LipidMS (version 1.1.0)

coelutingFrags: 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.

Examples

# NOT RUN {
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, 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$rawScans)
coelfrags <- coelutingFrags(candidates$RT, MSMS, rttol = 10, rawData = rawData,
coelCutoff = 0.8)
# }
# NOT RUN {
# }