plot_EIC: Plot an Extracted Ion Chromatogram (EIC)

In MetaboList: Annotation of Metabolites from Liquid Chromatography-Mass Spectrometry Data

Description

Plot an Extracted Ion Chromatogram (EIC) either from processed MS1 or MS/MS file with FullMS or AIF.

Usage

plot_EIC(fullms,peakID=333,ms=1,CE=0)

Arguments

fullms	A fullms or DIA file processed by FullMS or AIF.
peakID	Identity of the EIC desired to plot. The peakID is indicated in the ouput obtained with FullMS or AIF.
ms	numeric. MS level of EIC desired to plot.
CE	numeric. Collision energy for the file processed.

Author(s)

Manuel D Peris Diaz

References

1. R-MetaboList: a flexible tool for metabolite extraction from high-resolution data-independent acquisition mass spectrometry analysis. Metabolites. Soon

2. A Survey of Orbitrap All Ion Fragmentation Analysis Assessed by an R MetaboList Package to Study Small-Molecule Metabolites. Chromatographia. 2018, 81, 981-994.

Examples

library(MetaboList)
#Reading the file.mzXML
# file<-fullMS.mzXML

#Reading the database.csv file:
# database<- read.csv("C:/FullMS1.csv")

#Processing peak-picking and annotation with default parameters
# FullMS_results<-FullMS(file,database, ion_mode = "positive",)

#Output:
#FullMS_results$ms

#plot_EIC(fullmsposH,peakID=413)

MetaboList documentation built on Aug. 22, 2019, 5:03 p.m.