AIF: Automatic Metabolite Annotation from LC-MS DIA experiments.

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

Description

Analysis and annotation of LC-MS/MS DIA data with the use of in-house mass spectral libraries.

Usage

AIF(fileMS1,fileMS2,CE=0, database,rtw=7,
ppm_tol=10,dmzgap=50,drtdens =20,drtgap=25,
drtsmallMS1=100,drtsmallMS2=30,dmzdensMS1=15,
dmzdensMS2=30,drtfill=5,drttotal=100,minpeakMS1=5,
minpeakMS2=3,recurs=2,weight=2,SB=3, SN=2,
minintMS1=1000,minintMS2=100,maxint=9e+09,
ion_mode="positive",ppm=TRUE,ended=6)

Arguments

fileMS1	A .mzXML file extension with the MS/MS experiment obtained at particular collision energy (CE).
fileMS2	A .mzXML file extension with the MS/MS experiment obtained at particular collision energy (CE).
CE	Collision energy employed for the MS/MS experiment.
database	A csv file with data arranged in columns including the names in the first row: Metabolite; Monoisotopic mass for the precursor; Mass Fragment 1; Mass Fragment 2; Mass Fragment 3... There is no need to used retention times as a constraint.
rtw	numeric. The difference between the theoretical retention time value and the experimental. Default value=3
ppm_tol	numeric. Mass error in ppm between the theoretical m/z value and the experimental. Default value=10
dmzgap	Arguments to be passed from enviPickwrap
dmzdensMS1	Arguments to be passed from enviPickwrapfor MS1 mode
dmzdensMS2	Arguments to be passed from enviPickwrapfor MS2 mode
drtgap	Arguments to be passed from enviPickwrap
drtsmallMS1	Arguments to be passed from enviPickwrap for MS1 mode
drtsmallMS2	Arguments to be passed from enviPickwrap for MS2 mode
drtdens	Arguments to be passed from enviPickwrap
drtfill	Arguments to be passed from enviPickwrap
drttotal	Arguments to be passed from enviPickwrap
minpeakMS1	Mininum number of scans that comprise a peak for MS1 mode.
minpeakMS2	Mininum number of scans that comprise a peak for MS2 mode.
recurs	Arguments to be passed from enviPickwrap
weight	Arguments to be passed from enviPickwrap
SB	Arguments to be passed from enviPickwrap
SN	Arguments to be passed from enviPickwrap
minintMS1	Arguments to be passed from enviPickwrap. Value for the MS1 mode.
minintMS2	Arguments to be passed from enviPickwrap. Value for the MS2 mode
maxint	Arguments to be passed from enviPickwrap
ion_mode	Arguments to be passed from enviPickwrap
ppm	Arguments to be passed from enviPickwrap
ended	Arguments to be passed from enviPickwrap

Value

ms1	Peak picking for MS1 level
ms2	Peak picking for MS2 level
annotationfull	Matrix with the metabolites annotated.
RawData1	Raw scans from raw data.
RawData2	Raw scans from raw data.

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)

CE.isolation("AIFpos1000-AIF.mzXML","fileposB")

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

#Processing peak-picking and annotation with default parameters

#aif5<-AIF(fileMS,fileMS2CE5,database,CE=5, ion_mode = "positive")

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