idBAneg {LipidMS}

Bile Acids (BA) annotation for ESI-

Description

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

Usage

idBAneg(
  msobject,
  ppm_precursor = 5,
  ppm_products = 10,
  rttol = 3,
  rt,
  adducts = c("M-H"),
  conjfrag = c("baconj_M-H"),
  bafrag = c("ba_M-H-H2O", "ba_M-H-2H2O"),
  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 BA in ESI-. Adducts allowed can be modified in the adducsTable (dbs argument).

conjfrag

character vector containing the fragmentation rules for the BA-conjugates. By default just taurine and glycine are considered, but baconjdb can be modified to add more possible conjugates. See chainFrags for details. It can also be an empty vector.

bafrag

character vector containing the fragmentation rules for other BA fragments. See chainFrags for details. It can be an empty vector.

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

idBAneg function involves 3 steps. 1) FullMS-based identification of candidate BA as M-H. 2) Search of BA-conjugate fragments if required. 3) Search of fragments coming from the loss of H2O.

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 (MS-only if no rules are defined, or Subclass level if they are supported by fragments) 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 <- idBAneg(msobject)

## End(Not run)