cldetect.scan: 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. No needs of peakpicking step

Usage

cldetect.scan(outdir = "", file, noise=500, deprof = FALSE,  
 Thresh = 30, m1 = 1.003, m2 = 1.997, mdiff = 0.05, ppmerr = 25,  
 mdiff2 = 0.001, myfile = "halo_list.csv", myfile2 = "halo_list_short.csv",
 m1need=FALSE, N=NULL, scanrange=NULL)

Arguments

outdir	your results directory
file	complete path to your file (mzXML, CDF, mzML)

$

noise	noise level above which ions (m/z) are considered in count
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 et mdiff2 differences in Da applied to neutral loss search and to IFC chromatogram respectively
ppmerr	ppm margin tolerated by cldetect
mdiff2	mdiff et mdiff2 differences in Da applied to neutral loss search and to IFC chromatogram respectively
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
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.
N	N is an option by default put to NULL, N is the number of scan that can be merged before calculation, if N=5, scan 1 & 2 (and the two last scans) are not modified but scans 3 is equal to the mean of scans 1+2+3+4+5. mean scan is calculated with plotSpec from xcms on the basis of an xcmsRaw object with profstep=mzabs. Be careful this option generate a real slowing (in a future version we will add an nSlaves option). This option was added in order to re-create the same calculation as described in the Zhu et al paper. to the best of our knowledge the AMSA-IPF algorithm described is not available: "Zhu, P., Tong, W., Alton, K., Chowdhury, S., 2009. An Accurate-Mass-Based Spectral-Averaging Isotope-Pattern-Filtering Algorithm for Extraction of Drug Metabolites Possessing a Distinct Isotope Pattern from LC-MS Data. Analytical Chemistry 81, 5910-5917. doi:10.1021/ac900626d"
scanrange	scanrange is a vector with start : end scan (eg 50:60, or c(50:60), by default NULL which means all scans

Value

A matrix with the Cl or Br peaks annotated.
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

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)

#No peakpicking needed 
myfile=file.path(system.file("doc/mzData", package="MeHaloCoA"),"Q-ToF_Data1.mzData")
result<-cldetect.scan(outdir=getwd(),file=myfile)

## End(Not run)

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