idPCpneg: Plasmenyl Phosphocholines (PCp) annotation for ESI-

In LipidMS: Lipid Annotation for LC-MS/MS DDA or DIA Data

Plasmenyl Phosphocholines (PCp) annotation for ESI-

Description

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

Usage

idPCpneg(
  msobject,
  ppm_precursor = 5,
  ppm_products = 10,
  rttol = 3,
  rt,
  adducts = c("M+CH3COO", "M-CH3", "M+CH3COO-CH3"),
  clfrags = c(168.0426, 224.0688, "pcp_M-CH3"),
  clrequired = c(F, F, F),
  ftype = c("F", "F", "BB"),
  chainfrags_sn1 = c("lysopcp_M-CH3", "lysopcp_M-CH3-H2O"),
  chainfrags_sn2 = c("fa_M-H", "fa_M-CO2-H"),
  intrules = c("lysopcp_sn1/fa_sn2"),
  rates = c(1/3),
  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 PCp 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

idPCpneg function involves 5 steps. 1) FullMS-based identification of candidate PCp as M+CH3COO, M-CH3 or M+CH3COO-CH3. To avoid incorrect annotations of PEp as PCp, candidates which are present just as M-CH3 will be ignored. 2) Search of PCp class fragments: 168.0426, 224.0688 or loss of CH3 coeluting with the precursor ion. 3) Search of specific fragments that inform about chain composition in sn1 (LPCp as M-CH3 and M-CH3-H2O resulting from the loss of the FA chain at sn2) and sn2 (FA as M-H and M-CO2-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, FA fragments from sn2 are at least 3 times more intense than LPCp from sn1.

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 <- idPCpneg(msobject)

## End(Not run)

LipidMS documentation built on May 29, 2024, 11:24 a.m.