Metabolomics 20 years on: what have we learned and what hurdles remain?

Tomato Multiomics Reveals Consequences of Crop Domestication and Improvement

(2018) James Giovannoni   CELL

Rewiring of the Fruit Metabolome in Tomato Breeding

(2018) Guangtao Zhu et al.   CELL

A Map of Protein-Metabolite Interactions Reveals Principles of Chemical Communication

(2018) Ilaria Piazza et al.   CELL

Mapping the Arabidopsis Metabolic Landscape by Untargeted Metabolomics at Different Environmental Conditions

(2018) Si Wu et al.   Molecular Plant

An integrated multi-layered analysis of the metabolic networks of different tissues uncovers key genetic components of primary metabolism in maize

(2018) Weiwei Wen et al.   PLANT JOURNAL

Unraveling lipid metabolism in maize with time-resolved multi-omics data

(2018) Francisco de Abreu e Lima et al.   PLANT JOURNAL

Metabolite profiling of barley flag leaves under drought and combined heat and drought stress reveals metabolic QTLs for metabolites associated with antioxidant defense

(2017) Sven Eduard Templer et al.   JOURNAL OF EXPERIMENTAL BOTANY

Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics

(2017) Zijuan Lai et al.   NATURE METHODS

HMDB 4.0: the human metabolome database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

Canalization of Tomato Fruit Metabolism

(2017) Saleh Alseekh et al.   PLANT CELL

An InDel in the Promoter of Al-ACTIVATED MALATE TRANSPORTER9 Selected during Tomato Domestication Determines Fruit Malate Contents and Aluminum Tolerance

(2017) Jie Ye et al.   PLANT CELL

High spatial resolution mass spectrometry imaging reveals the genetically programmed, developmental modification of the distribution of thylakoid membrane lipids among individual cells of maize leaf

(2017) Maria Emilia Dueñas et al.   PLANT JOURNAL

Integrated omics analysis of specialized metabolism in medicinal plants

(2017) Amit Rai et al.   PLANT JOURNAL

Engineering central metabolism - a grand challenge for plant biologists

(2017) Lee J. Sweetlove et al.   PLANT JOURNAL

A chemical genetic roadmap to improved tomato flavor

(2017) Denise Tieman et al.   SCIENCE

Differentially evolved glucosyltransferases determine natural variation of rice flavone accumulation and UV-tolerance

(2017) Meng Peng et al.   Nature Communications

An evolutionarily young defense metabolite influences the root growth of plants via the ancient TOR signaling pathway

(2017) Frederikke Gro Malinovsky et al.   eLife

A Quantitative Profiling Method of Phytohormones and Other Metabolites Applied to Barley Roots Subjected to Salinity Stress

(2017) Da Cao et al.   Frontiers in Plant Science

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

(2017) Leonardo Perez de Souza et al.   GigaScience

System-wide detection of protein-small molecule complexes suggests extensive metabolite regulation in plants

(2017) Daniel Veyel et al.   Scientific Reports

Metabolite pools and carbon flow during C4photosynthesis in maize:13CO2labeling kinetics and cell type fractionation

(2016) Stéphanie Arrivault et al.   JOURNAL OF EXPERIMENTAL BOTANY

Evolutionary Metabolomics Reveals Domestication-Associated Changes in Tetraploid Wheat Kernels

(2016) Romina Beleggia et al.   MOLECULAR BIOLOGY AND EVOLUTION

Solanum pennelliibackcross inbred lines (BILs) link small genomic bins with tomato traits

(2016) Itai Ofner et al.   PLANT JOURNAL

A Tale of Two Sugars: Trehalose 6-Phosphate and Sucrose

(2016) Carlos M. Figueroa et al.   PLANT PHYSIOLOGY

Network-Guided GWAS Improves Identification of Genes Affecting Free Amino Acids

(2016) Ruthie Angelovici et al.   PLANT PHYSIOLOGY

Broadening Our Portfolio in the Genetic Improvement of Maize Chemical Composition

(2016) Weiwei Wen et al.   TRENDS IN GENETICS

Omic Relief for the Biotically Stressed: Metabolomics of Plant Biotic Interactions

(2016) Hezi Tenenboim et al.   TRENDS IN PLANT SCIENCE

More than Pictures: When MS Imaging Meets Histology

(2016) Yonghui Dong et al.   TRENDS IN PLANT SCIENCE

The WEIZMASS spectral library for high-confidence metabolite identification

(2016) Nir Shahaf et al.   Nature Communications

Characterization of a recently evolved flavonol-phenylacyltransferase gene provides signatures of natural light selection in Brassicaceae

(2016) Takayuki Tohge et al.   Nature Communications

Combined Use of Genome-Wide Association Data and Correlation Networks Unravels Key Regulators of Primary Metabolism in Arabidopsis thaliana

(2016) Si Wu et al.   PLoS Genetics

Sample Preparation for Mass Spectrometry Imaging of Plant Tissues: A Review

(2016) Yonghui Dong et al.   Frontiers in Plant Science

What the transcriptome does not tell — proteomics and metabolomics are closer to the plants’ patho-phenotype

(2015) Ivo Feussner et al.   CURRENT OPINION IN PLANT BIOLOGY

Metabolomics continues to expand: highlights from the 2015 metabolomics conference

(2015) Oliver Fiehn et al.   Metabolomics

Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects

(2015) Lloyd W. Sumner et al.   NATURAL PRODUCT REPORTS

ECMDB 2.0: A richer resource for understanding the biochemistry ofE. coli

(2015) Tanvir Sajed et al.   NUCLEIC ACIDS RESEARCH

Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato

(2015) Saleh Alseekh et al.   PLANT CELL

Quantitative Variation in Responses to Root Spatial Constraint withinArabidopsis thaliana

(2015) Bindu Joseph et al.   PLANT CELL

In vitro reconstruction and analysis of evolutionary variation of the tomato acylsucrose metabolic network

(2015) Pengxiang Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Variation in the Nuclear and Organellar Genomes Modulates Stochastic Variation in the Metabolome, Growth, and Defense

(2015) Bindu Joseph et al.   PLoS Genetics

Profiling of Stable Isotope Enrichment in Specialized Metabolites Using Liquid Chromatography and Multiplexed Nonselective Collision-Induced Dissociation

(2014) Zhenzhen Wang et al.   ANALYTICAL CHEMISTRY

On the regulation and function of secondary metabolism during fruit development and ripening

(2014) Takayuki Tohge et al.   JOURNAL OF EXPERIMENTAL BOTANY

Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean

(2014) E. Bellucci et al.   PLANT CELL

Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism

(2014) Fumio Matsuda et al.   PLANT JOURNAL

Revealing insect herbivory-induced phenolamide metabolism: from single genes to metabolic network plasticity analysis

(2014) Emmanuel Gaquerel et al.   PLANT JOURNAL

Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

(2014) C. Sauvage et al.   PLANT PHYSIOLOGY

Comprehensive analysis of lipids in biological systems by liquid chromatography-mass spectrometry

(2014) Tomas Cajka et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights

(2014) Weiwei Wen et al.   Nature Communications

Natural occurring epialleles determine vitamin E accumulation in tomato fruits

(2014) Leandro Quadrana et al.   Nature Communications

The Spatial Organization of Metabolism Within the Plant Cell

(2013) Lee J. Sweetlove et al.   Annual Review of Plant Biology

Making new molecules—evolution of structures for novel metabolites in plants

(2013) Daniel J Kliebenstein   CURRENT OPINION IN PLANT BIOLOGY

New Synthesis—Regulatory Evolution, the Veiled World of Chemical Diversification

(2013) Daniel J. Kliebenstein   JOURNAL OF CHEMICAL ECOLOGY

LipidBlast in silico tandem mass spectrometry database for lipid identification

(2013) Tobias Kind et al.   NATURE METHODS

Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids

(2013) Ryo Nakabayashi et al.   PLANT JOURNAL

Whole-Genome Mapping of Agronomic and Metabolic Traits to Identify Novel Quantitative Trait Loci in Bread Wheat Grown in a Water-Limited Environment

(2013) C. B. Hill et al.   PLANT PHYSIOLOGY

PLGG1, a plastidic glycolate glycerate transporter, is required for photorespiration and defines a unique class of metabolite transporters

(2013) T. R. Pick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AtABCG29 Is a Monolignol Transporter Involved in Lignin Biosynthesis

(2012) Santiago Alejandro et al.   CURRENT BIOLOGY

An alternative route to cyclic terpenes by reductive cyclization in iridoid biosynthesis

(2012) Fernando Geu-Flores et al.   NATURE

ECMDB: The E. coli Metabolome Database

(2012) An Chi Guo et al.   NUCLEIC ACIDS RESEARCH

Dissection of genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis

(2012) Fumio Matsuda et al.   PLANT JOURNAL

Untargeted Metabolic Quantitative Trait Loci Analyses Reveal a Relationship between Primary Metabolism and Potato Tuber Quality

(2012) N. Carreno-Quintero et al.   PLANT PHYSIOLOGY

The genetic architecture of branched-chain amino acid accumulation in tomato fruits

(2011) Andrej Kochevenko et al.   JOURNAL OF EXPERIMENTAL BOTANY

Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function

(2011) Takayuki Tohge et al.   Nature Protocols

KNApSAcK Family Databases: Integrated Metabolite–Plant Species Databases for Multifaceted Plant Research

(2011) Farit Mochamad Afendi et al.   PLANT AND CELL PHYSIOLOGY

Identification of Genes in the Phenylalanine Metabolic Pathway by Ectopic Expression of a MYB Transcription Factor in Tomato Fruit

(2011) V. Dal Cin et al.   PLANT CELL

Elemental formula annotation of polar and lipophilic metabolites using13C,15N and34S isotope labelling, in combination with high-resolution mass spectrometry

(2011) Patrick Giavalisco et al.   PLANT JOURNAL

Metabolomic analysis of Arabidopsis reveals hemiterpenoid glycosides as products of a nitrate ion-regulated, carbon flux overflow

(2011) J. L. Ward et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combining Genome-Wide Association Mapping and Transcriptional Networks to Identify Novel Genes Controlling Glucosinolates in Arabidopsis thaliana

(2011) Eva K. F. Chan et al.   PLOS BIOLOGY

MassBank: a public repository for sharing mass spectral data for life sciences

(2010) Hisayuki Horai et al.   JOURNAL OF MASS SPECTROMETRY

Network Analysis of Enzyme Activities and Metabolite Levels and Their Relationship to Biomass in a Large Panel of Arabidopsis Accessions

(2010) R. Sulpice et al.   PLANT CELL

Mass spectrometry screening reveals widespread diversity in trichome specialized metabolites of tomato chromosomal substitution lines

(2010) Anthony Schilmiller et al.   PLANT JOURNAL

Metabolome and water homeostasis analysis of Thellungiella salsuginea suggests that dehydration tolerance is a key response to osmotic stress in this halophyte

(2010) Raphaël Lugan et al.   PLANT JOURNAL

The Influence of Fruit Load on the Tomato Pericarp Metabolome in a Solanum chmielewskii Introgression Line Population

(2010) P. T. Do et al.   PLANT PHYSIOLOGY

Biosynthesis of glucosinolates – gene discovery and beyond

(2010) Ida E. Sønderby et al.   TRENDS IN PLANT SCIENCE

Dual Labeling of Metabolites for Metabolome Analysis (DLEMMA): A New Approach for the Identification and Relative Quantification of Metabolites by Means of Dual Isotope Labeling and Liquid Chromatography−Mass Spectrometry

(2009) Liron Feldberg et al.   ANALYTICAL CHEMISTRY

Metabolomics for Functional Genomics, Systems Biology, and Biotechnology

(2009) Kazuki Saito et al.   Annual Review of Plant Biology

Understanding the Evolution of Defense Metabolites in Arabidopsis thaliana Using Genome-wide Association Mapping

(2009) E. K. F. Chan et al.   GENETICS

Web-based resources for mass-spectrometry-based metabolomics: A user’s guide

(2009) Takayuki Tohge et al.   PHYTOCHEMISTRY

Starch as a major integrator in the regulation of plant growth

(2009) R. Sulpice et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alkaloid Biosynthesis: Metabolism and Trafficking

(2008) Jörg Ziegler et al.   Annual Review of Plant Biology

Temporally resolved GC-MS-based metabolic profiling of herbicide treated plants treated reveals that changes in polar primary metabolites alone can distinguish herbicides of differing mode of action

(2008) Sandra Trenkamp et al.   Metabolomics

1H NMR metabolite fingerprinting and metabolomic analysis of perchloric acid extracts from plant tissues

(2008) Nicholas J Kruger et al.   Nature Protocols

Biochemical Networks and Epistasis Shape the Arabidopsis thaliana Metabolome

(2008) H. C. Rowe et al.   PLANT CELL