FullMS: Processing and Annotation of LC-MS Full-Scan data

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

Description

Peak picking of MS data is performed by the enviPick algorithm embedded. Second, it is performed a targeted extraction with a mass tolerance and m/z interval windows constraints for general peak grouping and library interrogation. Retention time might be considered as optional constraints. Library listing needs to follow the format following the exampled attached.

Usage

FullMS(file, database, rtw = 10, mzw = 0.0004,ppm_tol=10,Peak_Assy=5,
dmzgap = 50,dmzdens = 20, drtgap = 25, drtsmall = 50,
drtdens = 20, drtfill = 5,drttotal = 100, minpeak = 5,
recurs = 3, weight = 1,SB = 2, SN = 1.5, minint = 1000,
maxint = 9e+09, ion_mode = "positive",
ppm = TRUE,ended=6)

Arguments

file	A mzXML file from the LC-MS/MS experiment in positive or negative ionization mode.
database	A file with data arranged in columns as follows: Molecular Formula; Retention time (optional); Neutral mass; Compound name
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 mass value and the experimental. Default value=10
Peak_Assy	numeric. Maximum peak assymetry threshold. Default value=5
mzw	numeric. The difference between the theoretical m/z value and the experimental (Da). Default value=0.004
dmzgap	Arguments to be passed from enviPickwrap
dmzdens	Arguments to be passed from enviPickwrap
drtgap	Arguments to be passed from enviPickwrap
drtsmall	Arguments to be passed from enviPickwrap
drtdens	Arguments to be passed from enviPickwrap
drtfill	Arguments to be passed from enviPickwrap
drttotal	Arguments to be passed from enviPickwrap
minpeak	Arguments to be passed from enviPickwrap
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
minint	Arguments to be passed from enviPickwrap
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

ms	Annotated metabolites.
RawData1	Raw scans from raw data.
PP	Results obtained throughout enviPick algorithm performed on MS level 1.
Peaklist	Matrix with the peak picked obtained throughout enviPick algorithm.

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

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