MetaboList (version 2.0)

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

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.

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

# NOT RUN {
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")



# }