An m/z error model of a run (calibration:recalibrate), fitted to the calibration PSMs and subtracted from the spectra before the main search. More...

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

Classes
struct	AtRT

struct	Chunk

Public Member Functions
bool	active () const

double	error (double mz, double rt) const
	the modelled error at (mz, rt)

double	correct (double mz, double rt) const
	`mz` without the modelled error

double	uncorrect (double corrected, double rt) const
	the inverse of correct(): the m/z it maps to `corrected`

AtRT	at (double rt) const
	the model at `rt` (the chunks must not change while the result is used)

std::string	toString () const
	"ppm; rt <s>: <intercept> + <slope> mz (<points>) \| ..." (empty: inactive)

Static Public Member Functions
static MzRecalibration_	fit (const std::vector< double > &errors, const std::vector< double > &mzs, const std::vector< double > &rts, Size n_chunks, Size min_points, bool linear, bool ppm)

Public Attributes
std::vector< Chunk >	chunks
	in RT order; empty: no correction

bool	ppm {true}
	the error unit: ppm (correction mz - e * mz * 1e-6) or Da (mz - e)

Detailed Description

An m/z error model of a run (calibration:recalibrate), fitted to the calibration PSMs and subtracted from the spectra before the main search.

Per retention-time chunk a linear function of m/z of the signed error (observed minus theoretical; the median alone, slope 0, with mode 'offset'), linearly interpolated between the chunks' centres and constant beyond them. The errors are in ppm or in the unit of the tolerance (Da); correct() removes the modelled error from an m/z.

Class Documentation

◆ OpenMS::ProSEAlgorithm::MzRecalibration_::Chunk

struct OpenMS::ProSEAlgorithm::MzRecalibration_::Chunk

Class Members
double	intercept
Size	points
double	rt
double	slope

Member Function Documentation

◆ active()

bool active ( ) const

inline

Referenced by ProSEAlgorithm::CalibrationResult_::appliedFragmentRecalibration(), and ProSEAlgorithm::CalibrationResult_::recalibrated().

◆ at()

AtRT at ( double rt ) const

the model at rt (the chunks must not change while the result is used)

◆ correct()

double correct	(	double	mz,
		double	rt
	)		const

mz without the modelled error

◆ error()

double error	(	double	mz,
		double	rt
	)		const

the modelled error at (mz, rt)

◆ fit()

static MzRecalibration_ fit	(	const std::vector< double > &	errors,
		const std::vector< double > &	mzs,
		const std::vector< double > &	rts,
		Size	n_chunks,
		Size	min_points,
		bool	linear,
		bool	ppm
	)

static

Fit the model: the points (error, m/z, RT) are split in RT order into n_chunks groups of equal size (fewer when a group would hold less than min_points points), each fitted to its points within three robust standard deviations of its median: the median (linear false) or the least-squares line in m/z (linear; the median when the line cannot be fitted). Deterministic (no RANSAC).

◆ toString()

std::string toString ( ) const

"ppm; rt <s>: <intercept> + <slope> mz (<points>) | ..." (empty: inactive)

◆ uncorrect()

double uncorrect	(	double	corrected,
		double	rt
	)		const

the inverse of correct(): the m/z it maps to corrected

Member Data Documentation

◆ chunks

std::vector<Chunk> chunks

in RT order; empty: no correction

◆ ppm

bool ppm {true}

the error unit: ppm (correction mz - e * mz * 1e-6) or Da (mz - e)

Classes

Public Member Functions

Static Public Member Functions

Public Attributes