cldetect: Search inside peaks mass spectrum clues for the presence of...

In yguitton/MeHaloCoA: Fast identification of Cl or Br containing compounds in LC-MS

Description

Fast search of compounds exhibiting chlorinated or brominated pattern (isotopic profile and mass defect) inside a hight-resolution LC-MS data set. First do CDF2RData then launch cldetect
with some expertise it is possible to search for any isotopic profile, not only Cl or Br.
In LC-MS ESI data acquired in negative mode cldetect gives you the [M+Cl]- adducts

Usage

cldetect(outdir = "", xsAnnotate, plotps = TRUE, deprof = FALSE, 
 Thresh = 30, m1 = 1.003, m2 = 1.997, mdiff = 0.05, ppmerr = 50, val = "into", 
 mdiff2 = 0.001, myfile = "halo_list.csv", myfile2 = "halo_list_short.csv", m1need=FALSE)

Arguments

outdir	your results directory
xsAnnotate	an R CAMERA object created by CDF2Data.R function made by Ron Wehrens and modified by Y. GUITTON or xs<-xcmsSet() then an<-annotate(xs)
plotps	Plot pseudospectra and EICs for each considered peaks in jpeg format the result repository default = TRUE. Put FALSE if you have error message like could not find file type (you may have moved your original datas)
deprof	default=FALSE if TRUE deprofile.scan from RMassBank is applied on each pspectra, mainly used if your LC-MS data are not well centroided by your file converter
Thresh	Threshold of intensity for M+2 here 30
m1	mass defect between M and M+1 isotope (here 1.0033)
m2	mass defect between M and M+2 isotope (here 1.997 for Cl)
mdiff	mdiff differences in Da applied to neutral loss search
ppmerr	ppm margin tolerated by cldetect
val	val for use of into or maxo in funM2 and deprofile.scan
mdiff2	mdiff2 differences in Da applied to IFC chromatogram drawing
myfile	name of the output file default "halo_list.csv"
myfile2	name of the output file default "halo_list_short.csv" is a resume from all individual myfile in the case off several files have been processed by the GUI
m1need	Should M+1 isotope be present? if FALSE (Default) peaks with no M+1 are considered (interesting for low intensity compounds). If TRUE only complete isotopic profiles are taken into account.

Value

A matrix with the Cl or Br peaks annotated with RT, Intensity, M, M+1,M+2.
Draw nice Isotopic Filtered Chromatogram (IFC) summary plot where Cl or Br containing peaks are pointed out on the TIC chromatogram in a PDF file inside the Result directory with runGUI type MeHaloCoAenv$an to see the CDF2RData object and type MeHaloCoAenv$matcl to see the result of cldetect

Author(s)

Yann GUITTON

References

"Sleno, L., 2012. The use of mass defect in modern mass spectrometry: Mass defect in mass spectrometry. Journal of Mass Spectrometry 47, 226-236. doi:10.1002/jms.2953"
"Wehrens, R., Weingart, G., Mattivi, F., n.d. metaMS: An open-source pipeline for GC-MS-based untargeted metabolomics. Journal of Chromatography B. doi:10.1016/j.jchromb.2014.02.051"

Examples

runGUI()
## Not run:
## Not run: 
library(MeHaloCoA)

#do the peak picking
data(xcmsSettings) #load peak picking parameters
an<-CDF2RData(indir = system.file("doc/mzData", package="MeHaloCoA"), settingslist=xcmsSettings)
#if indir="", interactive selection of data directory

#do isotopic profile search
data(cldetectSettings) #load halogens detection parameters
i=1 #just first file is processed with cldetect
matcl<-do.call("cldetect", c(an[[i]],cldetectSettings))

#if several files have been processed by CDF2RData
for (i in 1:length(an)){
	matcl<-do.call("cldetect", c(an[[i]],cldetectSettings))
}

## End(Not run)

yguitton/MeHaloCoA documentation built on May 3, 2019, 4:30 p.m.