BA identification based on fragmentation patterns for LC-MS/MS AIF data acquired in negative mode.
idBAneg(MS1, MSMS1, MSMS2, ppm_precursor = 5, ppm_products = 10,
rttol = 3, rt, adducts = c("M-H"), conjfrag = c("baconj_M-H"),
bafrag = c("ba_M-H-H2O", "ba_M-H-2H2O"), 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.
rt range where the function will look for candidates. By default, it will search within all RT range in MS1.
expected adducts for BA in ESI-. Adducts allowed can be modified in the adducsTable (dbs argument).
character vector containing the fragmentation rules for the BA-conjugates. By default just taurine and glycine are considered, but baconjdb can be modified to add more possible conjugates. See chainFrags for details. It can also be an empty vector.
character vector containing the fragmentation rules for other BA fragments. See chainFrags for details. It can be an empty vector.
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.
List with BA annotations (results) and some additional information (fragments).
idBAneg function involves 3 steps. 1) FullMS-based
identification of candidate BA as M-H. 2) Search of BA-conjugate fragments if
required. 3) Search of fragments coming from the loss of H2O.
Results data frame 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 (MS-only if no rules are defined, or Subclass level if they are supported by fragments) and PFCS (parent-fragment coelution score mean of all fragments used for the identification).
# NOT RUN {
library(LipidMSdata)
idBAneg(MS1 = MS1_neg, MSMS1 = MSMS1_neg, MSMS2 = MSMS2_neg)
# }
# NOT RUN {
# }
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