annotatemsbatch: Lipid annotation for an msbatch

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

Lipid annotation for an msbatch

Description

Summarize annotation results of an msbatch into the feature table

Usage

annotatemsbatch(
  msbatch,
  ppm_precursor = 5,
  ppm_products = 10,
  rttol = 5,
  coelCutoff = 0.8,
  lipidClassesPos = c("MG", "LPC", "LPE", "PC", "PCo", "PCp", "PE", "PEo", "PEp", "PG",
    "PI", "Sph", "SphP", "Cer", "CerP", "AcylCer", "SM", "Carnitines", "CE", "DG", "TG"),
  lipidClassesNeg = 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,
  simplifyAnnotations = FALSE,
  parallel = FALSE,
  ncores
)

Arguments

msbatch	msbatch
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.
lipidClassesPos	classes of interest in ESI+.
lipidClassesNeg	classes of interest in ESI-.
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.
simplifyAnnotations	logical. If TRUE, only the most frequent id will be kept (recommended when only pool samples have been acquired in DIA or DDA). If FALSE, all annotations will be shown.
parallel	logical.
ncores	number of cores to be used in case parallel is TRUE.

Value

msbatch

Author(s)

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

Examples

## Not run: 
msbatch <- annotatemsbatch(msbatch)

msbatch$features

## End(Not run)

LipidMS documentation built on March 18, 2022, 7:14 p.m.