LipidMS (version 0.1.0)

idBAneg: Bile Acids (BA) annotation for ESI-

Description

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

Usage

idBAneg(MS1, MSMS1, MSMS2 = data.frame(), ppm_precursor = 5,
  ppm_products = 10, rttol = 3, rt = c(min(MS1$RT), max(MS1$RT)),
  adducts = c("M-H"), conjfrag = c("baconj_M-H"),
  bafrag = c("ba_M-H-H2O"), dbs = list(badb = LipidMS::badb, baconjdb =
  LipidMS::baconjdb, adductsTable = LipidMS::adductsTable))

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.

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 BA in ESI-. Adducts allowed can be modified in the adducsTable (dbs argument).

conjfrag

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.

bafrag

character vector containing the fragmentation rules for other BA fragments. See chainFrags for details. It can be an empty vector.

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 changed. If data bases have been customized using createLipidDB, they also have to be modified here.

Value

List with BA annotations (results) and some additional information (fragments).

Details

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. If any fragmentation rule has been defined, only those with MSMS support are kept.

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 MSMS level if they are supported by fragments).

Examples

# NOT RUN {
idBAneg(MS1 = LipidMS::mix_neg_fullMS, MSMS1 = LipidMS::mix_neg_Ce20,
MSMS2 = LipidMS::mix_neg_Ce40)

idBAneg(MS1 = LipidMS::serum_neg_fullMS, MSMS1 = LipidMS::serum_neg_Ce20,
MSMS2 = LipidMS::serum_neg_Ce40)

# }