Review
Nutrition & Dietetics
Martin Kussmann
Summary: Nature's bioactive substances offer potential solutions to human, animal, and environmental health issues. However, the utilization of bioactive peptides and natural bioactives has been underdeveloped. The future lies in employing systems-level and artificial intelligence approaches to better understand their functions and accelerate the development and implementation of solutions.
Article
Chemistry, Applied
Tessa B. Moyer, Wyatt J. Schug, Leslie M. Hicks
Summary: This study utilizes in silico predictions, proteomics, and simulated gastrointestinal digestions to identify digestion resistant cysteine-rich peptides (CRPs) within Amaranthus hypochondriacus seeds. Thirteen in silico predicted CRPs were detected in a seed extract, providing evidence for the translation of five CRP families. Mature forms of six CRPs were characterized via top-down proteomics, revealing multiple post translational modifications. All six peptides demonstrated resistance to simulated gastrointestinal digestion, suggesting that A. hypochondriacus CRPs may exhibit bioactivity after consumption and should be prioritized for further characterization.
Editorial Material
Biochemistry & Molecular Biology
James W. Checco
Summary: Peptidomics is an underutilized method that uses mass spectrometry to identify and measure endogenous peptides, which play crucial biological roles and have potential as biomarkers. This article serves as a brief introduction to peptidomics, aiming to raise awareness and encourage its application among researchers interested in studying endogenous peptides.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Chemistry, Applied
Olivia Ogilvie, Sarah Roberts, Kevin Sutton, Nigel Larsen, Juliet Gerrard, Laura Domigan
Summary: The study investigated the impact of adding different concentrations of mTG to bread on gluten structure, digestibility, and immunogenic peptides. The results showed that the addition of mTG did not affect the deamidation state and digestibility of immunogenic peptides, indicating that mTG addition does not produce activated gluten peptides.
Article
Biochemistry & Molecular Biology
Yuzuru Nakagawa, Takashi Matsui, Ryo Konno, Yusuke Kawashima, Toshiya Sato, Makoto Itakura, Yoshio Kodera
Summary: The study developed a peptide extraction method for efficient and reproducible extraction of peptides from dissected hypothalamus of a single animal. This method helps understand individual differences and tissue specificity, facilitating the discovery of new peptides and biomarkers.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Claudia Neves Correa, Louise Oliveira Fiametti, Gabriel Marques de Barros, Leandro Mantovani de Castro
Summary: This study identified 1080 peptides in the gills of the seahorse H. reidi using fast heat inactivation of proteases and liquid chromatography coupled to mass spectrometry. Among these peptides, 1013 were present in all samples and 67 were identified in an additional LC-MS/MS run from an alkylated and reduced pool of samples. The majority of the identified peptides were fragments of the internal region of precursor proteins, including ribosomal proteins, histones, and hemoglobin, and some fragments from moronecidin-like protein with antimicrobial activity were also found.
Article
Biochemistry & Molecular Biology
Somayeh Mousavi, Haowen Qiu, Frazer I. Heinis, Md Shadman Ridwan Abid, Matthew T. Andrews, James W. Checco
Summary: The study evaluated the impact of short-term anesthetic administration on the abundance of cell-cell signaling peptides and found that isoflurane administration changed the levels of a small number of peptides, while sodium pentobarbital administration had negligible impact on peptide abundance.
ACS CHEMICAL NEUROSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Somayeh Mousavi, Haowen Qiu, Frazer I. Heinis, Md Shadman Ridwan Abid, Matthew T. Andrews, James W. Checco
Summary: Cell-cell signaling peptides play important roles in various physiological processes, and liquid chromatography-mass spectrometry-based peptidomics workflows are commonly used to identify and quantify their relative abundances. However, acute administration of anesthetics may affect the measured abundance of cell-cell signaling peptides, especially in the brain and endocrine system. This study evaluated the effect of short-term anesthetic administration on the measured abundance of these peptides and found that isoflurane had a minor impact on the levels of some peptides, while sodium pentobarbital had negligible impact.
ACS CHEMICAL NEUROSCIENCE
(2022)
Article
Food Science & Technology
Simonetta Caira, Gianluca Picariello, Giovanni Renzone, Simona Arena, Antonio Dario Troise, Sabrina De Pascale, Valentina Ciaravolo, Gabriella Pinto, Francesco Addeo, Andrea Scaloni
Summary: This study aims to provide a comprehensive overview of bioactive food-derived peptides identified in various body fluids and tissues, and to describe their absorption mechanisms and metabolic processes. Available information suggests that while these peptides are present in organism tissues/body fluids, only a few of them have demonstrated substantial bioavailability and potential bioactivity.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2022)
Review
Biochemical Research Methods
Rachel E. Foreman, Amy L. George, Frank Reimann, Fiona M. Gribble, Richard G. Kay
Summary: Improvements in LC and MS instrumentation have enhanced proteomic and metabolomic analysis, but there has been less focus on detecting and quantifying small bioactive peptides. It is important to preserve the structure of processed peptide products to prevent misidentification and consider the stability of peptides in biological matrices when developing methods to study them. Bioinformatic analysis of peptidomics data sets should include specific post-translational modifications critical for the function of bioactive peptides.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Somayeh Mousavi, Haowen Qiu, Matthew T. Andrews, James W. Checco
Summary: During winter, hibernating mammals undergo extreme physiological changes, such as decreased metabolism, near-freezing body temperatures, and reduced heart rate, allowing them to survive without food for several months. The neurochemical basis of this regulation is largely unknown. This study used a peptidomics approach to examine the changes in endogenous peptides in the hypothalamus and pituitary of a hibernating mammal, the thirteen-lined ground squirrel. The results provide critical insight into the molecular basis of hibernation and have potential implications for organ preservation, obesity treatment, and stroke treatment.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Alejandro Heres, Marta Gallego, Leticia Mora, Fidel Toldra
Summary: Reducing salt in meat products can affect the natural mechanisms of proteolysis, leading to changes in texture and flavor. This study quantified the presence of dipeptides in low-salt Spanish dry-cured ham using mass spectrometry. The results showed a correlation between these dipeptides and taste attributes, as well as potential health benefits.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Nhu Q. Vu, Hsu-Ching Yen, Lauren Fields, Weifeng Cao, Lingjun Li
Summary: Neuropeptides play important regulatory roles in biochemical, physiological, and behavioral processes. This study introduces HyPep, a novel database searching tool that utilizes sequence homology searching for neuropeptide identification. The performance of HyPep was optimized and compared with a commercial database searching software, PEAKS DB, using LC-MS/MS measurements. HyPep identified more neuropeptides than PEAKS DB at a 1% false discovery rate and both programs had a false match rate of 2%. The report also highlights how HyPep can aid in the discovery of novel neuropeptides.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Immunology
Erik Hartman, Karl Wallblom, Mariena J. A. van der Plas, Jitka Petrlova, Jun Cai, Karim Saleh, Sven Kjellstrom, Artur Schmidtchen
Summary: The study investigates the peptidomes of wound fluids and reveals highly individualized profiles in patients, with differences based on wound type. Peptides from infected wounds may contribute to an antimicrobial environment. Validation of findings through literature compilation and cross checking against data confirms the presence of immunologically significant peptides in infected wounds. The use of sorting algorithms and open source software demonstrates the power to analyze and visualize peptidomic data.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Spectroscopy
Kai-Ting Fan, Chia-Wei Hsu, Yet-Ran Chen
Summary: This article summarizes and discusses the application of mass spectrometry (MS) in discovering peptide hormones, including targeted and untargeted methods. Although peptidomics is expected to discover new peptide hormones in an unbiased manner, only a limited number of successful cases have been reported. The challenges and corresponding measures in peptidomics, as well as emerging technologies for comprehensive study of endogenous peptide hormones, are also discussed.
MASS SPECTROMETRY REVIEWS
(2023)
Article
Nutrition & Dietetics
Veronica Caldeo, Eimear Downey, Carol-Anne O'shea, Michael Affolter, Sheri Volger, Marie-Claude Courtet-Compondu, Carlos Antonio De Castros, James A. O'Mahony, C. Anthony Ryan, Alan L. Kelly
Summary: This study evaluated the composition, protein profile, and plasmin activity of human milk from mothers who delivered infants at different gestational ages. Results showed that protein content and levels of some individual proteins were significantly affected by gestational age at birth and duration of lactation, with differences in proteolytic activity in milk samples. Compositional differences between term and pre-term infant milk were most significant in terms of protein profile.
CLINICAL NUTRITION
(2021)
Article
Nutrition & Dietetics
Stephanie Andraos, Beatrix Jones, Clare Wall, Eric Thorstensen, Martin Kussmann, David Cameron-Smith, Katherine Lange, Susan Clifford, Richard Saffery, David Burgner, Melissa Wake, Justin O'Sullivan
Summary: The study reveals that family, age, and sex contribute to variations in the concentrations of plasma B vitamers in Australian children and adults. Concordance in B vitamer levels was found between parent-child pairs, with different generations showing specificity in their vitamer concentrations.
Article
Biochemical Research Methods
Loic Dayon, Charlotte Macron, Sabine Lahrichi, Antonio Nunez Galindo, Michael Affolter
Summary: A highly automated proteomic workflow for human milk sample analysis was developed, utilizing liquid chromatography mass spectrometry. Different workflows were evaluated and optimized, with the aim of allowing analysis of large sample cohorts in clinical research. This efficient workflow provides a new approach to studying the proteome of human milk.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Nutrition & Dietetics
Tristan Bourdeau, Michael Affolter, Lenaick Dupuis, Alexandre Panchaud, Sabine Lahrichi, Loraine Merminod, Christine Martin-Paschoud, Rachel Adams, Sophie Nutten, Carine Blanchard
Summary: Human clinical trials have demonstrated that a specific partially hydrolyzed 100% whey-based infant formula can reduce atopic dermatitis risk in the first year of life. However, differences in peptide composition and functional properties were found among different formulas, indicating that not all formulas have the same ability to reduce allergenicity and induce oral tolerance.
Article
Nutrition & Dietetics
Paloma K. Barrera-Reyes, Josue Cortes-Fernandez de Lara, Laure Poquet, Karine Redeuil, Martin Kussmann, Irma Silva-Zolezzi, Elizabeth M. Tejero
Summary: This study found that the concentrations of cocoa polyphenols were higher after sustained intake, with sulfate conjugates showing higher levels in females. Epicatechin-3'-glucuronide and epicatechin-3'-sulfate were the most abundant metabolites in all subjects.
Review
Genetics & Heredity
Aoife Doherty, Audrey Wall, Nora Khaldi, Martin Kussmann
Summary: Scientific research shows that diseases can be delayed, treated, or prevented through health-promoting functional food ingredients (FFIs) to maintain health. Consumers are increasingly seeking information on food, nutrition, nutrients, and associated health benefits, leading to the formation of a nutrition industry centered around natural foods and FFIs.
FRONTIERS IN GENETICS
(2021)
Review
Biochemical Research Methods
Loic Dayon, Ornella Cominetti, Michael Affolter
Summary: Biological fluids, such as blood and cerebrospinal fluid, are important samples for diagnostic testing and monitoring. Proteomic technologies have been used to identify protein biomarkers in these fluids, but with limited success. Recent advancements in technology and methodologies have allowed for better analysis of human biological fluids, and this review focuses on recent highlights in the field of proteomics using mass spectrometry. Despite being overshadowed by genomics, proteomic tools and methodologies have matured and are now better suited for discovering innovative and robust biofluid biomarkers.
EXPERT REVIEW OF PROTEOMICS
(2022)
Article
Agriculture, Dairy & Animal Science
Holger A. Ebhardt, Pierre Ponchon, Konstantinos Theodosiadis, Christophe Fuerer, Marie -Claude Courtet-Compondu, Jonathan O'Regan, Michael Affolter, Yousef Joubran
Summary: High resolution mass spectrometry can identify hundreds to thousands of proteins per sample with label-free quantification, but the gold standard for quantitative proteomics is MRM. The authors demonstrate a reductionist approach using correlation analysis of dairy ingredients, successfully explaining variance in proteomics data with only 9 proteins. Their method, Trinity-MRM, shows reproducibility below 5% in independent experiments with double cream.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Multidisciplinary Sciences
Starin McKeen, Nicole C. Roy, Jane Adair Mullaney, Hannah Eriksen, Amy Lovell, Martin Kussman, Wayne Young, Karl Fraser, Clare R. Wall, Warren C. McNabb
Summary: This study characterized the changes in the gut microbiome composition, metagenomic functional capacity, and associated metabolites during the introduction of solid foods in infants. The results showed that the microbiome composition diversified during the first year of life, while the functional capacity of the gut microbiome remained stable. The introduction of solid foods resulted in significant changes in the relative abundance of sequences assigned to KEGG pathways and taxonomic assignments, as well as stronger correlations with metabolites compared to continued diet diversification. This study provides insights into the trends in microbiome composition and functional capacity during the complementary feeding period and identifies potential metabolite targets for future investigations.
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)
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)
Review
Nutrition & Dietetics
Martin Kussmann
Summary: Nature's bioactive substances offer potential solutions to human, animal, and environmental health issues. However, the utilization of bioactive peptides and natural bioactives has been underdeveloped. The future lies in employing systems-level and artificial intelligence approaches to better understand their functions and accelerate the development and implementation of solutions.
Article
Medicine, Research & Experimental
Amy L. Lovell, Hannah Eriksen, Starin McKeen, Jane Mullaney, Wayne Young, Karl Fraser, Eric Altermann, Olivier Gasser, Martin Kussmann, Nicole C. Roy, Warren C. McNabb, Clare R. Wall
Summary: This 6-month prospective non-randomised feasibility study conducted in Auckland, New Zealand, aimed to investigate the feasibility and acceptability of a food intervention for infants before introducing complementary foods. The study found that recruiting infants before introducing complementary foods is feasible and the food-based intervention received acceptable adherence. These results will inform a full-scale randomized controlled trial with adjustments to the collection of biological samples to examine the effect of a prebiotic food on the prevalence of respiratory tract infections during infancy.
PILOT AND FEASIBILITY STUDIES
(2022)
Article
Biochemical Research Methods
Tanushree Halder, Elke Stroeher, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
Summary: Improving the root system of wheat is crucial for enhancing grain yield and climate resilience. This study identified proteins associated with root length and root mass in wheat using label-free quantitative proteomics. The findings revealed potential biomarkers that could be used for improving the root system of wheat.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Yinhua Pan, Quanqing Zou, Wu Yin, Zhen Huang, Yingzhu Zhao, Zongming Mo, Lihui Li, Jianrong Yang
Summary: A prognostic model of BC based on LNM-related genes was established in this study, providing guidance for prognosis evaluation and precise treatment of BC. The genes related to lymph node metastasis in BC are largely unknown and need further exploration. Searching for potential lymph node metastasis-related genes of BC will provide meaningful biomarkers for BC treatment. Our model, based on TCGA-BRCA data, effectively predicted patient outcomes and classified BC patients. The identified feature genes might have a predictive function in immunotherapy. The results of this study provide a new reference for the prognosis and treatment of BC patients with lymph node metastasis.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Qiushi Liang, Joon M. Pijnenburg, Erikjan Rijkers, Arnold G. Vulto, Ans T. van der Ploeg, Niek P. van Til, Eva C. Vlaar, Jeroen A. A. Demmers, W. W. M. Pim Pijnappel
Summary: Pompe disease is a lysosomal storage disorder characterized by glycogen accumulation in skeletal muscle, leading to profound pathology. This study showed that lentiviral gene therapy with LV-IGF2.GAAco can nearly completely correct disease-associated proteomic changes, supporting its future clinical development as a new treatment option for Pompe disease.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Chuang Liu, Wenjing Zhang, Qianli Dong, Haipeng Liu
Summary: This study fills the knowledge gap about the matrix proteins involved in the formation of mineralized exoskeletons in decapod crustaceans. By comparing with well-studied molluscan biomineralization proteins, it is proposed that decapod crustaceans evolved novel proteins while sharing some proteins with molluscs. This study provides insights into the evolution and adaptation of crustaceans and molluscs in forming their exoskeletons.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Rania D. Baka, Josipa Kules, Angelo Beletic, Vladimir Farkas, Dina Resetar Maslov, Blanka Beer Ljubic, Ivana Rubic, Vladimir Mrljak, Mark McLaughlin, David Eckersall, Zoe Polizopoulou
Summary: This study analyzed serum samples from dogs with epilepsy and identified potential markers of epilepsy, proteins involved in nerve tissue regeneration, and proteins altered by antiepileptic medication. The findings provide insight into the pathogenesis of epilepsy and the effects of medication on extracellular matrix proteins.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Viviane M. Codognoto, Fabiana F. de Souza, Thais R. Cataldi, Carlos A. Labate, Laiza S. de Camargo, Pedro H. Esteves Trindade, Roberto R. da Rosa Filho, Diego J. B. de Oliveira, Eunice Oba
Summary: This study aimed to compare urine proteomics from non- and pregnant buffaloes to identify potential biomarkers of early pregnancy. A total of 798 proteins were reported in the urine considering all groups, and the differential proteins play essential roles during pregnancy.
JOURNAL OF PROTEOMICS
(2024)