Deisotope: Deisotope MS/MS spectra

In chrismckennan/MSeQUiP: Quantifying uncertainty in peptide-spectrum matches

Description

Deisotope MS/MS spectra using a modified chi squared statistic scoring function.

Usage

Deisotope(
  mzml.file.path,
  n_cores = NULL,
  ppm = 20,
  ppm.filter = 40,
  ppm.precursor = 20,
  remove.precursor = F,
  max.addition = 2,
  min.ions = 20,
  min.chi = 0.26,
  write.mzml = F
)

Arguments

mzml.file.path	A character string containing the mzML or mzXML file path
n_cores	Number of cores. Defaults to the total number of available cores minus 1.
ppm	Fragment isotope mass error, in the ppm scale. Detaults to 20.
ppm.filter	The software will collapse any peaks <=ppm.filterppm apart into 1 peak. Defaults to 40.
remove.precursor	Should the precursor be removed. Defaults to F.
write.mzml	Should an mzML file be returned. Defaults to F.

Value

If write.mzml is set to T, returns an mzML file in the same directory as mzml.file.path. Otherwise, it returns a list with the following entries:

Headers	A data frame of headers for each MS and MS/MS spectrum.
Spectra	A list containing the MS and MS/MS spectra. The outputed MS/MS spectra contain 3 columns: m/z, intensity, and inferred charge.

chrismckennan/MSeQUiP documentation built on Dec. 19, 2021, 4:01 p.m.