#include <OpenMS/FILTERING/CALIBRATION/TOFCalibration.h>
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.
Public Types | |
typedef RawDataPoint1D | RawDataPointType |
Raw data point type. | |
typedef PickedPeak1D | PickedPeakType |
Picked Peak type. | |
Public Member Functions | |
TOFCalibration () | |
Default constructor. | |
~TOFCalibration () | |
Destructor. | |
template<typename PeakType> | |
void | calibrate (MSExperiment< RawDataPointType > &calib_spectra, MSExperiment< PeakType > &exp, std::vector< double > &exp_masses) |
Apply the external calibration using raw calibrant spectra. | |
template<typename PeakType> | |
void | calibrate (MSExperiment< PickedPeakType > &calib_spectra, MSExperiment< PeakType > &exp, std::vector< double > &exp_masses) |
Apply the external calibration using picked calibrant spectra. | |
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< PickedPeakType > &calib_peaks_ft) throw (UnableToCalibrate) |
Calculates the coefficients of the quadratic fit used for external calibration. | |
void | getMonoisotopicPeaks_ (MSExperiment< PickedPeakType > &calib_peaks, std::vector< std::vector< unsigned int > > &monoiso_peaks) |
determines the monoisotopic peaks | |
void | applyTOFConversion_ (MSExperiment< PickedPeakType > &calib_spectra) |
Applies the conversion from TOF to m/z-values to all peaks. | |
void | matchMasses_ (MSExperiment< PickedPeakType > &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< PickedPeakType > | 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_ |
Classes | |
class | UnableToCalibrate |
Inner Classes for Exception handling. More... |
typedef RawDataPoint1D RawDataPointType |
Raw data point type.
typedef PickedPeak1D PickedPeakType |
Picked Peak type.
TOFCalibration | ( | ) |
Default constructor.
~TOFCalibration | ( | ) |
Destructor.
void calibrate | ( | MSExperiment< RawDataPointType > & | calib_spectra, | |
MSExperiment< PeakType > & | exp, | |||
std::vector< double > & | exp_masses | |||
) | [inline] |
Apply the external calibration using raw calibrant spectra.
void calibrate | ( | MSExperiment< PickedPeakType > & | calib_spectra, | |
MSExperiment< PeakType > & | exp, | |||
std::vector< double > & | exp_masses | |||
) | [inline] |
Apply the external calibration using picked calibrant spectra.
const std::vector<double>& getML1s | ( | ) | const [inline] |
Non-mutable access to the first calibration constant.
void setML1s | ( | const std::vector< double > & | ml1s | ) | [inline] |
mutable access to the first calibration constant
const std::vector<double>& getML2s | ( | ) | const [inline] |
Non-mutable access to the second calibration constant.
void setML2s | ( | const std::vector< double > & | ml2s | ) | [inline] |
mutable access to the second calibration constant
const std::vector<double>& getML3s | ( | ) | const [inline] |
Non-mutable access to the third calibration constant.
void setML3s | ( | const std::vector< double > & | ml3s | ) | [inline] |
mutable access to the third calibration constant
void calculateCalibCoeffs_ | ( | MSExperiment< PickedPeakType > & | calib_peaks_ft | ) | throw (UnableToCalibrate) [private] |
Calculates the coefficients of the quadratic fit used for external calibration.
void getMonoisotopicPeaks_ | ( | MSExperiment< PickedPeakType > & | calib_peaks, | |
std::vector< std::vector< unsigned int > > & | monoiso_peaks | |||
) | [private] |
determines the monoisotopic peaks
void applyTOFConversion_ | ( | MSExperiment< PickedPeakType > & | 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 matchMasses_ | ( | MSExperiment< PickedPeakType > & | 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.
void averageErrors_ | ( | ) | [private] |
Calculate the average errors of the reference masses over all scans.
void averageCoefficients_ | ( | ) | [private] |
Average the coefficients of the quadratic fit.
MSExperiment<PickedPeakType> calib_peaks_ft_ [private] |
the calibrant spectra still using flight times instead of m/z-values
std::vector<double> exp_masses_ [private] |
the expected calibrant masses
std::map<double,std::vector<double> > errors_ [private] |
error in ppm after quadratic fit
std::vector<double> error_medians_ [private] |
median errors
std::vector<double> calib_masses_ [private] |
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] |
std::vector<double> coeff_quad_fit_ [private] |
all coefficients of the quadratic fit
double a_ [private] |
mean coefficients
double b_ [private] |
double c_ [private] |
gsl_interp_accel* acc_ [private] |
gsl_spline* spline_ [private] |
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |