ReviewNature methods2021
Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices.
Open access · hybridAbstract readReview
In one paragraph
Review in Nature methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 514 papers, 3 of them syntheses that pooled it.
0numbers the graph read from it
0cells of the map it votes in
514citing papers in PubMed, 3 pooled it
55.0field-weighted citation impact, top 1% of its field
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
514 citing papers in PubMed, 3 syntheses or guidelines pooled it, 1,004 citations in OpenAlex.
- Clinical lipidomics in bacterial sepsis: a systematic review of serum and plasma evaluations.Metabolomics : Official journal of the Metabolomic Society · 2026Pooled it
- Systematic Worldwide Review on the Performance of Non-Invasive Exhalation-Based Methods for the Diagnosis of Liver Fibrosis.International journal of environmental research and public health · 2026Pooled it
- Exhaled breath volatile organic compounds (VOCs) detection methods: GC-MS versus eNose in COPD diagnosis-a systematic review and meta-analysis.BMC pulmonary medicine · 2025Pooled it
- Homologous recombination deficiency (HRD) tests for ovarian cancer: a multicenter French phase II study (HERO).BMC cancer · 2025Trial
- Sub-3 μm porous graphitic carbon for highly polar metabolomics: orthogonal selectivity and comparison with HILIC and reversed-phase chromatography.Analytical and bioanalytical chemistry · 2026Article
- Structurally diverse acylsugars on wild tomatillo fruit surfaces.Horticulture research · 2026Article
- Integration of the D-Genome Reshapes Gene Transcription, Chromatin Architecture, and Metabolome of Allohexaploid Wheat, Leading to Enhanced Environmental Adaptability.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Fermentation Quality Divergence of Alfalfa Silage within the Same Batch: Insights from 16S rRNA Sequencing and Untargeted Metabolomics.ACS omega · 2026Article
- Universal charge-tag labelling of undetectable polymers for mass spectrometric characterization.Chemical science · 2026Article
- Redefining reference materials for the evolving metabolomics landscape.Analytical and bioanalytical chemistry · 2026Review
- Mechanisms Underlying Efficient n-Eicosane Degradation and Physiological Adaptation in Rhodococcus erythropolis KB1.Journal of basic microbiology · 2026Article
- An Ultrathin, Permeable, and Battery-Free Monolithically Integrated System for Emotion Sensing and Interaction.Advanced materials (Deerfield Beach, Fla.) · 2026Article
- Serum and Urine Metabolite Profiling Combined With Network Pharmacology to Predict the Renoprotective Mechanism of Huangkui Capsule Against Acute Kidney Injury.Biomedical chromatography : BMC · 2026Article
- PMPIHGLL: predicting metabolite-protein interactions using dual hypergraph convolutional networks and large language models.Briefings in bioinformatics · 2026Article
- Multi-Omics Analysis Reveals Molecular Networks and Key Pathways Associated with Cysteine- and Methionine-Mediated Biosynthesis of Sulfur-Containing Flavor Metabolites inInternational journal of molecular sciences · 2026Article
- Organ Identity Outweighs Geographic Origin in Shaping the Metabolome ofMetabolites · 2026Article
- Organ-Resolved Salicylate-Phenylpropanoid Metabolite Profiling ofMolecules (Basel, Switzerland) · 2026Article
- From Phytochemical Diversity to Clinical Translation: Preparation-Dependent Bioactivity ofInternational journal of molecular sciences · 2026Review
- Application of Metabolomics in the Exploration of Bioactive Compounds and Drug Development from Medicinal Fungi.Metabolites · 2026Review
- Oral Cavity Antibacterial Discovery Pipeline Driven by Advanced Analytical Techniques.Molecules (Basel, Switzerland) · 2026Review
454 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
32 authors at 20 institutions in 12 countries.
Saleh AlseekhMax Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. alseekh@mpimp-golm.mpg.de.ORCID http://orcid.org/0000-0003-2067-5235
Asaph AharoniDepartment of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.ORCID http://orcid.org/0000-0002-6077-1590
Yariv BrotmanDepartment of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel.
Kévin ContrepoisDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-9678-5161
John D'AuriaLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.ORCID http://orcid.org/0000-0002-4865-3938
Jan EwaldDepartment of Bioinformatics, University of Jena, Jena, Germany.ORCID http://orcid.org/0000-0002-9415-2317
Jennifer C EwaldInterfaculty Institute of Cell Biology, Eberhard Karls University of Tuebingen, Tuebingen, Germany.ORCID http://orcid.org/0000-0003-1822-4988
Paul D FraserBiological Sciences, Royal Holloway University of London, Egham, UK.
Patrick GiavaliscoMax Planck Institute for Biology of Ageing, Cologne, Germany.
Robert D HallBU Bioscience, Wageningen Research, Wageningen, the Netherlands.ORCID http://orcid.org/0000-0002-5786-768X
Matthias HeinemannMolecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.ORCID http://orcid.org/0000-0002-5512-9077
Hannes LinkMax Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Jie LuoCollege of Tropical Crops, Hainan University, Haikou, China.
Steffen NeumannBioinformatics and Scientific Data, Leibniz Institute for Plant Biochemistry, Halle, Germany.
Jens NielsenBioInnovation Institute, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-9955-6003
Leonardo Perez de SouzaMax Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.ORCID http://orcid.org/0000-0002-7200-8808
Kazuki SaitoPlant Molecular Science Center, Chiba University, Chiba, Japan.ORCID http://orcid.org/0000-0001-6310-5342
Uwe SauerInstitute for Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.ORCID http://orcid.org/0000-0002-5923-0770
Frank C SchroederBoyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.ORCID http://orcid.org/0000-0002-4420-0237
Stefan SchusterDepartment of Bioinformatics, University of Jena, Jena, Germany.
Gary SiuzdakCenter for Metabolomics and Mass Spectrometry, Scripps Research Institute, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-4749-0014
Aleksandra SkiryczMax Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.ORCID http://orcid.org/0000-0002-7627-7925
Lloyd W SumnerDepartment of Biochemistry and MU Metabolomics Center, University of Missouri, Columbia, MO, USA.ORCID http://orcid.org/0000-0002-4086-663X
Michael P SnyderDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-0784-7987
Huiru TangState Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Human Phenome Institute, Metabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular Phenomics, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0002-7139-2756
Takayuki TohgeDepartment of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan.
Yulan WangSingapore Phenome Center, Lee Kong Chian School of Medicine, School of Biological Sciences, Nanyang Technological University, Nanyang, Singapore.ORCID http://orcid.org/0000-0002-2831-8737
Weiwei WenKey Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China.ORCID http://orcid.org/0000-0002-3413-4766
Si WuDepartment of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
Guowang XuCAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.ORCID http://orcid.org/0000-0003-4298-3554
Nicola ZamboniInstitute for Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.ORCID http://orcid.org/0000-0003-1271-1021
Alisdair R FernieMax Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. fernie@mpimp-golm.mpg.de.ORCID http://orcid.org/0000-0001-9000-335X
Friedrich Schiller University Jena · DEStanford University · USCenter of Plant Systems Biology and Biotechnology · BGCornell University · USETH Zurich · CHBen-Gurion University of the Negev · ILBioInnovation Institute · DKChiba University · JPDalian Institute of Chemical Physics · CNFudan University · CNHainan University · CNHuazhong Agricultural University · CNLeibniz Institute of Plant Biochemistry · DELeibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) · DEMax Planck Institute for Biology of Ageing · DEMax Planck Institute for Terrestrial Microbiology · DEMax Planck Institute of Molecular Plant Physiology · DENanyang Technological University · SGNara Institute of Science and Technology · JPRoyal Holloway University of London · GB
Funding
PreCancer Atlas of Familial Adenomatous PolyposisU2CCA233311 · NCI · STANFORD UNIVERSITY · PI SNYDER, MICHAEL P. · 2018 to 2023
$11.6MStanford Tissue Mapping CenterU54HG010426 · NHGRI · STANFORD UNIVERSITY · PI SNYDER, MICHAEL P. · 2018 to 2021
$5.1MSmall molecule signaling in C. elegansR35GM131877 · NIGMS · BOYCE THOMPSON INST FOR PLANT RESEARCH · PI Frank Clemens Schroeder · 2019 to 2026
$5.0MPortal for Open Computational Metabolomics Tools - Yr 4 U2C SupplementU2CES030167 · NIEHS · UNIVERSITY OF GEORGIA · PI SCHROEDER, FRANK CLEMENS · 2018 to 2021
$4.2MMetabolomics Technologies to Advance Biomedical ResearchR35GM130385 · NIGMS · SCRIPPS RESEARCH INSTITUTE, THE · PI GARY E SIUZDAK · 2019 to 2026
$3.9MBiotechnology and Biological Sciences Research Council BB/P001742/1NCI NIH HHS U2C CA233311NHGRI NIH HHS U54 HG010426NIEHS NIH HHS U2C ES030167NIGMS NIH HHS R35 GM130385NIGMS NIH HHS R35 GM131877
Abstract
Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography- and gas chromatography-mass spectrometry-based metabolomics-derived data.
Indexed as
AnimalsChromatography, LiquidGas Chromatography-Mass SpectrometryHumansMass SpectrometryMetabolomicsRandom AllocationSpecimen HandlingWorkflow
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