Metabolomics - Welcome to the Metabolomics Journal Cover Gallery
September 2024: Volume 20, Number 5
Metabolites in the one-carbon metabolism-related pathways may modulate the DNA methylation levels of CpG-sites at specific loci and, in turn, epigenetically regulate the expression of adipose tissue transcripts involved in obesity and insulin resistance
August 2024: Volume 20, Number 4
The global incidence of type 2 diabetes has surged over the last two decades, affirming its epidemic status. Despite treatment administration/adherence, some individuals still experience poorly controlled diabetes, characterized by hyperglycemia and an increased risk of developing co-morbidities such as cardiovascular disease, tuberculosis, kidney damage, etc. In this 1H-NMR metabolomics study, we provide the first characterization of metabolic alterations in poorly controlled type 2 diabetes, identifying metabolite markers for probable causes, suggesting improved treatment strategies, and proposing methods for monitoring disease progression and treatment compliance.
July 2024: Volume 20, Number 4
This study analyzed the correlation between dietary habits and plasma lipid concentrations in a Japanese population. It revealed that various lipid subclasses responded to dietary habits, including known associations such as the link between seafood consumption and omega-3 fatty acids, and dairy consumption and odd-carbon-number fatty acids. These findings provide valuable insights into the connection between dietary habits and health outcomes.
June 2024: Volume 20, Number 3
The front cover features the winner of the 2024 Best Review Award. This award is for the best review article based on downloads during 2023. Congratulations to Xinsong Du and colleagues for their excellent work!
May 2024: Volume 20, Number 3
The front cover features the winner of the 2024 Best Article Award. This award is for the best original article based on downloads during 2023. Congratulations to Roberto Bonelli and colleagues for their excellent work!
March/April 2024: Volume 20, Number 2
Meta-analysis in metabolomics can be challenging due to differences in study design, collection procedures and technologies between cohorts. During our investigation, we identified potential solutions to increase the impact of metabolomic meta-analyses of human health, including increased reporting standards and opportunities for novel tool development in the field.
February 2024: Volume 20, Number 1
Global metabolic patterns predict metabolism-related diseases like diabetes before their manifestation. The diabetic closeness of metabolism can be predicted even in seemingly healthy individuals using altered metabolic patterns. Machine learning models trained on metabolomics data can raise an early alert for vulnerable individuals and can be used for early diagnostic, prognostic, and treatment of metabolic disorders.
January 2024: Volume 20, Number 1
Lactic Acid Bacteria (LAB) are powerhouses of food technology, used in a range of products including bread, cheese, yogurts, meat and wine. In this study we show how understanding metabolism of LAB, and potentially directing it, could lead to new products and applications with benefits for the food industry and the consumer.
December 2023: Volume 19, Number 12
This study investigates potential biomarkers for lower urinary tract symptoms using a metabolomics approach, demonstrating the role of advanced statistical methods in biomarker identification. The Northern Lights reflect the nature of chance findings in research, emphasizing the necessity for robust statistical analysis to discern true patterns from randomness.
November 2023: Volume 19, Number 11
This review covers all aspects of sterol and lipid metabolism in bees. This area is of increasing interest as the importance of the role of pollinators in crop production and protecting plant biodiversity is becoming more widely understood. We identify a number of unexpected results and knowledge gaps that may be filled in the next decade.
October 2023: Volume 19, Number 10
By applying metabolic profiling LC-MSn techniques, we provided evidence for QTLs for polyphenols in red raspberry. These QTLs represent areas of the genome that influence the accumulation of these health beneficial components and provide genetic markers that could accelerate breeding of new varieties.
September 2023: Volume 19, Number 9
Monitoring and modeling glutamine metabolic pathways is significant due to its role in cell metabolism. Innovative label-free methods can redefine metabolic biosensing and advance metabolomics research in live cells.
August 2023: Volume 19, Number 8
This investigation shows that BAYESIL can be used to automatically annotate 1H NMR spectra obtained from the analyses of limited sample volumes, and that this approach can be applied to identify biological variations in African elephant serum.
July 2023: Volume 19, Number 7
Soldiers selected for Special Forces training had higher levels of metabolites associated with healthier diets, better physical performance, and resistance to oxidative stress, while non-selected candidates had higher levels of metabolites indicating elevated oxidative stress.
June 2023: Volume 19, Number 6
Untargeted LCMS and GCMS-based metabolomics has revealed the dynamics of the white asparagus metabolome. Using advanced analytical and statistical tools the detected metabolites were clustered to form a network (overlay) and the behavior of the clustered metabolites allowed the evaluation of the impact of genotype and environment/seasonal effects.
May 2023: Volume 19, Number 5
The front cover features the winner of the 2023 Best Review Award. This award is for the best review article based on downloads during 2022. Congratulations to Katrice, Bal and mQACC for their excellent work!
April 2023: Volume 19, Number 4
The front cover features the winner of the 2023 Best Article Award. This award is for the best original article based on downloads during 2022. Congratulations to Iva and colleagues for their excellent work!
Roberts, I., Muelas, M.W., Taylor, J.M., Davison, A.S., Xu, Y., Grixti, J.M., Gotts, N., Sorokin, A., Goodacre, R. & Kell, D.B. (2022) Untargeted metabolomics of COVID-19 patient serum reveals potential prognostic markers of both severity and outcome. Metabolomics 18: 6.
March 2023: Volume 19, Number 3
A model that describes sources of variation in LC-MS-based untargeted metabolomics data is used to assist in building data curation pipelines. New quality control (QC) practices based on the use of pooled QC samples analyzed as technical replicates and as process replicates are introduced to assess the analytical quality of data.
February 2023: Volume 19, Number 2
This study evaluated 61 LC-HRMS metabolomics data processing software based on criteria related to FAIR Principles for Research Software. Our results provide an evaluation guideline that can also be used to assess the FAIRness of other multi-omics data processing software.
January 2023: Volume 19: Number 1
NMR-based metabolomics demonstrated that maternal exposure to microplastics results in a reduction in glucose and lysine in the mouse placenta.
December 2022: Volume 18: Number 12
The application of Blooms cognitive domain in the development and delivery of education and training in metabolomics.
November 2022: Volume 18: Number 11
There are similarities that are both instructive in understanding the biology of renal disease and calcium oxalate stones and there are similarities that obfuscate the understanding of the underlying biology.
This paper uses the power of metabolomics to better understand the biological similarities and differences in these diseases in cats.
October 2022: Volume 18: Number 10
Single Cell Metabolism Techniques.
Individual cells can be analyzed either after nanoscale extraction and ionization via various methods, or directly by confocal microscopy using e.g. optical or Raman spectroscopy.
Redrawn and adapted from Duncan et al. (2019). Advances in mass spectrometry based single-cell metabolomics. Analyst 144, 782-79 and Lita, A., et al. (2019). Toward Single-Organelle Lipidomics in Live Cells. Anal Chem 91, 11380-11387
We thank E. He, from Medical Arts of the National Institutes of Health for help with the cover figure.
September 2022: Volume 18: Number 9
A novel ensemble machine learning approach is applied to predict lung cancer patient survival from tumor core biopsy metabolomic data. Increased relative abundance of guanine, choline, and creatine corresponded with shorter Overall Survival (OS), while increased leucine and tryptophan corresponded with shorter Progression-Free Survival (PFS).
August 2022: Volume 18: Number 8
PeakForest.org, an open-source FAIR infrastructure supporting MS and NMR experimental spectral metadata storage, information curation, integration into data processing pipelines and spectral data sharing across laboratories.
July 2022: Volume 18: Number 7
Here, we show the use of Fusarium as a model system to evaluate the chemical production of microbes by utilizing the full capabilities of PLS with microbial-specific modeling that considers incubation days, media culture availability, and growth rate in solid media
June 2022: Volume 18: Number 6
The metabolomics quality assurance and quality control consortium (mQACC) is enabling the identification, development, prioritization, and promotion of suitable reference materials (RMs) to be used in quality assurance (QA) and quality control (QC) for MS-based untargeted metabolomics and lipidomics. RMs are critical QC tools to assure standardization, comparability, repeatability and reproducibility for untargeted data analysis, interpretation, and to compare data within and across studies and across multiple laboratories.
May 2022: Volume 18: Number 5
The front cover features the winner of the 2022 Best Review Award.
This award is for the best review article based on downloads during 2021.
Congratulations to Biswa for his excellent work:
April 2022: Volume 18: Number 4
The front cover features the winner of the 2022 Best Article Award. This award is for the best original article based on downloads during 2021.
Congratulations to the authors for their excellent work:
March 2022: Volume 18: Number 3
Lipid traffic analysis was used to investigate the effect of the paternal nutrition on the lipid metabolism of the offspring. Our worked showed that both sperm and seminal plasma contribute to paternal nutritional programming.
February 2022: Volume 18: Number 2
In this study, we integrated in vitro metabolomics into a 96-well high-throughput screening platform, employing only 50,000 hepatocytes of HepaRG per well. The intracellular metabolome was measured using optimised high-resolution spectral-stitching nanoelectrospray direct infusion mass spectrometry, which demonstrated good sensitivity and repeatability, allowing for subsequent application of this workflow to study the effect of cadmium chloride on the HepaRG metabolome. The approach presented here demonstrates that metabolomics is able to complement other high-throughput assays to drive animal-free toxicity testing, and could be applied to relevant case studies.
The cover image was generated using BioRender (BioRender.com).
January 2022: Volume 18: Number 1
Glyphosate contaminated grain feeding of dairy cows introduces odd-chain fatty acids with branched chain amino acids into metabolism via the TCA cycle and disrupts mitochondrial proton tunneling by high deuterium metabolic water production with health compromising effects in the human consumer.
December 2021: Volume 17: Number 12
Lipid extraction using fresh-frozen samples with ultrasound assistance provides the most original lipid composition and gave a relatively high lipid content.
November 2021: Volume 17: Number 11
IonFlow, a standardised Galaxy workflow for ionomics, was used to study elemental profiling data from the yeast S. cerevisiae BY4741.
October 2021: Volume 17: Number 10
Comparison between SBSE and SPME on sampling tomato soup metabolites on reproducibility, composition, and predictive ability of sensoric properties.
September 2021: Volume 17: Number 9
Infrared matrix-assisted laser desorption electrospray ionization mass spectrometry imaging (IR-MALDESI MSI) analysis of human bladder samples provides spatially resolved metabolomic profiles, which reveals tumor heterogeneity and predicts sample pathology using novel statistical methods.
August 2021: Volume 17: Number 8
The article by Alger et al. in this issue considers the problem of determining which of alternate possible candidate models of tricarboxylic acid cycle metabolism, shown schematically in the cover figure, best fits experimentally-acquired 13C NMR data in metabolic studies that use 13C isotopic tracers.
Alger, J.R., Minhajuddin, A., Sherry, A.D. & Malloy, C.R. (2021) Analysis of steady-state carbon tracer experiments using akaike information criteria. Metabolomics 17: 61
July 2021: Volume 17: Number 7
Environmental factors influence skin microbiota. As a result, microorganisms release volatile organic compounds (VOCs) that are synthesized by different metabolism pathways. These VOCs are involved in interaction processes between skin microbiota and the environment.
June 2021: Volume 17: Number 6
In response to the growing interest in metabolomic epidemiology, the Metabolomics Society has established the Metabolomic Epidemiology Task Group. The objective of the task group is to promote the growth and understanding of metabolomic epidemiology as an independent research discipline. This includes establishing a network of collaborations to facilitate the coordinated development of the required infrastructure and resources to support the lifecycle of metabolomic epidemiology research as illustrated in the cover image.
May 2021: Volume 17: Number 5
The front cover features the winner of the 2021 Best Review Award.
This award is for the best review article based on downloads during 2020. Congratulations to the authors for their excellent work:
A Word Cloud is created from Table 1 of this review article that depicts terms enriched for metabolomics, tools, softwares, and resources that appeared in 2020. The WordCloud was created using WordItOut https://worditout.com/
April 2021: Volume 17: Number 4
The front cover features the winner of the 2021 Best Article Award.
This award is for the best original article based on downloads during 2020. Congratulations to the authors for their excellent work:
March 2021: Volume 17: Number 3
The image illustrates the phases of the study, where metabolomics verified that the metabolic profile of obese dogs differs from healthy dogs. In addition, after weight loss the metabolites showed similarities with dogs in ideal body condition, highlighting their importance.
Metabolomics 17: 27, Serum metabolomics analysis reveals that weight loss in obese dogs results in a similar metabolic profile to dogs in ideal body condition
February 2021: Volume 17: Number 2
The present study provides information regarding sex and race variations of cerebrospinal fluid (CSF) metabolite levels in healthy individuals. CSF metabolites within the tryptophan, tyrosine, and purine pathways were measured using a targeted electrochemistry-based metabolomics platform and univariate and multivariate analyses were used to identify differences between men and women and African American and white participants. The study highlights the importance of understanding sex and race differences in healthy individuals as those differences could influence health trajectories and have implications for the effectiveness of treatments.
Metabolomics 17:13, Sex and race differences of cerebrospinal fluid metabolites in healthy individuals.
January 2021: Volume 17: Number 1
This study has highlighted altered glycerophospholipids in plasma samples taken at 20 weeks of gestation, from women who delivered a small for gestational age baby.
Metabolomics 17:5, Glycerophospholipid and detoxification pathways associated with small for gestation age pathophysiology: discovery metabolomics analysis in the SCOPE cohort.
December 2020: Volume 16: Number 12
1H NMR metabolomics seems to be a valuable tool in forensic sciences. An in-depth programme of collaborative exercises are needed to standardize ad-hoc protocols before its use in courts.
Metabolomics 16:118, Forensic NMR metabolomics: one more arrow in the quiver
November 2020: Volume 16: Number 11
In previous epidemiological studies, certain classes of plasma sphingolipids, particularly ceramides, were associated with risk of cardiovascular diseases. Our results from a large-scale sphingolipidomic analysis of a prospective cohort do not support the hypothesis that ceramide concentrations are linked to CVD risk, but suggest that other classes of sphingolipids may affect CVD risk.
Metabolomics 16:89, Plasma sphingolipids and risk of cardiovascular diseases: a large-scale lipidomic analysis
October 2020: Volume 16: Number 10
SWATH Data independent acquisition with different Q1 windows sizes enables comprehensive quantitative analysis at MS1 and MS2 levels and qualitative analysis of complex samples.
Metabolomics 16:71, SWATH-MS for metabolomics and lipidomics: critical aspects of qualitative and quantitative analysis
September 2020: Volume 16: Number 9
Advanced metabolomics studies require sophisticated analytical instruments such as GC-MS, LC-MS, NMR and hyphenated techniques. GC-MS is probably the most widely used analytical technique in metabolomics laboratories. In this paper, different aspects of sample collection, preparation, analysis and data interpretation involved in the untargeted urinary metabolomics studies using GC-MS are presented. Although, a number of protocols have been published in this regards, users are advised to pay attention to details and optimise every step of the adopted method in house. Areas of compound identification and data interpretation may benefit from optimisation in particular.
Metabolomics 16:66, A review of strategies for untargeted urinary metabolomic analysis using gas chromatography–mass spectrometry
August 2020: Volume 16: Number 8
Conidiospore germination represents an excellent target for novel and improved plant protection agents, and within this context, untargeted metabolomics could ideally serve as a hypothesis-generation tool. The hydrolysis of intracellular trehalose during the conidiospore germination of Aspergillus nidulans marks the end of their dormancy, and it is followed by the rapid biosynthesis of glycerol, which results in major early osmotic changes.
Metabolomics 16:79, Untargeted metabolomics as a hypothesis-generation tool in plant protection product discovery: Highlighting the potential of trehalose and glycerol metabolism of fungal conidiospores as novel targets
July 2020: Volume 16: Number 7
By comparing the classic CPMG approach to the LED, using ultrafiltration as a baseline, we aimed to determine a viable untargeted plasma NMR metabolomics protocol for large sample cohorts. Optimization steps included the usage of a quantitative internal standard and an improved method (peak picking) for extracting useful spectral information compared to the conventional one (equidistant bucketing). Our results show an overall improved performance in sample group separation compared to the conventional approach. The metabolite quantitative capabilities of the proposed method are also presented.
Metabolomics 16:64, A comparison of high-throughput plasma NMR protocols for comparative untargeted metabolomics
June 2020: Volume 16: Number 6
The front cover features the winner of the 2020 Best Review Award. This award is for the best review based on downloads during 2019.
Congratulations to the authors for their excellent work: Mendez, K.M., Pritchard, L., Reinke, S.N. & Broadhurst, D.I. (2019) Toward collaborative open data science in metabolomics using Jupyter Notebooks and cloud computing. Metabolomics 15:125, Toward collaborative open data science in metabolomics using Jupyter Notebooks and cloud computing
May 2020: Volume 16: Number 5
The front cover features the winner of the 2020 Best Article Award. This award is for the best original article based on downloads during 2019.
Congratulations to the authors for their excellent work: King, M., Mullin, L.G., Wilson, I.D., Coen, M., Rainville, P.D., Plumb, R.S., Gethings, L.A., Maker, G. & Trengove, R.
Metabolomics 15:17, Development of a rapid proiling method for the analysis of polar analytes in urine using HILIC-MS and ion mobility enabled HILIC-MS
April 2020, Volume 16: Number 4
The figure on the front cover shows the mapping of the MetaboHub lipid library onto the Human metabolic network; by using chemical ontologies, it was possible to map more lipids (orange nodes) than by regular exact mapping (green nodes).
Improving lipid mapping in Genome Scale Metabolic Networks using ontologies
March 2020, Volume 16: Number 3
The effect of glufosinate to inhibit a key enzyme involved in nitrogen metabolism, glutamine synthetase (GS). GS coupling with glutamine oxoglutarate aminotransferase (GOGAT) forms a principal mechanism to incorporate ammonia (NH4+) into living organisms (GS/GOGAT) pathways. Inhibition of GS disrupts the pathway and subsequently leads to an accumulation of toxic ammonia. Alternative reactions for the biosynthesis and degradation of glutamate are catalyzed by glutamate dehydrogenase (GDH) under a low NH4+ condition. NB: Arrows crossed by double parallel lines indicate interrupted reactions.
February 2020, Volume 16: Number 2
DESI-MS imaging technology coupled with the new annotation engine-METASPACE will serve as powerful tools to provide insight on fundamental pathways in diabetic kidney disease.
January 2020, Volume 16: Number 1
Integrative analysis of multiple data sets by PE-ASCA model provides an improved understanding of the common and distinct variation in response to different experimental factors.
Common and distinct variation in data fusion of designed experimental data
December 2019, Volume 15: Number 12
Neurocognitive deficits affect nearly 50% of infants who underwent surgery for complex congenital heart disease. Emerging evidence suggests a correlation between perioperative events, such as hypoxemia and hypothermia, and adverse neurodevelopmental outcomes. Discovery of potential biomarkers of brain damage is of paramount importance to discriminate newborns at higher risk of worse post-operative outcome. In this paper we present an innovative experimental design that allow the identification of perturbed metabolic pathways limiting drug interference in the analysis. Our findings suggest changes in the kynurenine pathway of tryptophan degradation.
November 2019, Volume 15: Number 11
Insulin resistance is a multifaceted disorder and is at the center of many obesity-related diseases. By integrating targeted lipidomics and shotgun metagenomic sequencing, we highlight potential links between a proinflammatory gut microbiome and host ceramide levels, which may contribute to impaired Glucose homeostasis.
October 2019, Volume 15: Number 10
A machine learning model was established using LC-MS-based metabolomic data for discrimination of chrysanthemum cultivars.
September 2019, Volume 15: Number 9
The benefit of MS and NMR data combination using chemometrics for fungi biotransformation reactions optimization.
Processing of NMR and MS metabolomics data using chemometrics methods: a global tool for fungi biotransformation reactions monitoring. Metabolomics 15: 107
August 2019, Vol. 15: Number 8
Irritable bowel syndrome (IBS) is a debilitating functional gut disorder that is increasing in prevalence worldwide despite its poorly understood aetiology. In this work, we identify a panel of urinary metabolites that distinguish IBS from healthy controls that may avoid the need for invasive colonoscopy procedures while revealing new insights into disease pathophysiology, such as accelerated collagen degradation and epithelial cell turn-over.
July 2019, Volume 15: Number 7
Metabolomics goes beyond the last frontier: Thanatometabolomics after "The Disintegration of the Persistence of Memory" from Salvatore Dali. In tribute to the 30th anniversary of Dali's Death, we let the NMR data (NOESY FID, 1D NOESY spectra, 2D COSY spectrum) of our mouse study enter the realm of one of his painting where Biophysics meet Metaphysics.
June 2019, Volume 15: Number 6
The front cover features the winner of the 2019 Best Review Award. This award is for the best review based on downloads during 2018.
Congratulations to the authors: Broadhurst, D., Goodacre, R., Reinke, S.N., Kuligowski, J., Wilson, I.D., Lewis, M. & Dunn, W.B. (2018) Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies. Metabolomics 14: 72
NEWS: the 2019 Metabolomics publication awards
May 2019, Volume 15: Number 5
The front cover features the winner of the 2019 Best Article Award. This award is for the best original article based on downloads during 2018.
Congratulations to the authors: Pan, D., Lindau, C., Lagies, S., Wiedemann, N. & Kammerer, B. (2018) Metabolic profiling of isolated mitochondria and cytoplasm reveals compartment-specific metabolic responses. Metabolomics 14: 59
NEWS: the 2019 Metabolomics publication awards
April 2019, Volume 15: Number 4
Environmental lipidomics may help understand the severity and distribution of a disease leading to mass mortality of aquatic wildlife in South Africa. Metabolomics 15:38
March 2019, Volume 15: Number 3
The calculation of similarity is an important tool to reveal variability between samples and spectra and can be used to verify data sets and improve alignment or binning procedures. With differential spectroscopy marker compounds are easily discovered. The methods can be seen as an important addition to the routine procedures of metabolomics experiments. Metabolomics 2019, 15:39
February 2019, Volume 15: Number 2
A rapid HILIC-MS method, combined with ion mobility spectrometry, for high throughput metabotyping. Metabolomics 2019, 15:17
January 2019, Volume 15: Number 1
HPLC-PDA-MS metabolite profiling was applied to study the effect of changing climate conditions on the metabolism of blackcurrants within a controlled growth system environment. Clear gradients of metabolite change were observed as the growth temperature was increased from 12-to-18-to-24oC.
Phenylalanine, a key polyphenolic compound pre-cursor, was up-regulated as the growth temperature increased, which correlated with an increase in concentration across the majority of flavonoids. Interestingly, delphinidin-3-O-rutinoside and cyanidin-3-O-rutinoside, the most abundant blackcurrant anthocyanins, showed a peak in concentration at the intermediate growth temperature and under ambient conditions.
High levels of accumulation of the most abundant anthocyanins in ambient (outdoor) conditions, was predicted to be associated with greater levels of UV-B exposure than plants would be subjected to under glass or within polytunnels.
Metabolite profiling approaches will aid our understanding of the effect that future climate changes will likely have upon our fresh fruit produce and will assist breeders in developing fruits that are better adapted to cope with such changes.
The authors gratefully acknowledge Thermo Fisher for their permission to use the image of the LTQ Series Orbitrap Mass Spectrometer system used in the cover art. Metabolomics 2019, 15:12.