iwNormQE.5: Q-Exactive +/- 0.5 range, normalisation for isolation window...

In computational-metabolomics/msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

Q-Exactive +/- 0.5 range, normalisation for isolation window efficiency

Description

Creates a function based on a previous experimental analysis of a Q-Exactive at +/- 0.5 isolation window efficiency. See http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b04358

The function that is created will output a value between 0 to 1 based on the position between the minOff and maxOff params

NOTE: The resulting function will work for values greater that 0.5 and less than -0.5.

This is because (on our instrument tested at least) when using a window of +/- 0.5, the isolation is NOT confined to the +/-0.5 Da window. Resulting in ions from outside the window being isolated. For this reason the function can normalise values outside of the the +/- 1 Da range. Please see above paper figure 3 for more details.

Usage

iwNormQE.5()

Value

normalisation function for +/- 0.5 range for Q-Exactive

Examples

iwNormFun <- iwNormQE.5()
pm <- data.frame(mz=c(99.5, 99.9, 100, 100.1, 100.5),i=c(1000, 1000, 1000, 1000, 1000))
mzmax = 100.5
mzmin = 99.5
middle <- mzmax-(mzmax-mzmin)/2
adjustmz = pm$mz-middle

# normalise the intensities
pm$normi = pm$i*iwNormFun(adjustmz)

computational-metabolomics/msPurity documentation built on May 13, 2024, 7:36 p.m.