calibration {ptairMS} | R Documentation |
To convert Time Of Flight (TOF) axis to mass axis, we use the formula: mz = ((tof-b)/a )^2 (Muller et al. 2013) To estimate those parameters, references peaks with accurate know masses and without overlapping peak are needed. The best is that the references masses covers a maximum of the mass range.
calibration( x, mzCalibRef = c(21.022, 29.013424, 41.03858, 60.0525, 203.943, 330.8495), calibrationPeriod = 60, tol = 70 ) ## S4 method for signature 'ptrRaw' calibration( x, mzCalibRef = c(21.022, 29.013424, 41.03858, 59.049141, 75.04406, 203.943, 330.8495), calibrationPeriod = 60, tol = 70 ) ## S4 method for signature 'ptrSet' calibration( x, mzCalibRef = c(21.022, 29.013424, 41.03858, 75.04406, 203.943, 330.8495), calibrationPeriod = 60, tol = 70 )
x |
a |
mzCalibRef |
Vector of accurate mass values of intensive peaks and 'unique' in a nominal mass interval (without overlapping) |
calibrationPeriod |
in second, coefficient calibration are estimated for
each sum spectrum of |
tol |
the maximum error tolerated in ppm. If more than |
the same ptrRaw or ptrSet as in input, with the following modified element:
mz: the new mz axis calibrated
rawM: same raw matrix with the new mz axis in rownames
calibMassRef: reference masses used for the calibration
calibMzToTof and calibTofToMz: function to convert TOF to mz
calibError: the calibration error to the reference masses in ppm
calibrationIndex: index time of each calibration period
### ptrRaw object library(ptairData) filePath <- system.file('extdata/exhaledAir/ind1', 'ind1-1.h5', package = 'ptairData') raw <- readRaw(filePath, calib = FALSE) rawCalibrated <- calibration(raw)