Recommendations for Reporting Metabolite Data
Alisdair R. Fernie,Asaph Aharoni,Lothar Willmitzer,Mark Stitt,Takayuki Tohge,Joachim Kopka,Adam J. Carroll,Kazuki Saito,Paul D. Fraser,Vincenzo DeLuca +9 more
TL;DR: The last decade has witnessed dramatic advances in the authors' ability to determine the levels of an ever broadening range of metabolites, and transcriptomic approaches and proteomics approaches are now capable of providing almost complete coverage.
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Abstract: The last decade has witnessed dramatic advances in our ability to determine the levels of an ever broadening range of metabolites. That said, while transcriptomic approaches provide almost complete coverage ([Gonzalez-Ballester et al., 2010][1]) and proteomics approaches are now capable of
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A novel integrated method for large-scale detection, identification, and quantification of widely targeted metabolites: application in the study of rice metabolomics.
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TL;DR: A comprehensive study of maize metabolism, combining genetic, metabolite and expression profiling methodologies to dissect the genetic basis of metabolic diversity in maize kernels, finds metabolite features associated with kernel weight could be used as biomarkers to facilitate genetic improvement of maize.
References
Proposed minimum reporting standards for chemical analysis
Lloyd W. Sumner,Alexander Amberg,Dave Barrett,Michael H. Beale,Richard D. Beger,Clare A. Daykin,Teresa W.-M. Fan,Oliver Fiehn,Royston Goodacre,Julian L. Griffin,Thomas Hankemeier,Nigel Hardy,James M. Harnly,Richard M. Higashi,Joachim Kopka,Andrew N. Lane,John C. Lindon,Philip J. Marriott,Andrew W. Nicholls,Michael D. Reily,John J. Thaden,Mark R. Viant +21 more
TL;DR: This article proposes the minimum reporting standards related to the chemical analysis aspects of metabolomics experiments including: sample preparation, experimental analysis, quality control, metabolite identification, and data pre-processing.
Metabolomics - the link between genotypes and phenotypes
TL;DR: In this review, the differences among metabolite target analysis, metabolite profiling, and metabolic fingerprinting are clarified, and terms are defined.
3.7K
Metabolite profiling for plant functional genomics.
Oliver Fiehn,Joachim Kopka,Peter Dörmann,Thomas Altmann,Richard N. Trethewey,Lothar Willmitzer +5 more
TL;DR: The use of metabolite profiling is described as a new tool for a comparative display of gene function and has the potential not only to provide deeper insight into complex regulatory processes but also to determine phenotype directly.
2.2K
Gas chromatography mass spectrometry–based metabolite profiling in plants
TL;DR: A detailed protocol for gas chromatography mass spectrometry (GC-MS)-based metabolite profiling that offers a good balance of sensitivity and reliability, being considerably more sensitive than NMR and more robust than liquid chromatography–linked mass spectromaetry.
1.9K
GMD@CSB.DB: the Golm Metabolome Database
Joachim Kopka,Nicolas Schauer,Stephan Krueger,Claudia Birkemeyer,Björn Usadel,Eveline Bergmüller,Peter Dörmann,Wolfram Weckwerth,Yves Gibon,Mark Stitt,Lothar Willmitzer,Alisdair R. Fernie,Dirk Steinhauser +12 more
TL;DR: GD, The Golm Metabolome Database is presented, an open access metabolome database, which provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools, e.g. with regard to methods, spectral information or compounds.
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