LipidMS (version 3.0.0)

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 {
devtools::install_github("maialba3/LipidMSdata2")

library(LipidMS)
dbs <- assignDB()

MS1 <- LipidMSdata2::msobjectDIAneg$peaklist$MS1
MS1 <- MS1[MS1$isotope %in% c("[M+0]"), !colnames(MS1) %in% c("isotope", "isoGroup")]
MS2 <- LipidMSdata2::msobjectDIAneg$peaklist$MS2[,c("mz", "RT", "int", "peakID")]
rawData <- rbind(LipidMSdata2::msobjectDIAneg$MS1, LipidMSdata2::msobjectDIAneg$MS2)

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

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