DecoMetDIA: DecoMetDIA: Deconvolution of Multiplexed MS/MS Spectra for...

In ZhuMSLab/DecoMetDIA: DecoMetDIA: Deconvolution of Multiplexed MS/MS Spectra for Metabolite Identification in SWATH-MS based Untargeted Metabolomics

DecoMetDIA: Deconvolution of Multiplexed MS/MS Spectra for Metabolite Identification in SWATH-MS based Untargeted Metabolomics

Description

DecoMetDIA picks peaks from SWATH acquired data with XCMS and extracts MS2 EICs under related SWATH window for each feature of different sample. Deconvolution algorithms are applied to MS2 EICs for each feature and thus MS2 spectra are generated. The features are identified by matching the obtained spectra with librarial ones.

Usage

DecoMetDIA(d.in = ".", d.out = "DecoMetDIA_Result", nSlaves = 6,
  peakwidth = c(5, 30), sn = 6, ppm.pd = 25,
  polarity = c("positive", "negative"), lc = c("HILIC", "RP"),
  minfrac = 0.5, bw = 5, mzwid = 0.015, is.ms1.filter = FALSE,
  thr.ms1.filter = NULL, filed.ms1.filter = c("maxo", "into", "intb"),
  is.plot.eic.feature = F, is.check.eic = FALSE,
  is.PlotEIC.MS2 = FALSE, snthr.ms2 = 5,
  fp.swath.setup = "../SWATHsetup.csv", ppm.ms2.mtp = 15,
  int.filter = 50, minfrac.vote = 0.5, is.plot.eic.spec = F,
  is.output.spec.smp = TRUE, is.span.constant = FALSE, rerun = FALSE,
  rerun.ms2 = FALSE, is.ms1.only = FALSE, is.dec.all = FALSE,
  is.dec.smoothed = FALSE, is.norm.consensus = TRUE)

Arguments

d.in	Working directory, where the well orgnized data are stored
d.out	Directory for saving results
nSlaves	No. of threads for data processing
peakwidth	Chromatographic peak width, given as range (min,max) in seconds (xcms)
sn	Signal to noise ratio cutoff for peak detection using xcms
ppm.pd	Maxmial tolerated m/z deviation in consecutive scans, in ppm for MS1 peak detection
polarity	Polarity setup for ionization
lc	LC column used for chromatographic seperation
minfrac	minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group when group peaks with 'denisty' method in xcms
bw	bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram when group peaks with 'denisty' method in xcms
mzwid	width of overlapping m/z slices to use for creating peak density chromatograms and grouping peaks across samples when group peaks with 'denisty' method in xcms
is.ms1.filter	logical value for indicating if filter isotopic or low abundant peaks
thr.ms1.filter	MS1 peak filter threshold for filtering low abundant peaks
filed.ms1.filter	MS1 peak filter method (maxo:intensity, into:raw peak area or intb:base-line corrected peak area)
is.plot.eic.feature	logical value for indicating if plot EICs of features
is.check.eic	logical value for indicating if plot peak boundaries when plotting feature EICs
is.PlotEIC.MS2	logical value for indicating if plot EICs of fragment ions
snthr.ms2	signal to noise threshold for MS2 peak detection
fp.swath.setup	file path for SWATH setup file (.csv format recording swath windows)
ppm.ms2.mtp	ppm threshold for EIC extraction of fragment ions in multiplexed spectrum
int.filter	intensity threshold for removing low abundant fragment ions in multiplexed spectrum
minfrac.vote	= 0.5,
is.output.spec.smp	logical value for indicating if output deconvoluted spectra for each sample
is.span.constant	logical value for indicating if using constant span when smoothing EICs
rerun	logical value for indicating if rerun the already processed peak detection results
rerun.ms2	logical value for indicating if rerun the already prcoessed MS2 data analysis process
is.ms1.only	logical value for indicating if only detect peaks
is.dec.all	logical value for indicating if deconvolute all EICs, if not, the 'simple' peaks are ignored
is.dec.smoothed	logical value for indicating if using smoothed peaks as model peaks.
is.norm.consensus	logical value for indicating if normalize intensities to 1 when consensusing spectra cross samples.

ZhuMSLab/DecoMetDIA documentation built on March 21, 2022, 9:57 a.m.