autoQ: Read files and quantify isotopologues in low- or...
In jcapelladesto/isoSCAN: Automatic Integration for GC-CI-MS Isotope Labeling Data

autoQ

R Documentation

Read files and quantify isotopologues in low- or high-resolution data

Description

Read each file and quantify both Area and Maxo of each metabolite isotopologues, by evaluating the RT window of each metabolite to minimize background noise. Low resolution data requires that massdiff and mzerror parameters are indicated to process the data. High resolution data requires a limit of ppm (maxppm) and that column Formula from formulaTable includes the molecular formula of the derivatized metabolite for accurate isotopologue mass estimation by enviPat package.

Usage

autoQ(
  SampleFiles = NULL,
  formulaTable = NULL,
  SNR = 3,
  minscans = 6,
  RTwin = 5,
  fit.p = 0.05,
  resolution = NA,
  minwidth = 1,
  maxwidth = 4,
  thr = 0.1,
  mzerror = 0.1,
  massdiff = 1.003355,
  maxppm = 5,
  isotopes,
  labelatom = "13C"
)

Arguments

`SampleFiles`	List of mzML files to be processed (see base::list.files())
`formulaTable`	Dataframe including CompoundName, Formula, mz, RT and NumAtoms (see buildFormulaTable)
`SNR`	Minimum signal-to-noise ratio for EIC peak quantification.
`minscans`	Minimum number of recorded scans to use to evaluate a peak.
`RTwin`	Retention time window (in seconds) to extract the metabolite isotopologues
`fit.p`	Max linear model p-value (used to determine peak symmetry) for a peak to have its area quantified, otherwise only Maxo is returned.
`resolution`	Set to c(1) in the case of low-resolution data. Set to a fixed average resolution value if qTOF instrument is used (for example, c(20000)). Set to 'R at MZ' as c(1e5,200) in Orbitrap instruments.
`minwidth`	Minimum width (in seconds) of a detected EIC peak to be considered
`maxwidth`	Maximum width (in seconds) of a detected EIC peak to be considered
`thr`	Inherited from isopattern. Probability below which isotope peaks can be omitted. Default = 0.1. Recommended values between: 0.5 and 0.01.
`mzerror`	Symmetric (+/-) absolute mass error to consider in low-resolution data.
`massdiff`	Stable isotope mass difference, for C13: 1.003355, necessary for low-resolution.
`maxppm`	Symmetric (+/-) maximum ppm mass error to consider in high-resolution data.
`isotopes`	Dataframe with stable isotopes information as in isotopes
`labelatom`	Labeling atom used as in isotopes$isotope. For example, "13C".

Details

In the case of high-resolution and additional column indicating the estimated mass accuracy error (in ppm) per each isotopologue and sample is included.