LipidMS (version 0.1.0)

idSphpos: Sphingoid bases (Sph) annotation for ESI-

Description

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

Usage

idSphpos(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"), clfrags = c(), clrequired = c(), ftype = c(),
  chainfrags_sn1 = c("sph_M+H-H20", "sph_M+H-2H2O"), dbs = list(sphdb =
  LipidMS::sphdb, 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.

MSMS1

data frame cointaining all peaks from the first high energy function. It must have three columns: m.z, RT (in seconds) and int.

MSMS2

data frame cointaining all peaks from the second high energy function if it is the case. It must have three columns: m.z, RT (in seconds) 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 precursors and product ions. By default, 3 seconds.

rt

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

adducts

expected adducts for Sph 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 the 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 uploaded here.

Value

list with Sph annotations (results) and some additional information (class fragments and chain fragments).

Details

idSphpos function involves 3 steps. 1) FullMS-based identification of candidate Sph as M+H. 2) Search of Sph class fragments in case some is defined. 3) Search of specific fragments that confirm chain composition (neutral loss of 1 or 2 H2O molecules).

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 Sph only have one chain, only Subclass and FA level are possible).

Examples

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

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

# }