adduct.search: Detecting and grouping adduct m/z relations among peaks in a...

In blosloos/nontarget: Detecting Isotope, Adduct and Homologue Relations in LC-MS Data

Detecting and grouping adduct m/z relations among peaks in a HRMS dataset

Description

Algorithm for detecting m/z differences among peaks that may correspond to m/z differences among different adducts.

Usage

adduct.search(peaklist, adducts, rttol = 0, mztol = 2,ppm = TRUE, 
use_adducts = c("M+H", "M+K", "M+Na"), ion_mode = "positive", get_pairs = FALSE)

Arguments

peaklist	Dataframe of HRMS peaks with three numeric columns for (a) m/z, (b) intensity and (c) retention time, such as peaklist.
adducts	Data.frame adducts or equivalent.
rttol	Retention time tolerance. Units as given in column 3 of peaklist argument, e.g. [min].
mztol	m/z tolerance setting: +/- value by which the m/z of a measured peak may vary from its expected m/z value. If parameter ppm=TRUE (see below) given in ppm, otherwise, if ppm=FALSE, in absolute m/z [u].
ppm	Should mztol be set in ppm (TRUE) or in absolute m/z (FALSE)
use_adducts	Vector of adducts to be screened for. Corresponds to names in the first column of adducts, thus referring to equations from the second column of adducts to be used for calculating adduct m/z differences.
ion_mode	"positive" or "negative".
get_pairs	enviMass output, please ignore.

Details

Given a peak from the peaklist, the adduct.search algorithm screens within tolerances mztol and rttol whether any other peaks may correspond to this one peak via adduct m/z differences. More precisely, the one peak m/z is reset to all possible candidate molecular mass values (M; uncharged, non-adduct). The latter are then used to calculate for all other candidate adduct peaks, which, if found, are subsequently grouped.

For example, consider use_adducts=c("M+H", "M+K"). Given the m/z-value of the one peak, two other peaks with ((m/z*z("M+H")-X("M+H"))/z("M+K"))+X("M+K") and ((m/z*z("M+K")-X("M+K"))/z("M+H"))+X("M+H") are searched for. The peak found for the first term (i.e. with "M+H" being the candidate adduct of the one peak) leads to one group of associated adduct peaks (M+H<->M+K). Another adduct peak (i.e. with "M+K" being the candidate adduct of the one peak) would lead to a second group of associated adduct peaks (M+K<->M+H). Logically, larger adduct groups than the one exemplified can be present, if argument "use_adducts" allows for it (e.g. M+H<->M+K,M+H<->M+Na,M+Na<->M+K).

For clarification, mztol states the maximum m/z deviation of a measured peak from its true value, i.e., the theoretical mass-to-charge ratio of the (often unknown) analyte adduct measured. The latter true value thus ranges +/-mztol from the measured value, leading to a lower and an upper m/z bound for this true value. These bounds are then modified by pairwise adduct m/z differences, leading to new bounds for the true value at other m/z positions. In turn, the values of measured peaks at exactly these positions can again deviate by +/-mztol from these bounds, which are hence adapted accordingly at these positions for a final search window. This entails: (a) the bounds are calculated from measured instead of true values (using ppm==TRUE, bound differences are assumed negligible between utilizing measured or true values) and (b) the final search window is larger than 2*mztol and can therefore lead to contradictory assignments (i.e., peaks B and C can be assigned to peak A for different adduct m/z differences within mztol but peaks B and C cannot be paired within mztol).

Value

List of type adduct with 5 entries

adduct[[1]]	Adducts. Dataframe with peaks (mass,intensity,rt,peak ID) and their adduct relations (to ID,adduct(s),mass tolerance,charge level) within adduct groups (group ID,interaction level).
adduct[[2]]	Parameters. Parameters used.
adduct[[3]]	Peaks in adduct groups.Dataframe listing all peaks (peak IDs) for an adduct group (group ID) and the individual adducts found in that group (adducts).
adduct[[4]]	Number of adducts. Counts of hits per adduct over all adduct groups found.
adduct[[5]]	Overlaps. Count on how many peaks were assigned to be two different adducts

Note

Peak IDs refer to the order in which peaks are provided. Different IDs exist for adduct groups, isotope pattern groups, grouped homologue series (HS) peaks and homologue series cluster. Yet other IDs exist for the individual components (see note section of combine).

The same peak may appear as different adducts in column adduct[[1]][,7], indicating a conflict in assigning the correct adduct. Beware, some adduct combinations from adducts may lead to the same results (e.g. M+H<->M+Na vs M+3H<->M+3Na).

Author(s)

Martin Loos

See Also

rm.sat adducts peaklist plotadduct combine plotgroup

Examples

######################################################
# load required data: ################################
# HRMS peak list: ####################################
data(peaklist)
# list of adducts ####################################
data(adducts) 
######################################################
# run grouping of peaks for different adducts ########
# of the same candidate molecule #####################
adduct<-adduct.search(
  peaklist,
  adducts,
  rttol=0.05,
  mztol=3,
  ppm=TRUE,
  use_adducts=c("M+K","M+H","M+Na","M+NH4"),
  ion_mode="positive"
);
# plot results #######################################
plotadduct(adduct);
######################################################

blosloos/nontarget documentation built on June 2, 2022, 3:53 p.m.