LipidMS (version 0.1.0)

idCarpos: Carnitine annotation for ESI+

Description

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

Usage

idCarpos(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", "M+Na"), clfrags = c(60.0807, 85.0295, "fa_M+H-H2O"),
  clrequired = c(F, F, F), ftype = c("F", "F", "BB"),
  chainfrags_sn1 = c("fa_M+H-H2O"), dbs = list(carnitinesdb =
  LipidMS::carnitinesdb, fadb = LipidMS::fadb, 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 Carnitines 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.

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 Carnitine annotations (results) and some additional information (class fragments and chain fragments).

Details

idCarpos function involves 3 steps. 1) FullMS-based identification of candidate carnitines as M+H and M+Na. 2) Search of carnitine class fragments: 60.0807 and 85.0295 or its loss (FA as M+H-H20) coeluting with the precursor ion. 3) Search of specific fragments coming from the FA chain (FA 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 Carnitines only have one chain, only Subclass and FA level are possible).

Examples

# NOT RUN {
idCarpos(MS1 = LipidMS::mix_pos_fullMS, MSMS1 = LipidMS::mix_pos_Ce20,
MSMS2 = LipidMS::mix_pos_Ce40)

idCarpos(MS1 = LipidMS::serum_pos_fullMS, MSMS1 = LipidMS::serum_pos_Ce20,
MSMS2 = LipidMS::serum_pos_Ce40)

# }