calibration {ptairMS}R Documentation

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
)

## 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
)

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.

Value

the same ptrRaw or ptrSet as in input, with the following modified element:

Examples


### ptrRaw object 

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

[Package ptairMS version 1.2.0 Index]