idNEG: Lipids annotation for ESI-

Description

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

Usage

idNEG(MS1, MSMS1, MSMS2 = data.frame(), ppm_precursor = 5,
  ppm_products = 10, rttol = 3)

Arguments

MS1

data frame cointaining all peaks from the full MS function. It must have three columns: m.z, RT (in seconds) and int (intensity).

MSMS1

data frame cointaining all peaks from the low energy function. It must have three columns: m.z, RT and int.

MSMS2

data frame cointaining all peaks from the high energy function if it is the case. It must have three columns: m.z, RT and int. Optional.

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, 3 seconds.

Value

The output is a list with 2 elements: 1) 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), mz, RT (in seconds), I (intensity, which comes directly from de input), Adducts, ppm (m.z error), confidenceLevel (Subclass, FA level, where chains are known but not their positions, or FA position level); and 2) the original MS1 peaklist with the annotations on it.

Examples

Run this code

# NOT RUN {
idNEG(MS1 = LipidMS::serum_neg_fullMS, MSMS1 = LipidMS::serum_neg_Ce20,
MSMS2 = LipidMS::serum_neg_Ce40)
# }
# NOT RUN {
# }

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