coelutingFrags {LipidMS}R Documentation

Coeluting fragments extraction

Description

Given a RT and a list of peaks, this function subsets all coeluting fragments within a rt windows. It is used by identification functions to extract coeluting fragments from high energy functions for candidate precursor ions.

Usage

coelutingFrags(
  precursors,
  products,
  rttol,
  rawData = data.frame(),
  coelCutoff = 0
)

Arguments

precursors

candidates data frame. Output of findCandidates.

products

peaklist for MS2 function (MSMS).

rttol

rt window in seconds.

rawData

raw scans data. Output of dataProcessing function (MSMS$rawData).

coelCutoff

coelution score threshold between parent and fragment ions. Only applied if rawData info is supplied.

Value

List of data frames with the coeluting fragments for each candidate.

Author(s)

M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>

Examples


library(LipidMSdata)
dbs <- assignDB()

candidates <- findCandidates(MS1 = MS1_neg$peaklist,
db = dbs$pgdb, ppm = 10, rt = c(0, 2000), adducts = c("M-H"),
rttol = 10, dbs = dbs, rawData = MS1_neg$rawScans, coelCutoff = 0.8)

MSMS <- rbind(MSMS1_neg$peaklist, MSMS2_neg$peaklist)
rawData <- rbind(MS1_neg$rawScans, MSMS1_neg$rawScans, MSMS2_neg$rawScans)
coelfrags <- coelutingFrags(candidates, MSMS, rttol = 10, rawData = rawData,
coelCutoff = 0.8)



[Package LipidMS version 1.2.0 Index]