LipidMS (version 1.0.0)

chainFrags: Search of chain specific fragments

Description

Search of specific fragments that inform about the chains structure.

Usage

chainFrags(coelfrags, chainfrags, ppm = 10, candidates, f = NULL, dbs)

Arguments

coelfrags

coeluting fragments for each candidate. Output of coelutingFrags.

chainfrags

character vector containing the fragmentation rules for the chain fragments. If it is an empty vector, chains will be calculated based on the difference between the precursor and the other chain. See details.

ppm

m/z tolerance in ppm.

candidates

candidates data frame. If any chain needs to be calculated based on the difference between the precursor and the other chain, this argument will be required. Output of chainFrags.

f

known chains. If any chain needs to be calculated based on the difference between the precursor and the other chain, this argument will be required. Output of chainFrags.

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.

Value

List of data frames with the chain fragments found.

Details

The chainfrags argument must contain the fragmentation rules which inform about the chains structure. For example, in the case of PG subclass, the chain in sn1 position is identified by the lysoPG as M-H resulting from the loss of the FA chain of sn2; and the chain in sn2 position is identified as the free FA chain as M-H. These two fragments need to be searched in two different steps: in the fist step we will look for lysoPGs coeluting with the precursor using chainfrags = c("lysopg_M-H"); then, we will look for FA chains using chainfrags = c("fa_M-H"). This information can be combined later using combineChains function.

To indicate the fragments to be searched, the class of lipid is writen using the same names as the LipidMS databases without the "db" at the end (i.e. pa, dg, lysopa, mg, CE, etc.), and the adduct has to be indicated as it appears in the adductsTable, both parts separated by "_". In case some chain needs to be searched based on a neutral loss, this can be defined using "NL-" prefix, followed by the database and adduct. If this neutral loss is employed to find the remaining chain, "cbdiff-" prefix allows to calculate the difference in carbons and doubles bounds between the precursor and the building block found. For example, "cbdiff-dg_M+H-H2O" will look for DG as M+H-H2O and then, it will return the difference between their number of carbons and double bounds and the ones from the precursor. Otherwise, "NL-mg_M+H-H2O" will look for fragments coming from the loss of MGs.

In case these fragments identified as losses from the precursors are going to be employed for the intensity rules, this same prefix has to be added.

If a chain is calculated based on the difference of total number of carbons and double bounds between the precursor and a previously searched chain, chainfrags argument must be a character vector c("") and candidates data frame and chain fragments list must be provided.

Examples

# NOT RUN {
dbs <- assignDB()

candidates <- findCandidates(MS1 = LipidMS::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(LipidMS::MSMS1_neg$peaklist, LipidMS::MSMS2_neg$peaklist)
rawData <- rbind(LipidMS::MS1_neg$rawScans, LipidMS::MSMS1_neg$rawScans,
LipidMS::MSMS2_neg$rawScans)
coelfrags <- coelutingFrags(candidates$RT, MSMS, rttol = 10, rawData = rawData,
coelCutoff = 0.8)

sn1 <- chainFrags(coelfrags, chainfrags = c("lysopg_M-H"), ppm = 10,
dbs = dbs)
sn2 <- chainFrags(coelfrags, chainfrags = c("fa_M-H"), ppm = 10, dbs = dbs)
# }
# NOT RUN {
# }

Run the code above in your browser using DataCamp Workspace