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.
idNEG(MS1, MSMS1, MSMS2, ppm_precursor = 10, ppm_products = 10,
rttol = 10, coelCutoff = 0.8, dbs)list with two data frames cointaining all peaks from the full MS function ("peaklist" data frame) and the raw MS scans data ("rawScans" data frame). They must have four columns: m.z, RT (in seconds), int (intensity) and peakID (link between both data frames). "rawScans" data frame also needs a extra column named "Scan", which indicates the scan order number. Output of dataProcessing function. In case no coelution score needs to be applied, this argument can be just the peaklist data frame.
list with two data frames cointaining all peaks from the high energy function ("peaklist" data frame) and the raw MS scans data ("rawScans" data frame). They must have four columns: m.z, RT (in seconds), int (intensity) and peakID (link between both data frames). "rawScans" data frame also needs a extra column named "Scan", which indicates the scan order number. Output of dataProcessing function. In case no coelution score needs to be applied, this argument can be just the peaklist data frame.
list with two data frames cointaining all peaks from a second high energy function ("peaklist" data frame) and the raw MS scans data ("rawScans" data frame). They must have four columns: m.z, RT (in seconds), int (intensity) and peakID (link between both data frames). "rawScans" data frame also needs a extra column named "Scan", which indicates the scan order number. Output of dataProcessing function. In case no coelution score needs to be applied, this argument can be just the peaklist data frame. Optional.
mass tolerance for precursor ions. By default, 5 ppm.
mass tolerance for product ions. By default, 10 ppm.
total rt window for coelution between precursor and product ions. By default, 3 seconds.
coelution score threshold between parent and fragment ions. Only applied if rawData info is supplied. By default, 0.8.
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.
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 PFCS (parent-fragment coelution score mean of all fragments used for the identification); and 2) the original MS1 peaklist with the annotations on it.
# NOT RUN {
library(LipidMSdata)
idNEG(MS1 = MS1_neg, MSMS1 = MSMS1_neg, MSMS2 = MSMS2_neg)
# }
# NOT RUN {
# }
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