search_NLM: search_NLM Wrappper function to search for the neutral loss...

In scottwalmsley/wSIMCity: Searching wide SIM - wide-MS2 data (DIA) for neutral losses

Description

search_NLM Wrappper function to search for the neutral loss in wide SIM DIA data.

Usage

search_NLM(
  file = NULL,
  type = "SIM",
  raw = FALSE,
  delta_search_mass = NULL,
  search_name = "",
  scandef_file = NULL,
  sim_width = NULL,
  overlapMZ = NULL,
  ppm_tol = 20,
  rt_tol = 9,
  mzmin = 135,
  mzmax = 634,
  mzwid = 0.01,
  plot = F
)

Arguments

file	the mzml file to search. Must be wide SIM MS1 / MS2 DIA data with SIM segments the same mz range
type	'SIM' for true wide SIM DIA data or any other value for pseudo MS1 0 volt data \(true MS2\)
raw	the Thermo .raw file
delta_search_mass	decimal value indicating the Da loss or gain. Must be signed if negative \(-\)
search_name	character value indicating the value used
scandef_file	the name of the scan definition file. Currently not used.
sim_width	the mz width of the wSIM windows
overlapMZ	the mz overlap (if any) between wSIM windows
ppm_tol	the ppm mass tolerance in parts per million
rt_tol	the retention time tolerance for the search in minutes
mzmin	the minimum mz, default = 135
mzmax	the maximum mz, default = 634
mzwid	the mz slice size, default = 0.01 for Orbitrap
plot	plot diagnostic plots

scottwalmsley/wSIMCity documentation built on May 3, 2021, 2:35 p.m.