Result of a calibration pass. More...

#include <OpenMS/ANALYSIS/ID/PROSE/ProSEAlgorithm.h>

Public Member Functions
bool	recalibrated () const

const MzRecalibration_ *	appliedFragmentRecalibration () const
	the fragment model applyRecalibration_() subtracts from the peaks (nullptr: the peaks are not corrected)

Public Attributes
double	precursor_shift {0}
	median of the signed precursor errors of the calibration PSMs (the mass offset)

double	precursor_sigma {0}
	their robust standard deviation, 1.4826 * MAD

double	precursor_raw_shift {0}
	offset and spread of the precursor errors as measured (= precursor_shift / precursor_sigma without recalibration)

double	precursor_raw_sigma {0}

double	fragment_raw_shift {0}
	the same of the fragment errors

double	fragment_raw_sigma {0}

MzRecalibration_	precursor_recalibration
	the models subtracted from the spectra (calibration:recalibrate; inactive otherwise)

MzRecalibration_	fragment_recalibration

double	precursor_spread {0}
	the larger side of the window before the caps, max(cal_lower, cal_upper) (diagnostic)

double	cal_lower {0}
	calibrated lower magnitude (valid iff !extreme_bias && success)

double	cal_upper {0}
	calibrated upper magnitude (valid iff !extreme_bias && success)

double	fragment_tolerance {0}
	estimated fragment tolerance (same unit as configured)

double	fragment_shift {0}
	median of the signed errors of the matched fragment peaks (covered by the window, not corrected)

double	fragment_sigma {0}
	their robust standard deviation, 1.4826 * MAD

double	precursor_coverage {0}
	share of the calibration PSMs inside the precursor window median +/- k sigma

double	fragment_coverage {0}
	share of the matched fragment peaks inside the fragment tolerance

Size	psms {0}

double	precursor_measured_coverage {0}
	share of the calibration PSMs whose precursor error (as measured, before a recalibration) lies within offset +/- 4 sigma

double	fragment_measured_coverage {0}
	share of the matched fragment peaks whose error (as measured) lies within \|offset\| + 4 sigma

bool	precursor_measurement_trusted {false}
	whether the measured precursor error describes the run: it covers at least 98 % of the calibration PSMs

bool	fragment_measurement_trusted {false}
	whether the measured fragment error describes the run: from calibration:min_psms peaks or more, covering at least 95 % of them

Size	fragment_peaks {0}
	matched fragment peaks the fragment window was estimated from

bool	extreme_bias {false}
	zero spread of the precursor errors: the precursor window is kept (test observability)

bool	success {false}
	true if enough PSMs were found for reliable estimation

Detailed Description

Result of a calibration pass.

Holds the estimated precursor and fragment tolerances computed from confident PSMs during the calibration pass. When success is false, the tolerance values are undefined and should not be used. With calibration:recalibrate the shifts and sigmas are those of the residual errors after the models (*_recalibration) are subtracted, i.e. the errors the main search sees; *_raw_* hold the errors as measured.

Member Function Documentation

◆ appliedFragmentRecalibration()

const MzRecalibration_ * appliedFragmentRecalibration ( ) const

inline

the fragment model applyRecalibration_() subtracts from the peaks (nullptr: the peaks are not corrected)

References ProSEAlgorithm::MzRecalibration_::active().

◆ recalibrated()

bool recalibrated ( ) const

inline

References ProSEAlgorithm::MzRecalibration_::active().

Member Data Documentation

◆ cal_lower

double cal_lower {0}

calibrated lower magnitude (valid iff !extreme_bias && success)

◆ cal_upper

double cal_upper {0}

calibrated upper magnitude (valid iff !extreme_bias && success)

◆ extreme_bias

bool extreme_bias {false}

zero spread of the precursor errors: the precursor window is kept (test observability)

◆ fragment_coverage

double fragment_coverage {0}

share of the matched fragment peaks inside the fragment tolerance

◆ fragment_measured_coverage

double fragment_measured_coverage {0}

share of the matched fragment peaks whose error (as measured) lies within |offset| + 4 sigma

◆ fragment_measurement_trusted

bool fragment_measurement_trusted {false}

whether the measured fragment error describes the run: from calibration:min_psms peaks or more, covering at least 95 % of them

◆ fragment_peaks

Size fragment_peaks {0}

matched fragment peaks the fragment window was estimated from

◆ fragment_raw_shift

double fragment_raw_shift {0}

the same of the fragment errors

◆ fragment_raw_sigma

double fragment_raw_sigma {0}

◆ fragment_recalibration

MzRecalibration_ fragment_recalibration

◆ fragment_shift

double fragment_shift {0}

median of the signed errors of the matched fragment peaks (covered by the window, not corrected)

◆ fragment_sigma

double fragment_sigma {0}

their robust standard deviation, 1.4826 * MAD

◆ fragment_tolerance

double fragment_tolerance {0}

estimated fragment tolerance (same unit as configured)

◆ precursor_coverage

double precursor_coverage {0}

share of the calibration PSMs inside the precursor window median +/- k sigma

◆ precursor_measured_coverage

double precursor_measured_coverage {0}

share of the calibration PSMs whose precursor error (as measured, before a recalibration) lies within offset +/- 4 sigma

◆ precursor_measurement_trusted

bool precursor_measurement_trusted {false}

whether the measured precursor error describes the run: it covers at least 98 % of the calibration PSMs

◆ precursor_raw_shift

double precursor_raw_shift {0}

offset and spread of the precursor errors as measured (= precursor_shift / precursor_sigma without recalibration)

◆ precursor_raw_sigma

double precursor_raw_sigma {0}

◆ precursor_recalibration

MzRecalibration_ precursor_recalibration

the models subtracted from the spectra (calibration:recalibrate; inactive otherwise)

◆ precursor_shift

double precursor_shift {0}

median of the signed precursor errors of the calibration PSMs (the mass offset)

◆ precursor_sigma

double precursor_sigma {0}