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

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

Inheritance diagram for TOFCalibration:

Collaboration diagram for TOFCalibration:

Public Member Functions
	TOFCalibration ()
	Default constructor. More...

	~TOFCalibration () override
	Destructor. More...

void	pickAndCalibrate (PeakMap &calib_spectra, PeakMap &exp, std::vector< double > &exp_masses)

void	calibrate (PeakMap &calib_spectra, PeakMap &exp, std::vector< double > &exp_masses)

const std::vector< double > &	getML1s () const
	Non-mutable access to the first calibration constant. More...

void	setML1s (const std::vector< double > &ml1s)
	mutable access to the first calibration constant More...

const std::vector< double > &	getML2s () const
	Non-mutable access to the second calibration constant. More...

void	setML2s (const std::vector< double > &ml2s)
	mutable access to the second calibration constant More...

const std::vector< double > &	getML3s () const
	Non-mutable access to the third calibration constant. More...

void	setML3s (const std::vector< double > &ml3s)
	mutable access to the third calibration constant More...

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress () const
	Ends the progress display. More...

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Private Member Functions
void	calculateCalibCoeffs_ (PeakMap &calib_peaks_ft)
	Calculates the coefficients of the quadratic fit used for external calibration. More...

void	getMonoisotopicPeaks_ (PeakMap &calib_peaks, std::vector< std::vector< unsigned int > > &monoiso_peaks)
	determines the monoisotopic peaks More...

void	applyTOFConversion_ (PeakMap &calib_spectra)
	Applies the conversion from TOF to m/z-values to all peaks. More...

void	matchMasses_ (PeakMap &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 More...

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. More...

double	mQAv_ (double ft) const
	Calculate the mass value for a given flight time using the averaged coefficients of the quadratic fit. More...

void	averageErrors_ ()
	Calculate the average errors of the reference masses over all scans. More...

void	averageCoefficients_ ()
	Average the coefficients of the quadratic fit. More...

Private Attributes
PeakMap	calib_peaks_ft_
	the calibrant spectra still using flight times instead of m/z-values More...

std::vector< double >	exp_masses_
	the expected calibrant masses More...

std::map< double, std::vector< double > >	errors_
	error in ppm after quadratic fit More...

std::vector< double >	error_medians_
	median errors More...

std::vector< double >	calib_masses_

std::vector< double >	ml1s_
	calibration constants from the instrument needed for the conversion of the calibrant spectra More...

std::vector< double >	ml2s_

std::vector< double >	ml3s_

std::vector< double >	coeff_quad_fit_
	all coefficients of the quadratic fit More...

double	a_
	mean coefficients More...

double	b_

double	c_

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...

Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

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 dependence 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()

TOFCalibration ( )

Default constructor.

◆ ~TOFCalibration()

~TOFCalibration ( )

override

Destructor.

Member Function Documentation

◆ applyTOFConversion_()

void applyTOFConversion_ ( PeakMap & 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.

◆ averageCoefficients_()

void averageCoefficients_ ( )

private

Average the coefficients of the quadratic fit.

◆ averageErrors_()

void averageErrors_ ( )

private

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

◆ calculateCalibCoeffs_()

void calculateCalibCoeffs_ ( PeakMap & calib_peaks_ft )

private

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

◆ calibrate()

void calibrate	(	PeakMap &	calib_spectra,
		PeakMap &	exp,
		std::vector< double > &	exp_masses
	)

◆ getML1s()

const std::vector<double>& getML1s ( ) const

inline

Non-mutable access to the first calibration constant.

◆ getML2s()

const std::vector<double>& getML2s ( ) const

inline

Non-mutable access to the second calibration constant.

◆ getML3s()

const std::vector<double>& getML3s ( ) const

inline

Non-mutable access to the third calibration constant.

◆ getMonoisotopicPeaks_()

void getMonoisotopicPeaks_	(	PeakMap &	calib_peaks,
		std::vector< std::vector< unsigned int > > &	monoiso_peaks
	)

private

determines the monoisotopic peaks

◆ matchMasses_()

void matchMasses_	(	PeakMap &	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

◆ mQ_()

double mQ_	(	double	ft,
		unsigned int	spec
	)

inlineprivate

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

◆ mQAv_()

double mQAv_ ( double ft ) const

inlineprivate

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

◆ pickAndCalibrate()

void pickAndCalibrate	(	PeakMap &	calib_spectra,
		PeakMap &	exp,
		std::vector< double > &	exp_masses
	)

◆ setML1s()

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

inline

mutable access to the first calibration constant

◆ setML2s()

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

inline

mutable access to the second calibration constant

◆ setML3s()

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

inline

mutable access to the third calibration constant

Member Data Documentation

◆ a_

double a_

private

mean coefficients

◆ b_

double b_

private

◆ c_

double c_

private

◆ calib_masses_

std::vector<double> calib_masses_

private

◆ calib_peaks_ft_

PeakMap calib_peaks_ft_

private

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

◆ coeff_quad_fit_

std::vector<double> coeff_quad_fit_

private

all coefficients of the quadratic fit

◆ error_medians_

std::vector<double> error_medians_

private

median errors

◆ errors_

std::map<double, std::vector<double> > errors_

private

error in ppm after quadratic fit

◆ exp_masses_

std::vector<double> exp_masses_

private

the expected calibrant masses

◆ ml1s_

std::vector<double> ml1s_

private

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

◆ ml2s_

std::vector<double> ml2s_

private

◆ ml3s_

std::vector<double> ml3s_

private

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ TOFCalibration()

◆ ~TOFCalibration()

Member Function Documentation

◆ applyTOFConversion_()

◆ averageCoefficients_()

◆ averageErrors_()

◆ calculateCalibCoeffs_()

◆ calibrate()

◆ getML1s()

◆ getML2s()

◆ getML3s()

◆ getMonoisotopicPeaks_()

◆ matchMasses_()

◆ mQ_()

◆ mQAv_()

◆ pickAndCalibrate()

◆ setML1s()

◆ setML2s()

◆ setML3s()

Member Data Documentation

◆ a_

◆ b_

◆ c_

◆ calib_masses_

◆ calib_peaks_ft_

◆ coeff_quad_fit_

◆ error_medians_

◆ errors_

◆ exp_masses_

◆ ml1s_

◆ ml2s_

◆ ml3s_