This class implements an external calibration for TOF data using external calibrant spectra. More...

#include <OpenMS/FILTERING/CALIBRATION/TOFCalibration.h>

Inheritance diagram for TOFCalibration:

Public Member Functions
	TOFCalibration ()
	Default constructor.
	~TOFCalibration ()
	Destructor.
template<typename PeakType >
void	pickAndCalibrate (MSExperiment< Peak1D > &calib_spectra, MSExperiment< PeakType > &exp, std::vector< double > &exp_masses)
template<typename PeakType >
void	calibrate (MSExperiment< Peak1D > &calib_spectra, MSExperiment< PeakType > &exp, std::vector< double > &exp_masses)
const std::vector< double > &	getML1s () const
	Non-mutable access to the first calibration constant.
void	setML1s (const std::vector< double > &ml1s)
	mutable access to the first calibration constant
const std::vector< double > &	getML2s () const
	Non-mutable access to the second calibration constant.
void	setML2s (const std::vector< double > &ml2s)
	mutable access to the second calibration constant
const std::vector< double > &	getML3s () const
	Non-mutable access to the third calibration constant.
void	setML3s (const std::vector< double > &ml3s)
	mutable access to the third calibration constant
Private Member Functions
void	calculateCalibCoeffs_ (MSExperiment<> &calib_peaks_ft)
	Calculates the coefficients of the quadratic fit used for external calibration.
void	getMonoisotopicPeaks_ (MSExperiment<> &calib_peaks, std::vector< std::vector< unsigned int > > &monoiso_peaks)
	determines the monoisotopic peaks
void	applyTOFConversion_ (MSExperiment<> &calib_spectra)
	Applies the conversion from TOF to m/z-values to all peaks.
void	matchMasses_ (MSExperiment<> &calib_peaks, std::vector< std::vector< unsigned int > > &monoiso_peaks, std::vector< unsigned int > &obs_masses, std::vector< double > &exp_masses, unsigned int idx)
	determine the monoisotopic masses that have matching expected masses
double	mQ_ (double ft, unsigned int spec)
	Calculate the mass value for a given flight time using the coefficients of the quadratic fit in a specific spectrum.
double	mQAv_ (double ft)
	Calculate the mass value for a given flight time using the averaged coefficients of the quadratic fit.
void	averageErrors_ ()
	Calculate the average errors of the reference masses over all scans.
void	averageCoefficients_ ()
	Average the coefficients of the quadratic fit.
Private Attributes
MSExperiment	calib_peaks_ft_
	the calibrant spectra still using flight times instead of m/z-values
std::vector< double >	exp_masses_
	the expected calibrant masses
std::map< double, std::vector < double > >	errors_
	error in ppm after quadratic fit
std::vector< double >	error_medians_
	median errors
std::vector< double >	calib_masses_
std::vector< double >	ml1s_
	calibration constants from the instrument needed for the conversion of the calibrant spectra
std::vector< double >	ml2s_
std::vector< double >	ml3s_
std::vector< double >	coeff_quad_fit_
	all coefficients of the quadratic fit
double	a_
	mean coefficients
double	b_
double	c_
gsl_interp_accel *	acc_
gsl_spline *	spline_

Detailed Description

This class implements an external calibration for TOF data using external calibrant spectra.

The procedure is very similar to the one described in Gobom et al. (Anal Chem. 2002, 74 (15) pp 3915-23). The input experiment data need to be flight times. They are converted into m/z-values using the calibrant spectra. The calibrant spectra and their expected masses are used to determine the quadratic dependance of tof and m/z values.

Note:: The input spectra need to contain flight times.; The peaks must be sorted according to ascending m/z!

Constructor & Destructor Documentation

TOFCalibration ( )

Default constructor.

~TOFCalibration ( )

Destructor.

Member Function Documentation

void applyTOFConversion_ ( MSExperiment<> & calib_spectra ) [private]

Applies the conversion from TOF to m/z-values to all peaks.

Either a 2-point or a 3-point time of flight conversion can be used, as well as different constants for each calibrant spectra or one set for all of them.

The 2-point equation is mass = ml1/10^12 * (tof * 1000 - ml2). The 3-point equation is time = ml2 + sqrt(10^12/ml1 * mass) + ml3*mass.

void averageCoefficients_ ( ) [private]

Average the coefficients of the quadratic fit.

void averageErrors_ ( ) [private]

Calculate the average errors of the reference masses over all scans.

void calculateCalibCoeffs_ ( MSExperiment<> & calib_peaks_ft ) [private]

Calculates the coefficients of the quadratic fit used for external calibration.

Referenced by TOFCalibration::calibrate().

void calibrate	(	MSExperiment< Peak1D > &	calib_spectra,
		MSExperiment< PeakType > &	exp,
		std::vector< double > &	exp_masses
	)

References TOFCalibration::acc_, TOFCalibration::calculateCalibCoeffs_(), TOFCalibration::exp_masses_, TOFCalibration::mQAv_(), and TOFCalibration::spline_.

Referenced by TOFCalibration::pickAndCalibrate().

const std::vector<double>& getML1s ( ) const [inline]

Non-mutable access to the first calibration constant.

const std::vector<double>& getML2s ( ) const [inline]

Non-mutable access to the second calibration constant.

const std::vector<double>& getML3s ( ) const [inline]

Non-mutable access to the third calibration constant.

void getMonoisotopicPeaks_	(	MSExperiment<> &	calib_peaks,
		std::vector< std::vector< unsigned int > > &	monoiso_peaks
	)			`[private]`

determines the monoisotopic peaks

void matchMasses_	(	MSExperiment<> &	calib_peaks,
		std::vector< std::vector< unsigned int > > &	monoiso_peaks,
		std::vector< unsigned int > &	obs_masses,
		std::vector< double > &	exp_masses,
		unsigned int	idx
	)			`[private]`

determine the monoisotopic masses that have matching expected masses

double mQ_	(	double	ft,
		unsigned int	spec
	)			`[inline, private]`

Calculate the mass value for a given flight time using the coefficients of the quadratic fit in a specific spectrum.

double mQAv_ ( double ft ) [inline, private]

Calculate the mass value for a given flight time using the averaged coefficients of the quadratic fit.

Referenced by TOFCalibration::calibrate().

void pickAndCalibrate	(	MSExperiment< Peak1D > &	calib_spectra,
		MSExperiment< PeakType > &	exp,
		std::vector< double > &	exp_masses
	)

References TOFCalibration::calibrate(), Param::copy(), DefaultParamHandler::param_, PeakPickerCWT::pickExperiment(), and DefaultParamHandler::setParameters().

void setML1s ( const std::vector< double > & ml1s ) [inline]

mutable access to the first calibration constant

void setML2s ( const std::vector< double > & ml2s ) [inline]

mutable access to the second calibration constant

void setML3s ( const std::vector< double > & ml3s ) [inline]

mutable access to the third calibration constant

Member Data Documentation

double a_ [private]

mean coefficients

gsl_interp_accel* acc_ [private]

Referenced by TOFCalibration::calibrate().

double b_ [private]

double c_ [private]

std::vector<double> calib_masses_ [private]

MSExperiment calib_peaks_ft_ [private]

the calibrant spectra still using flight times instead of m/z-values

std::vector<double> coeff_quad_fit_ [private]

all coefficients of the quadratic fit

std::vector<double> error_medians_ [private]

median errors

std::map<double, std::vector<double> > errors_ [private]

error in ppm after quadratic fit

std::vector<double> exp_masses_ [private]

the expected calibrant masses

Referenced by TOFCalibration::calibrate().

std::vector<double> ml1s_ [private]

calibration constants from the instrument needed for the conversion of the calibrant spectra

std::vector<double> ml2s_ [private]

std::vector<double> ml3s_ [private]

gsl_spline* spline_ [private]

Referenced by TOFCalibration::calibrate().

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:53 using doxygen 1.7.1

TOFCalibration Class Reference [SignalProcessing]

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

TOFCalibration Class Reference
[SignalProcessing]