idAcylCerneg {LipidMS} | R Documentation |
Acylceramides (AcylCer) annotation for ESI-
Description
AcylCer identification based on fragmentation patterns for LC-MS/MS DIA or DDA data acquired in negative mode.
Usage
idAcylCerneg(
msobject,
ppm_precursor = 5,
ppm_products = 10,
rttol = 3,
rt,
adducts = c("M-H", "M+CH3COO"),
clfrags = c(),
clrequired = c(),
ftype = c(),
chainfrags_sn1 = c("cbdiff-cer_M-H"),
chainfrags_sn2 = c("sph_Mn-62.06001", "sph_M-H-H2O"),
chainfrags_sn3 = c("fa_Mn-1.9918", "fa_Mn-19.0179"),
intrules = c("cbdiff-cer_sn1/sph_sn2", "sph_sn2/fa_sn3"),
rates = c("5/1", "2/1"),
intrequired = c(T, T),
coelCutoff = 0.8,
dbs,
verbose = TRUE
)
Arguments
msobject |
an msobject returned by dataProcessing. |
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 AcylCer 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 sphingoid base. See chainFrags for details. |
chainfrags_sn2 |
character vector containing the fragmentation rules for the chain fragments in sn2 position. See chainFrags for details. If empty, it will be estimated based on the difference between precursors and sn1 chains. |
chainfrags_sn3 |
character vector containing the fragmentation rules for the acyl chain. See chainFrags for details. |
intrules |
character vector specifying the fragments to compare. See checkIntensityRules. |
rates |
character vector with the expected ratesbetween fragments given as a string (e.g. "3/1"). See checkIntensityRules. |
intrequired |
logical vector indicating if any of the rules is required. If not, at least one must be verified to confirm the structure. |
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. |
verbose |
print information messages. |
Details
idAcylCerneg
function involves 5 steps. 1) FullMS-based
identification of candidate AcylCer as M-H and M+CH3COO. 2) Search of AcylCer
class fragments: no class fragments by default. 3) Search of specific fragments
that inform about the acyl chain (Cer as M-H), the sphingoid base (neutral
loss of 62.0600 of the Sph) and the FA chain (FA as M-H and M-H2O but with a N
instead of an O, what results in a mass differences of 1.9918 and 19.0179
respectively). 4) Look for possible chains structure based on the combination
of chain fragments. 5) Check intensity rules to confirm chains position. In
this case, the fragment coming from the loss of the acyl chain must be at least
5 times more intense the fragment from the sphingoid base and this one, two
times more intense than the FA chain from sn3.
Results data frame shows: ID, lipid class, 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 (mz error), confidenceLevel (Subclass, FA level, where chains are known but not their positions, or FA position level) and Score (parent-fragment coelution score mean in DIA data or relative sum intensity in DDA of all fragments used for the identification).
Value
annotated msobject (list with several elements). The results element is a data frame that shows: ID, lipid class, CDB (total number of carbons and double bounds), FA composition (specific chains composition if it has been confirmed), mz, RT (in seconds), I (intensity), Adducts, ppm (mz error), confidenceLevel (Subclass, FA level, where chains are known but not their positions, or FA position level), peakID, and Score (parent-fragment coelution score mean in DIA data or relative sum intensity in DDA of all fragments used for the identification).
Note
This function has been writen based on fragmentation patterns observed for three different platforms (QTOF 6550 from Agilent, Synapt G2-Si from Waters and Q-exactive from Thermo), but it may need to be customized for other platforms or acquisition settings.
Author(s)
M Isabel Alcoriza-Balaguer <maialba@alumni.uv.es>
Examples
## Not run:
msobject <- idAcylCerneg(msobject)
## End(Not run)