The metabolomics standards initiative (MSI)

Fiehn, Oliver; Robertson, D. J.; Griffin, Jules; Werf, Mariet vab der; Nikolau, Basil J.; Morrison, Norman; Sumner, Lloyd W.; Goodacre, Royston; Hardy, Nigel; Taylor, Chris; Fostel, Jennifer; Kristal, Bruce S.; Kaddurah‐Daouk, Rima; Mendes, Pedro; Ommen, Ben van; Lindon, John C.; Sansone, Susanna Assunta

doi:10.1007/s11306-007-0070-6

Cited by 409 publications

(295 citation statements)

References 14 publications

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“…Special interest should also be directed to applications of proper and robust physicochemical methods during proteome and metabolome analyses, appropriate strategies of biological material preparation are also important Fiehn et al 2007) In particular the number of sample repetitions have a great influence on the results during proteome and/or metabolome analyses (Moco et al 2007;Mann et al 2013). …”

Section: Discussionmentioning

confidence: 99%

“…Molecular masses and polarity of the components present in the samples should be taken into account while choosing a proper identification system (Villas-Bôas et al 2004). It is also very important to design the experiments according to the standards of Metabolomic Standard Initiative Fiehn et al 2007), which recommends defined procedures for the proper biological material preparation, metabolite extraction procedures and analytical protocols. According to the published rules, suitable number of sample repetitions (biological and technical), plant growth conditions have to be monitored and described, also control of MS parameters during mass spectra registration is required.…”

Section: Instrumentation Applied In Proteomic and Metabolomic Studiesmentioning

confidence: 99%

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Influence of abiotic stresses on plant proteome and metabolome changes

et al. 2013

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Plant responses to abiotic stresses are very complex phenomena with individual characteristics for various species. Abiotic stresses (e.g. drought, salinity, flooding, cold, heat, UV radiation, heavy metals, etc.) strongly affect plant growth and development. It is estimated that they are the cause of more than 50 % of crop yield losses. Abiotic stresses are known to activate a multigene response resulting in the changes in various proteins and primary and secondary metabolite accumulation. Therefore, proteomic and metabolomic approaches are becoming very important and powerful tools used in studying plants' reaction to various stimuli. Precise analysis of proteome and metabolome is essential for understanding the fundamentals of stress physiology and biochemistry. In this review, we focus on recent reports concerned to the influence of abiotic stresses on changes in the level of different protein groups and metabolite classes. Basic information about physicochemical methods applied to qualitative and quantitative analyses of biopolymers and natural products is also briefly presented.

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Section: Discussionmentioning

confidence: 99%

Section: Instrumentation Applied In Proteomic and Metabolomic Studiesmentioning

confidence: 99%

Influence of abiotic stresses on plant proteome and metabolome changes

et al. 2013

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“…As with genomics, databases need to be expanded and methods, including data handling, need to be standardized to facilitate comparison of data (Verpoorte et al, 2008). The need for standardization in metabolomics research has been underlined by the 'metabolomics standards initiative' (Fiehn et al, 2007), which emphasizes that meta-data from metabolomics studies are especially important, as the metabolome is highly responsive to the biological milieu.…”

Section: Discussionmentioning

confidence: 99%

Metabolic fingerprinting reveals differences between northern and southern strains of the cryptic diatomChaetoceros socialis

Huseby

Degerlund

Zingone

et al. 2012

European Journal of Phycology

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Morphology and molecular phylogeny constitute the structural elements of diatom taxonomy. These approaches do not, however, give information on the functioning of taxa. Additional methods to serve a more integrated and wide-ranging taxonomy have therefore been called for. Metabolic fingerprinting is one approach used within the field of metabolomics, often applied in classification of samples. Here we apply metabolic fingerprinting in a taxonomic study of a cryptic diatom species. Strains of the cosmopolitan diatom Chaetoceros socialis from two geographical areas; the north-east Atlantic and Arctic and the Gulf of Naples, were cultivated at three different temperatures; 2.5, 8 and 13 C. The strains from the two different geographical areas exhibited different growth rates as well as different photosynthetic efficiencies. Algal extracts, collected at the end of the growth experiments, were analysed by Ultra-Performance Liquid Chromatography High Resolution Mass Spectrometry. The two groups of strains were separated by principal component analysis of their metabolic fingerprints. Analysis of the data revealed both qualitative and quantitative differences in metabolite markers. These phenotypic differences reinforce differences also found for morphology, phylogenetic markers and growth rates, and point at different adaptive characteristics in organisms living under different temperature regimes.

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“…In 2007 the Metabolomics Standards Initiative (MSI) 2, 3 published a set of seminal papers with recommendations on minimal reporting standards for a number of aspects in metabolomics, summarized in 4. This work built on earlier efforts by the Standard Metabolic Reporting Structure initiative 5 and the Architecture for Metabolomics consortium (ArMet) 6 .…”

Section: Identification Of Challengesmentioning

confidence: 99%

The future of metabolomics in ELIXIR

Rijswijk

Beirnaert

Caron³

et al. 2017

F1000Res

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Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the “Future of metabolomics in ELIXIR” was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases.

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The metabolomics standards initiative (MSI)

Cited by 409 publications

References 14 publications

Influence of abiotic stresses on plant proteome and metabolome changes

Influence of abiotic stresses on plant proteome and metabolome changes

Metabolic fingerprinting reveals differences between northern and southern strains of the cryptic diatomChaetoceros socialis

The future of metabolomics in ELIXIR

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