp_spectrum, const DataArrays::IntegerDataArray &  exp_charges, const PeakSpectrum &  theo_spectrum, const DataArrays::IntegerDataArray &  theo_charges, std::vector< double > &  intensity_sum  )

static

compute() [3/3]

static double compute ( double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, const PeakSpectrum &  exp_spectrum, const PeakSpectrum &  theo_spectrum  )

static

compute the (ln transformed) X!Tandem HyperScore

1. the dot product of peak intensities between matching peaks in experimental and theoretical spectrum is calculated
2. the HyperScore is calculated from the dot product by multiplying by factorials of matching b- and y-ions

   Note

   Peak intensities of the theoretical spectrum are typically 1 or TIC normalized, but can also be e.g. ion probabilities

   Parameters

   [in]	fragment_mass_tolerance	mass tolerance applied left and right of the theoretical spectrum peak position
   [in]	fragment_mass_tolerance_unit_ppm	Unit of the mass tolerance is: Thomson if false, ppm if true
   [in]	exp_spectrum	measured spectrum
   [in]	theo_spectrum	theoretical spectrum Peaks need to contain an ion annotation as provided by TheoreticalSpectrumGenerator.

computeMassAccuracy()

static double computeMassAccuracy ( double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, const PeakSpectrum &  exp_spectrum, const PeakSpectrum &  theo_spectrum, double  mass_error_sd_ppm, PSMDetail &  detail  )

static

HyperScore with mass-accuracy-weighted fragment evidence.

A matched ion with signed mass error e (ppm) contributes exp(-0.5*(e/sigma)^2) to its terminal ion count and intensity product. Fractional factorial rewards use max(0, lgamma(count+1)), agreeing with HyperScore for exact matches. The kernel is centred at zero and its width is fixed; it is a ranking statistic, not a PSM p-value.

Parameters

[in]	fragment_mass_tolerance	Positive finite match tolerance (Da or ppm).
[in]	fragment_mass_tolerance_unit_ppm	Whether matching tolerance is in ppm.
[in]	exp_spectrum	Experimental spectrum, sorted by m/z.
[in]	theo_spectrum	Theoretical spectrum, sorted by m/z, with ion names.
[in]	mass_error_sd_ppm	Positive finite Gaussian standard deviation in ppm.
[out]	detail	Unweighted match counts and mean absolute error in matching units.

Returns

Nonnegative weighted log HyperScore; zero without matches.

Exceptions

Exception::InvalidParameter	for invalid tolerance or standard deviation.
Exception::InvalidValue	for incomplete theoretical ion annotations.

computeWithDetail()

static double computeWithDetail ( double  fragment_mass_tolerance, bool  fragment_mass_tolerance_unit_ppm, const PeakSpectrum &  exp_spectrum, const PeakSpectrum &  theo_spectrum, PSMDetail &  d  )

static

logfactorial_()

static double logfactorial_ ( const int  x, int  base = 2  )

staticprivate

helper to compute the log factorial