calibration: Calibrates the mass axis with references masses

In camilleroquencourt/ptairMS: Pre-processing PTR-TOF-MS Data

Calibrates the mass axis with references masses

Description

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.

Usage

calibration(
  x,
  mzCalibRef = c(21.022, 29.013424, 41.03858, 60.0525, 203.943, 330.8495),
  calibrationPeriod = 60,
  tol = 70,
  checkAroundPeakCalib = FALSE,
  ...
)

## 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,
  checkAroundPeakCalib = FALSE,
  ...
)

## 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,
  fileNames = getParameters(x)$listFile
)

Arguments

x	a ptrRaw-class or ptrSet-class object
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 calibrationPeriod seconds
tol	the maximum error tolerated in ppm. If more than tol warnings.
checkAroundPeakCalib	If FALSE it autorises that a pic could be close to less than200 ppm for the calibration peaks
...	" "
fileNames	file to recalibrate

Value

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

Examples

### ptrRaw object 

library(ptairData)
filePath <- system.file('extdata/exhaledAir/ind1', 'ind1-1.h5', 
package = 'ptairData')
raw <- readRaw(filePath, calib = FALSE)
rawCalibrated <- calibration(raw)

camilleroquencourt/ptairMS documentation built on June 9, 2024, 10:35 a.m.