LipidMS (version 2.1.2)

idPOS: Lipids annotation for ESI+

Description

Lipids annotation based on fragmentation patterns for LC-MS/MS DIA or DDA data acquired in positive mode. This function compiles all functions writen for ESI+ annotations.

Usage

idPOS(
  msobject,
  ppm_precursor = 5,
  ppm_products = 10,
  rttol = 5,
  coelCutoff = 0.8,
  lipidClasses = c("MG", "LPC", "LPE", "PC", "PE", "PG", "Sph", "SphP", "Cer", "SM",
    "Carnitines", "CE", "DG", "TG"),
  dbs
)

Arguments

msobject

an msobject returned by dataProcessing.

ppm_precursor

mass tolerance for precursor ions. By default, 5 ppm.

ppm_products

mass tolerance for product ions. By default, 10 ppm.

rttol

total rt window for coelution between precursor and product ions. By default, 5 seconds.

coelCutoff

coelution score threshold between parent and fragment ions. Only applied if rawData info is supplied. By default, 0.8.

lipidClasses

classes of interest to run the identification functions.

dbs

list of data bases required for 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 supplied. See createLipidDB and assignDB.

Value

annotated msobject (list with several elements). The results element is a data frame that shows: ID, class of lipid, CDB (total number of carbons and double bounds), FA composition (specific chains composition if it has been confirmed), m.z, RT (in seconds), I (intensity), Adducts, ppm (m.z error), confidenceLevel (Subclass, FA level, where chains are known but not their positions, or FA position level), peakID, and PFCS (parent-fragment coelution score mean of all fragments used for the identification); and the annotatedPeaklist element shows the original MS1 peaklist with the annotations on it.

Examples

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

library(LipidMS)
msobject <- idPOS(LipidMSdata2::msobjectDIApos)
# }
# NOT RUN {
# }