idPEneg {LipidMS}

Phosphoethanolamines (PE) annotation for ESI-

Description

PE identification based on fragmentation patterns for LC-MS/MS DIA or DDA data acquired in negative mode.

Usage

idPEneg(
  msobject,
  ppm_precursor = 5,
  ppm_products = 10,
  rttol = 5,
  rt,
  adducts = c("M-H"),
  clfrags = c(140.0118, 196.038, 214.048, "pe_M-CH3"),
  clrequired = c(F, F, F, "excluding"),
  ftype = c("F", "F", "F", "BB"),
  chainfrags_sn1 = c("lysope_M-H"),
  chainfrags_sn2 = c("lysope_M-H", "fa_M-H"),
  intrules = c("lysope_sn1/lysope_sn2"),
  rates = c("3/1"),
  intrequired = c(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 PE 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 in sn1 position. 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.

intrules

character vector specifying the fragments to compare. See checkIntensityRules.

rates

character vector with the expected rates between 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

idPEneg function involves 5 steps. 1) FullMS-based identification of candidate PE as M-H. 2) Search of PE class fragments: 140.0115, 196.038, 214.048 ion coeluting with the precursor ion. If a loss of CH3 group is found coeluting with any candidate, this will be excluded as it is a characteristic fragment of PC. 3) Search of specific fragments that inform about chain composition in sn1 (lysoPE as M-H resulting from the loss of the FA chain at sn2) and sn2 (lysoPE as M-H resulting from the loss of the FA chain at sn1 or FA chain as M-H). 4) Look for possible chains structure based on the combination of chain fragments. 5) Check intensity rules to confirm chains position. In this case, lysoPE from sn1 is at least 3 times more intense than lysoPE from sn2.

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 <[e-mail]>

Examples

## Not run: 
msobject <- idPEneg(msobject)

## End(Not run)