| OpenMS 2.5.0

Public Member Functions | Private Member Functions | Private Attributes | List of all members
TOFCalibration Class Reference
Analysis » SignalProcessing

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. 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...
virtual 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...
| ~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)
| 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...
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
| ) |  |

inline private

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 | ) |

inline private

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