LipidMS (version 1.0.0)

idLPEpos: Lysophosphoethanolamines (LPE) annotation for ESI+

Description

LPE identification based on fragmentation patterns for LC-MS/MS AIF data acquired in positive mode.

Usage

idLPEpos(MS1, MSMS1, MSMS2, ppm_precursor = 5, ppm_products = 10,
  rttol = 3, rt, adducts = c("M+H", "M+Na"), clfrags = c(141.01909),
  clrequired = c(F), ftype = c("NL"),
  chainfrags_sn1 = c("mg_M+H-H2O"), coelCutoff = 0.8, dbs)

Arguments

MS1

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.

MSMS1

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.

MSMS2

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.

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.

rt

rt range where the function will look for candidates. By default, it will search within all RT range in MS1.

adducts

expected adducts for LPE in ESI+. Adducts allowed can be modified in adductsTable (dbs argument).

clfrags

vector containing the expected fragments for a given lipid class. See checkClass for details.

clrequired

logical vector indicating if each class fragment is required or not. If any of them is required, at least one of them must be present within the coeluting fragments. See checkClass for details.

ftype

character vector indicating the type of fragments in clfrags. It can be: "F" (fragment), "NL" (neutral loss) or "BB" (building block). See checkClass for details.

chainfrags_sn1

character vector containing the fragmentation rules for the chain fragments. See chainFrags for details.

coelCutoff

coelution score threshold between parent and fragment ions. Only applied if rawData info is supplied. By default, 0.8.

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.

Value

List with LPE annotations (results) and some additional information (class fragments and chain fragments).

Details

idLPEpos function involves 3 steps. 1) FullMS-based identification of candidate LPE as M+H and M+Na. 2) Search of LPE class fragments: neutral loss of 141.01909 coeluting with the precursor ion. 3) Search of specific fragments that confirm chain composition in sn1 (MG as M+H-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 (in this case, as LPE only have one chain, only Subclass and FA level are possible) and PFCS (parent-fragment coelution score mean of all fragments used for the identification).

Examples

Run this code
# NOT RUN {
idLPEpos(MS1 = LipidMS::MS1_pos, MSMS1 = LipidMS:MSMS1_pos,
MSMS2 = LipidMS::MSMS2_pos)
# }
# NOT RUN {
# }

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