From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

GigaScience
Leonardo Perez de SouzaAlisdair R Fernie

Abstract

The grand challenge currently facing metabolomics is the expansion of the coverage of the metabolome from a minor percentage of the metabolic complement of the cell toward the level of coverage afforded by other post-genomic technologies such as transcriptomics and proteomics. In plants, this problem is exacerbated by the sheer diversity of chemicals that constitute the metabolome, with the number of metabolites in the plant kingdom generally considered to be in excess of 200 000. In this review, we focus on web resources that can be exploited in order to improve analyte and ultimately metabolite identification and quantification. There is a wide range of available software that not only aids in this but also in the related area of peak alignment; however, for the uninitiated, choosing which program to use is a daunting task. For this reason, we provide an overview of the pros and cons of the software as well as comments regarding the level of programing skills required to effectively exploit their basic functions. In addition, the torrent of available genome and transcriptome sequences that followed the advent of next-generation sequencing has opened up further valuable resources for metabolite identification. All things consi...Continue Reading

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Citations

Jan 24, 2018·Bioinformatics·Michael J Dagley, Malcolm J McConville
May 8, 2018·The Plant Journal : for Cell and Molecular Biology·Saleh Alseekh, Alisdair R Fernie
Aug 4, 2018·International Journal of Molecular Sciences·Shumei LiQing Jin
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Nov 20, 2019·Current Protocols in Plant Biology·Leonardo Perez de SouzaAlisdair Fernie
Jan 11, 2020·The Plant Journal : for Cell and Molecular Biology·Paul D FraserAlisdair R Fernie
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Methods Mentioned

BETA
Feature Extraction
NMR
ISA
PCA

Software Mentioned

IDEOM
MetNormalizer
yamss )
DW
MetFrag
Multiple Reaction Monitoring – Based Differential Analysis ( M...
MFSearcher
MassBank
MetaboLights
AMDIS

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