EvaluatePairsFromXCMSSet: Identify and evaluate mz pairs from a peak list.

In HiResTEC: Non-Targeted Fluxomics on High-Resolution Mass-Spectrometry Data

Identify and evaluate mz pairs from a peak list.

Description

EvaluatePairsFromXCMSSet will analyze an 'xcmsSet' result or a generic peak list from a mass spectrometry experiment for mass pairs (mz1, mz2) with changes due to any tracer incorporation.

Usage

EvaluatePairsFromXCMSSet(
  xg = NULL,
  tp = NULL,
  gr = NULL,
  drt = 1,
  dmz = 0.025,
  mz_iso = 1.00335,
  n = 6,
  method = c("APCI", "ESI")[1],
  specific_row = NULL,
  testing = FALSE,
  silent = FALSE
)

Arguments

xg	xcmsSet object with group information. Alternatively, can be a numeric matrix containing 'mz' and 'rt' information in the first two columns followed by peak intensities of all samples in the same order as in parameters 'tp' and 'gr'.
tp	Time point information for all samples (obviously required, internally converted to factor).
gr	Group information for all samples, e.g. different genotypes or concentrations (optional, factor).
drt	Allowed rt deviation in time units of xcmsSet (usually seconds) to test for candidates.
dmz	Allowed mass deviation in Da.
mz_iso	Mass defect of the isotope under investigation (use 1.00335 for ^13^C experiments.
n	Number of maximal incorporated carbons to test.
method	Currently APCI or ESI. If APCI, dmz will be modified depending on n (see details).
specific_row	A single row of the peak list to process.
testing	Stop in function using browser() if specific_row is specified; can be a isotope number, i.e. 3 will stop at third isotope.
silent	Suppress warnings and console output if TRUE.

Details

Using 'APCI' as method assumes that (i) you analyze TMS-derivatized compounds and (ii) your MS resolution does not allow to separate Si and C isotopes but reports an intermediate mass as m/z. In this case you will find carbon isotopes below there expected masses, i.e. M+1 would be 1.001 mDa apart from M+0 instead of 1.003. The effect is increased with isotope number, i.e. M+6 will be ~20 mDa below the expected value. Hence, selecting method 'APCI' will combine your selected dmz with a allowed deviation due to mass shifts caused by Si isotopes. Use 'ESI' if you are not sure if this effect takes place in your settings.

Value

A dataframe with all observable pairs within the provided xg object (usually an 'xcmsSet' peak) list including mean group intensities and P values.

Examples

# The example measurement data provided with HiResTEC contain a peak at 1026s
raw <- HiResTEC::raw
sam <- HiResTEC::sam
mz <- c(556.26, 561.26, 564.26)

# extract the peak intensities for 3 m/z of this peak
int <- sapply(raw, function(x) {
  tmp <- getMultipleBPC(x = x, mz = mz, mz_dev = 0.04, rt = 1026)
  tmp[attr(tmp, "maxBPC"),]
})
colnames(int) <- sam$ID; rownames(int) <- NULL
xg <- data.frame(
 "mz" = mz,
 "rt" = rep(1026.5, 3),
 int
)

# evaluate this peak list for interesting pairs
EvaluatePairsFromXCMSSet(xg=xg, tp=sam$TP, gr=sam$Group, silent=TRUE, n=8)

HiResTEC documentation built on April 3, 2025, 9:35 p.m.