LipidMS (version 3.0.0)

ddaFrags: MS/MS scan extraction of a precursor in DDA

Description

This function searches for the closest precursor selected for MS2 in DDA that matches mz tolerance and RT window of a list of candidates and extracts their fragments.

Usage

ddaFrags(candidates, precursors, rawData, ppm)

Arguments

candidates

candidates data frame. Output of findCandidates.

precursors

data frame with the whole list of precursors selected for MS2.

rawData

peaklist for MS2 function (MSMS).

ppm

m/z tolerance in ppm.

Value

List of data frames with the fragments for each candidate.

Details

MS2 scans for a given precursor are searched within a rt window from minrt-rttol/2 to maxrt+rttol/2. If the same precursor was selected several times along the peak, the closest scan to the rt at the peak maximum is selected for annotation.

Coelution score for DDA fragments represents their relative intensity within the MS2 scan.

Examples

# NOT RUN {
devtools::install_github("maialba3/LipidMSdata2")

library(LipidMS)
dbs <- assignDB()

MS1 <- LipidMSdata2::msobjectDDAneg$peaklist$MS1
MS1 <- MS1[MS1$isotope %in% c("[M+0]"), !colnames(MS1) %in% c("isotope", "isoGroup")]
MS2 <- LipidMSdata2::msobjectDDAneg$peaklist$MS2[,c("mz", "RT", "int", "peakID")]
rawData <- rbind(LipidMSdata2::msobjectDDAneg$MS1, LipidMSdata2::msobjectDDAneg$MS2)
precursors <- LipidMSdata2::msobjectDDAneg$metaData$scansMetadata[
LipidMSdata2::msobjectDDAneg$metaData$scansMetadata$collisionEnergy > 0 &
msobjectDDAneg$metaData$scansMetadata$msLevel == 2, c("RT", "precursor", "Scan")]
candidates <- findCandidates(MS1 = MS1, db = dbs$cerdb, ppm = 10,
rt = c(0, 2000), adducts = c("M-H"),
rttol = 10, dbs = dbs, rawData = rawData_neg$rawScans, coelCutoff = 0.8)

coelfrags <- ddaFrags(candidates, precursors, rawData, ppm = 10)
# }
# NOT RUN {
# }