DeconvoluteSpectrum: Deconvolute a Mass Spectrum from a list of raw data files.

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

Deconvolute a Mass Spectrum from a list of raw data files.

Description

DeconvoluteSpectrum will evaluate a list of 'xcmsRaw' or 'xcmsRawLike' objects at a given time (rt) and potential mass (mz1). The main purpose is to deconvolute the mass spectrum at rt including mz1.

Usage

DeconvoluteSpectrum(
  dat = NULL,
  rt = NULL,
  rt_dev = 3,
  mz1 = NULL,
  mz_dev = 0.003,
  use.mz.adjust = FALSE,
  ionization = c("APCI", "ESI")[1],
  smooth = 0
)

Arguments

dat	A list of 'xcmsRaw' or 'xcmsRawLike' objects.
rt	Retention time of the expected peak.
rt_dev	Allowed retention time deviation.
mz1	If specified, ensure that this mass is included in the spectrum (assumed base peak). Can be NULL otherwise in which case the most intense peak at rt will be selected as mz1.
mz_dev	Allowed mz deviation [Da].
use.mz.adjust	Will adjust mz on an experiment wide basis.
ionization	Either APCI or ESI. Choice will modify some internal parameters and checks performed.
smooth	Smoothing parameter passed on to getMultipleBPC.

Details

The specific advantage of DeconvoluteSpectrum is, that it does not deconvolute signals within a single measurement file but uses correlation tests over a set of measurements to improve statistical power. It will test all mz around a specified rt to co-apex with some mz1, have a low rt difference and consistent intensity ratio over all samples.

Value

A pseudo spectrum at rt (containing mz1 if specified). Effectively a 2-column matrix (mz, int) with rt as attribute.

Examples

# The example measurement data provided with HiResTEC contain a peak at 1026s
raw <- HiResTEC::raw
HiResTEC::DeconvoluteSpectrum(raw, rt = 1026)

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