idNEG: Lipids annotation for ESI-

In LipidMS: Lipid Annotation for LC-MS/MS DDA or DIA Data

Lipids annotation for ESI-

Description

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

Usage

idNEG(
  msobject,
  ppm_precursor = 5,
  ppm_products = 10,
  rttol = 5,
  coelCutoff = 0.8,
  lipidClasses = c("FA", "FAHFA", "LPC", "LPE", "LPG", "LPI", "LPS", "PC", "PCo", "PCp",
    "PE", "PEo", "PEp", "PG", "PI", "PS", "Sph", "SphP", "Cer", "CerP", "AcylCer", "SM",
    "CL", "BA"),
  dbs,
  verbose = TRUE
)

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.
verbose	print information messages.

Value

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

Author(s)

M Isabel Alcoriza-Balaguer <[e-mail]>

Examples

## Not run: 
msobject <- idNEG(msobject)

## End(Not run)

LipidMS documentation built on Nov. 6, 2025, 1:13 a.m.