LipidMS (version 1.1.0)

findCandidates: Search of lipid candidates of a certain class.

Description

Search of lipid candidates from a peaklist based on a set of expected adducts.

Usage

findCandidates(MS1, db, ppm, rt, adducts, rttol = 3, dbs,
  rawData = data.frame(), coelCutoff = 0)

Arguments

MS1

peaklist of the MS function. Data frame with 3 columns: m.z, RT (in seconds) and int (intensity).

db

database (i.e. pcdb, dgdb, etc.). Data frame with at least 2 columns: Mass (exact mass) and total (total number of carbons and double bound of the FA chains, i.e. "34:1").

ppm

m/z tolerance in ppm.

rt

rt range where the function will look for candidates. By default, it will search within all RT range in MS1.

adducts

character vector containing the expected adducts to search for (i.e. "M+H", "M+Na", "M-H", etc.). See details.

rttol

rt tolerance in seconds to match adducts.

dbs

list of data bases required for the annotation. By default, dbs contains the required data frames based on the default fragmentation rules. If these rules are modified, dbs may need to be changed. If data bases have been customized using createLipidDB, they also have to be modified here.

rawData

raw scans data. Output of dataProcessing function (MS1$rawData).

coelCutoff

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

Value

Data frame with the found candidates. It contains 6 columns: m.z, RT, int (from the peaklist data.frame), ppms, cb (total number of carbons and double bounds of the FA chains) and adducts.

Details

findCandidates looks for matches between the m/z of the MS1 peaklist and the expected m/z of the candidates in the database for each adduct. If several adducts are expected, results are combined.

Adducts allowed are contained in adductsTable data frame, which can be modified if required (see adductsTable).

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)


# If any adduct is not in the adductsTable, it can be added:

adductsTable2 <- rbind(adductsTable,
c(adduct = "M+HCOO", mdiff = 44.9982, n = 1, charge = -1))
dbs <- assignDB()
dbs$adductsTable <- adductsTable2

candidates <- findCandidates(MS1 = MS1_neg$peaklist,
db = dbs$pgdb, ppm = 10, rt = c(0, 2000), adducts = c("M-H", "M+HCOO"),
rttol = 10, rawData = MS1_neg$rawScans, coelCutoff = 0.8)
# }
# NOT RUN {
# }