Article
Chemistry, Analytical
Yoann Gloaguen, Jennifer A. Kirwan, Dieter Beule
Summary: NeatMS is a machine learning tool based on convolutional neural networks that reduces false peaks in untargeted metabolomics. It includes a pre-trained model and functions for training new models, improving peak curation, and facilitating the analysis of large-scale experiments.
ANALYTICAL CHEMISTRY
(2022)
Article
Medicine, General & Internal
Rintaro Saito, Masahiro Sugimoto, Akiyoshi Hirayama, Tomoyoshi Soga, Masaru Tomita, Toru Takebayashi
Summary: Large-scale metabolomic studies are common, but there is less focus on the reliability of uncharacterized peaks in untargeted metabolomics data. This study tested criteria to assess the reliability of uncharacterized peaks and identified some reliable peaks potentially related to important physiological processes like disease progression.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Biochemical Research Methods
Sara Forcisi, Franco Moritz, Christopher J. Thompson, Basem Kanawati, Jenny Uhl, Carlos Afonso, Chantal D. Bader, Aiko Barsch, Berin A. Boughton, Rosalie K. Chu, Justine Ferey, Francisco Fernandez-Lima, Celine Gueguen, Dimitri Heintz, Mario Gomez-Hernandez, Kyoung-Soon Jang, Nikolas Kessler, Vaughn Mangal, Rolf Mueller, Ryo Nakabayashi, Edith Nicol, Simone Nicolardi, Magnus Palmblad, Ljiljana Pasa-Tolic, Jacob Porter, Isabelle Schmitz-Afonso, Jong Bok Seo, Eduardo Sommella, Yuri E. M. van der Burgt, Claire Villette, Matthias Witt, Ashley Wittrig, Jeremy J. Wolff, Michael L. Easterling, Frank H. Laukien, Philippe Schmitt-Kopplin
Summary: Ultrahigh resolution mass spectrometry combined with direct infusion ionization is a fast and accurate method for untargeted metabolomics analysis. Fourier transform ion cyclotron resonance mass spectrometers play an important role in studying complex chemical systems by enabling unambiguous molecular formula assignment. Through a comparison study involving 17 laboratories worldwide, we found that five laboratories showed comparable and representative performances, providing a reference for future ring trials on blood plasma.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemical Research Methods
Arnaud M. Wolfer, Goncalo D. S. Correia, Caroline J. Sands, Stephane Camuzeaux, Ada H. Y. Yuen, Elena Chekmeneva, Zoltan Takats, Jake T. M. Pearce, Matthew R. Lewis
Summary: peakPantheR is an R package designed for targeted extraction and integration of annotated features from LC-MS profiling experiments. It utilizes chromatographic and spectral databases as well as prior information of sample matrix composition to generate interpretable metabolic phenotypic datasets and power workflows for real-time data quality assessment.
Review
Medicine, Research & Experimental
Tomislav Caval, Frederico Alisson-Silva, Flavio Schwarz
Summary: Cell surface glycosylation plays important roles in cancer, including impaired signaling, metastasis, and evading immune responses. Several glycosyltransferases, such as B3GNT3, FUT8, and B3GNT2, have been linked to reduced anti-tumor immune responses. There is a need for unbiased methods to investigate cell surface glycosylation. The field of glycoproteomics has advanced to allow large-scale profiling of intact glycopeptides for discovering new targets against cancer.
Article
Nutrition & Dietetics
Sarah Brajkovic, Nils Rugen, Carlos Agius, Nicola Berner, Stephan Eckert, Amirhossein Sakhteman, Claus Schwechheimer, Bernhard Kuster
Summary: Plants are crucial for sustainable global food supply, but the understanding of crop proteomes is limited. The presence of secondary metabolites in crop plants has hindered proteomic analyses, requiring individually optimized protein extraction protocols. In this study, a universal protein extraction protocol combined with an automated SP3 protocol and optimized micro-LC-MS/MS conditions was developed for high-quality proteomic analysis of crop plants. The workflow was successfully applied to analyze the proteomes of mature tomato fruits, demonstrating its robustness and potential for large-scale projects mapping crop tissue proteomes.
Article
Multidisciplinary Sciences
Taiyun Kim, Owen Tang, Stephen T. Vernon, Katharine A. Kott, Yen Chin Koay, John Park, David E. James, Stuart M. Grieve, Terence P. Speed, Pengyi Yang, Gemma A. Figtree, John F. O'Sullivan, Jean Yee Hwa Yang
Summary: A new computational workflow is developed to remove unwanted data variation while preserving biologically relevant information in large scale metabolomics studies.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Frantisek Malinka, Ashkan Zareie, Jan Prochazka, Radislav Sedlacek, Vendula Novosadova
Summary: Aligning and combining individually preprocessed batches in large-scale multi-batch experiments is a challenging task. We present two methods and demonstrate that retention order swaps are not rare in untargeted LC-MS data.
Article
Chemistry, Analytical
Xian Ding, Fen Yang, Yanhua Chen, Jing Xu, Jiuming He, Ruiping Zhang, Zeper Abliz
Summary: A novel data normalization and integration method, Norm ISWSVR, is proposed in this study to effectively remove systematic errors and improve the statistical power and quality of metabolomics data. Experimental results show that this method can decrease cross-validated relative standard deviation, increase the correlation of quality control samples, improve the classification accuracy of biomarkers, and is compatible with quantitative data.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Ken H. Liu, Choon M. Lee, Grant Singer, Preeti Bais, Francisco Castellanos, Michael H. Woodworth, Thomas R. Ziegler, Colleen S. Kraft, Gary W. Miller, Shuzhao Li, Young-Mi Go, Edward T. Morgan, Dean P. Jones
Summary: The study introduces a novel method in which xenobiotic metabolites are enzymatically generated and identified using high-resolution mass spectrometry, offering a new approach for exposomics research.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Nanna Vestergaard, Lasse Jorgensen Cehofski, Alexander Norgard Alsing, Anders Kruse, Jonas Ellegaard Nielsen, Anders Schlosser, Grith Lykke Sorensen, Bent Honore, Henrik Vorum
Summary: This study found that retinal artery occlusion (RAO) results in the upregulation of multiple inflammatory proteins and the downregulation of proteins involved in visual pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Zhuo Wang, Hsin-Yao Wang, Chia-Ru Chung, Jorng-Tzong Horng, Jang-Jih Lu, Tzong-Yi Lee
Summary: This study successfully identified associations of methicillin resistance with demographics and mass spectrometry data, and developed a machine-learning-based predictive model that can predict methicillin resistance in both discovery and replication populations, with an AUC >0.85. The predictive model enables early detection of methicillin resistance in patients with Staphylococcus aureus infection, highlighting potential candidates for improving treatment efficacy and prescription decisions.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Chemistry, Analytical
Teresa S. McMillen, Andrew Leslie, Kenneth Chisholm, Susanne Penny, Jeffrey Gallant, Alejandro Cohen, Arik Drucker, James P. Fawcett, Devanand M. Pinto
Summary: This study presents a comprehensive and quantitatively robust method for metabolomic analysis, using HILIC and RP stationary phases combined with positive and negative electrospray ionization. The method allows for complete analysis of a single sample in as little as 40 minutes and has been validated with clinical samples.
ANALYTICA CHIMICA ACTA
(2023)
Article
Oncology
Cheng-Le Zhuang, Qian-Tong Dong, Han-Ping Shi, Feng-Min Zhang, Xin Luo, Wen-Bin Wang, Zhen Yu, Xiao-Lei Chen, Su-Lin Wang
Summary: The study compared the characteristics and prognostic value of cachexia and sarcopenia in patients after gastrectomy, revealing that they have different clinical characteristics and prognostic values, with different impacts on the survival of patients at different stages.
ANNALS OF SURGICAL ONCOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Daniel Demus, Annemieke Naber, Viktoria Dotz, Bas C. Jansen, Marco R. Bladergroen, Jan Nouta, Eric J. G. Sijbrands, Mandy Van Hoek, Simone Nicolardi, Manfred Wuhrer
Summary: This study evaluated the role of apo-CIII in lipid metabolism using a new high-throughput workflow. The results support the hypothesis that apo-CIII sialylation may regulate triglyceride clearance, and the association with triglyceride levels was found to be independent of body mass index.
FRONTIERS IN CHEMISTRY
(2021)
Article
Endocrinology & Metabolism
Mads N. Thomsen, Mads J. Skytte, Amirsalar Samkani, Martin H. Carl, Philip Weber, Arne Astrup, Elizaveta Chabanova, Mogens Fenger, Jan Frystyk, Bolette Hartmann, Jens J. Holst, Thomas M. Larsen, Sten Madsbad, Faidon Magkos, Henrik S. Thomsen, Steen B. Haugaard, Thure Krarup
Summary: The study indicates that moderate carbohydrate restriction in individuals with type 2 diabetes can improve glycemic control, reduce circulating and intrahepatic triglyceride levels beyond the effects of weight loss itself. This improvement may be attributed to differences in protein and fat intakes, and the quality of dietary macronutrients.
Editorial Material
Nutrition & Dietetics
Mads F. Hjorth, Arne Astrup
JOURNAL OF NUTRITION
(2022)
Article
Pediatrics
Michelle D. Pang, Hulya Yilmaz, Arne Astrup, Ellen E. Blaak, Marleen A. Baak
Summary: This study found a positive association between changes in body mass index of parents and their children during a weight-maintenance family-based dietary intervention. Including parents in family-based dietary approaches for weight management of their children is effective, regardless of the child's weight status.
Article
Nutrition & Dietetics
Nicole Jacqueline Jensen, Helena Zander Wodschow, Mads Juul Skytte, Amirsalar Samkani, Arne Astrup, Jan Frystyk, Bolette Hartmann, Jens Juul Holst, Thomas Meinert Larsen, Sten Madsbad, Faidon Magkos, Kamilla Woznica Miskowiak, Steen Bendix Haugaard, Thure Krarup, Jorgen Rungby, Mads Norvin Thomsen
Summary: The study evaluated the effects of dietary carbohydrate restriction on health-related quality of life (HRQoL) and cognition in individuals with type 2 diabetes. The results showed that weight loss improved physical health, while the amount of carbohydrates, protein, and fat in the diet may affect mental health and cognition.
CLINICAL NUTRITION
(2022)
Letter
Endocrinology & Metabolism
Mads N. Thomsen, Arne Astrup, Jens J. Holst, Sten Madsbad, Faidon Magkos, Steen B. Haugaard, Thure Krarup
Article
Nutrition & Dietetics
Nikita Misella Hansen, Peder Berg, Marianne Rix, Manan Pareek, Jens Leipziger, Anne -Lise Kamper, Arne Astrup, Mads Vaarby Sorensen, Louise Salomo
Summary: The objective of this study was to evaluate the effects of the New Nordic Renal Diet (NNRD) on metabolic acidosis and uremic toxins in patients with moderate CKD. The results showed that one week of NNRD effectively improved metabolic acidosis and reduced urinary excretion of uric acid and uremic toxins. These results provide encouragement for further investigations on the long-term renal protection effects of NNRD in patients with CKD.
JOURNAL OF RENAL NUTRITION
(2023)
Review
Nutrition & Dietetics
Silvia Berciano, Juliana Figueiredo, Tristin D. Brisbois, Susan Alford, Katie Koecher, Sara Eckhouse, Roberto Ciati, Martin Kussmann, Jose M. Ordovas, Katie Stebbins, Jeffrey B. Blumberg
Summary: Precision Nutrition (PN) is an individualized approach to nutritional recommendations based on various factors. It recognizes that healthful diets can differ between individuals and that health and dietary responses change over time. Despite concerns about the scientific support for current products and services, PN shows promise in improving healthspan and reducing healthcare costs. Advancing PN will require investment in multidisciplinary collaborations, engagement of healthcare professionals and payers, and system-wide collaboration to advocate for evidence-based PN and regulatory support.
FRONTIERS IN NUTRITION
(2022)
Article
Biochemistry & Molecular Biology
Helena Deris, Petra Tominac, Frano Vuckovic, Arne Astrup, Ellen E. Blaak, Gordan Lauc, Ivan Gudelj
Summary: The aberrant plasma protein glycosylation associated with various diseases was studied by analyzing glycomes from participants of the Diogenes study. Significant alterations in glycan structures were observed 8 weeks after the low-calorie diet, but these effects were nullified during the weight-maintenance diets period.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Nutrition & Dietetics
Philip Weber, Mads N. N. Thomsen, Mads Juul Skytte, Amirsalar Samkani, Martin Hansen Carl, Arne Astrup, Jan Frystyk, Jens J. J. Holst, Bolette Hartmann, Sten Madsbad, Faidon Magkos, Thure Krarup, Steen B. B. Haugaard
Summary: In a real-life setting, the benefits of a fully provided, hypocaloric, carbohydrate-reduced high-protein diet were not maintained when individuals with type 2 diabetes switched to self-prepared diets aiming for the same nutritional goals for 6 months.
Article
Medicine, General & Internal
Sebastien Bailly, Odile Fabre, Mallory Cals-Maurette, Laurent Pantagis, Robin Terrail, Remy Legrand, Arne Astrup, Jean-Louis Pepin
Summary: This study assessed the impact of a weight-loss program on OSA risk and daytime sleepiness. The results showed that the program led to significant weight loss and improvement in both OSA and subjective daytime sleepiness.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Chemistry, Analytical
Anton N. Kozhinov, Alex Johnson, Konstantin O. Nagornov, Michael Stadlmeier, Warham Lance Martin, Loic Dayon, John Corthesy, Martin Wuhr, Yury O. Tsybin
Summary: In multiplexed quantitative proteomics based on tandem mass spectrometry (MS2), complement reporter ion approaches (TMTc and TMTproC) have been developed to solve the ratio-compression problem of conventional MS2-level approaches. However, current mass resolution and scan speeds of OrbitrapTM instruments limit the quantification of complement reporter ions to a limited number of channels. This study demonstrates the feasibility of resolving 6.32 mDa-spaced complement reporter ions using a FusionTM LumosTM Orbitrap instrument with extended acquisition modes, and achieving shotgun proteomics-compatible scan rates through a super-resolution mass spectrometry approach using the least-squares fitting (LSF) method.
ANALYTICAL CHEMISTRY
(2023)
Article
Cell Biology
Jaime Santo-Domingo, Steve Lassueur, Antonio Nunez Galindo, Pilar Alvarez-Illera, Silvia Romero-Sanz, Elena Caldero-Escudero, Sergio de la Fuente, Loic Dayon, Andreas Wiederkehr
Summary: Glucose sensing in pancreatic D-cells relies on mitochondrial signals and oxidative phosphorylation to promote insulin secretion. SLC25A46, an outer mitochondrial membrane protein, was identified as a downstream effector of glucose-dependent signal transduction. It plays a role in mitochondrial dynamics and protects mitochondria from apoptosis under nutrient stress in INS-E cells.
JOURNAL OF CELL SCIENCE
(2023)
Editorial Material
Nutrition & Dietetics
Martin Kussmann
Review
Nutrition & Dietetics
Eva Kiesswetter, Julia Stadelmaier, Maria Petropoulou, Jakub Morze, Kathrin Grummich, Isabelle Roux, Roberta Lay, Lisa Himmelsbach, Martin Kussmann, Christine Roeger, Malte Rubach, Hans Hauner, Lukas Schwingshackl
Summary: The health effects of dairy products on cardiometabolic markers remain debated. A systematic review and network meta-analysis found that high-dairy intake had no detrimental effects on anthropometric outcomes, blood lipids, and blood pressure. Low-fat and full-fat dairy improved blood pressure but may impair glycemic control. Yogurt showed beneficial effects on waist circumference, triglycerides, and high-density lipoprotein cholesterol.
ADVANCES IN NUTRITION
(2023)
Article
Physics, Atomic, Molecular & Chemical
Martin Kussmann
Summary: Mass spectrometry (MS) has become the most informative and versatile analytical technology in molecular and structural biology. It enables the discovery, identification, and characterization of biomolecules and facilitates the understanding of their interactions and effects. MS has also played a crucial role in the field of molecular nutrition, providing comprehensive and rapid identification and characterization of nutrients and bioactives. Furthermore, it has the potential to contribute to personalized and systems nutrition, leading to science-based recommendations and actions for public and personal health.
EUROPEAN JOURNAL OF MASS SPECTROMETRY
(2023)
