Proceedings of the EuBIC-MS developers meeting 2023.

The 2023 European Bioinformatics Community for Mass Spectrometry (EuBIC-MS) Developers Meeting was held from January 15th to January 20th, 2023, in Congressi Stefano Franscin at Monte Verità in Ticino, Switzerland. The participants were scientists and developers working in computational mass spectrometry (MS), metabolomics, and proteomics. The 5-day program was split between introductory keynote lectures and parallel hackathon sessions focusing on "Artificial Intelligence in proteomics" to stimulate future directions in the MS-driven omics areas. During the latter, the participants developed bioinformatics tools and resources addressing outstanding needs in the community. The hackathons allowed less experienced participants to learn from more advanced computational MS experts and actively contribute to highly relevant research projects. We successfully produced several new tools applicable to the proteomics community by improving data analysis and facilitating future research.

Discovery of Urinary Biomarkers of Spinach Consumption Using Untargeted LC-MS Metabolomics in a Human Intervention Trial.

SCOPE: Biomarkers for intake of green leafy vegetables such as spinach can help investigate their health effects. However, only few potential intake markers have been reported in the literature so far. METHODS AND RESULTS: Based on a cross-over study on whole leaf and minced spinach, we investigate changes in metabolites before and after spinach intake and differences between the two treatments and health status. Nineteen volunteers (12 healthy subjects and 7 short bowel patients) completed the study within 48 days. Urine samples (24-h intervals before and after spinach intake) and serum samples (baseline, post 8 d, and post 15 d) are collected and analyzed by ultra-high performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS). The acquired data is analyzed by multivariate and univariate analyses. Three candidate biomarkers are observed in urine only after the spinach intake, including des-amino arginine pentenol ester, D/L-malic acid ester of cis-p-coumarate, D/L-malic acid ester of trans-p-coumarate, and 69 metabolites are present before spinach intake but showing an altered level after treatment. These metabolites are related to dietary habits or meal structure, and some changes are possibly affected by spinach intake. The candidate biomarkers are independent of spinach pre-processing and healthy status. No markers are discovered in serum samples. CONCLUSION: We propose structures for three candidate spinach intake biomarkers; these markers will need further validation in independent studies.

Combined Urinary Biomarkers to Assess Coffee Intake Using Untargeted Metabolomics: Discovery in Three Pilot Human Intervention Studies and Validation in Cross-Sectional Studies.

Coffee is a widely consumed beverage worldwide and has a high content of chlorogenic acids, polyphenols, methylxanthines, and volatile flavor compounds. Scientific evidence to support the beneficial health effects of coffee is limited, and validated urinary biomarkers of coffee intake are therefore needed. We observed 23 common putative biomarkers of coffee intake in three separate parallel intervention studies by ultra-high-performance liquid chromatography-electrospray ionization-quadrupole time-of-flight-mass spectrometry (UHPLC-ESI-QTOF-MS) and multivariate analyses. Baseline samples from the NU-AGE study were used to confirm and validate 16 of these candidate biomarkers, including their robustness, time response, and dose response. These validated candidate biomarkers are N-methylpyridinium cation, 1-methyl-1H-pyrrole-2-carboxaldehyde, 1H-pyrrole-2-carboxaldehyde sulfate, 3-piperidinemethanol, furfurylidene-furfurylamine, 2-furoylglycine, N-substituted-5-(aminoethyl) furan-2-carbaldehyde derivative, 3',4'-dihydroxyacetophenone sulfate, caffeine, dihydroxystyrene glucuronide, ferulic acid sulfate, 4-ethylcatechol glucuronide, 3-feruloylquinic acid, 3,4-dihydroxystyrene sulfate, one unknown glucuronide, and one unknown sulfate. Combinations of candidate biomarkers gave a better prediction of coffee consumption than individual biomarkers. The robustness of the combined biomarkers requires additional validation in cohort studies covering other populations.

Discovery of Urinary Biomarkers of Seaweed Intake Using Untargeted LC-MS Metabolomics in a Three-Way Cross-Over Human Study.

Seaweeds are a marine source rich in potentially bioactive components, and therefore have attracted attention since the middle of the twentieth century. Accurate and objective assessment of the intake of seaweeds to study their health effects is hampered by a lack of validated intake biomarkers. In this three-armed, randomized, cross-over study, an untargeted metabolomics approach was applied for discovering novel intake biomarkers. Twenty healthy participants (9 men and 11 women) were provided each of three test meals in a randomized order: 5 g of Laminaria digitate (LD), 5 g of Undaria pinnatifida (UP), or a control meal with energy-adjusted pea protein. Four urine samples and a 24 h pooled urine were collected along with blood samples at seven time-points. All samples were profiled by LC-ESI-QTOF-MS and the data were analyzed by univariate analysis and excretion kinetics to select putative intake biomarkers. In total, four intake biomarkers were selected from urine samples. They were identified as hydroxyl-dihydrocoumarin at Level III, loliolid glucuronide at level I, and isololiolid glucuronide at level II, while the last one remains unknown. Further identification and validation of these biomarkers by a cross-sectional study is essential to assess their specificity and robustness.

Biomarkers of seaweed intake.

Seaweeds are marine macroalgae, some of which are edible. They are rich in specific dietary fibers and also contain other characteristic biological constituents. Biological activities have been investigated mainly in animal studies, while very few results are available from human studies. Biomarkers of food intake (BFIs) specific to seaweed could play an important role as objective measurements in observational studies and dietary intervention studies. Thus, the health effects of seaweeds can be explored and understood by discovering and applying BFIs. This review summarizes studies to identify candidate BFIs of seaweed intake. These BFIs are evaluated by a structured validation scheme. Hydroxytrifuhalol A, 7-hydroxyeckol, C-O-C dimer of phloroglucinol, diphloroethol, fucophloroethol, dioxinodehydroeckol, and/or their glucuronides or sulfate esters which all belong to the phlorotannins are considered candidate biomarkers for brown seaweed. Fucoxanthinol, the main metabolite of fucoxanthin, is also regarded as a candidate biomarker for brown seaweed. Further validation will be needed due to the very limited number of human studies. Further studies are also needed to identify additional candidate biomarkers, relevant specifically for the red and green seaweeds, for which no candidate biomarkers emerged from the literature search. Reliable BFIs should also ideally be found for the whole seaweed food group.

Biomarkers of meat and seafood intake: an extensive literature review.

Meat, including fish and shellfish, represents a valuable constituent of most balanced diets. Consumption of different types of meat and fish has been associated with both beneficial and adverse health effects. While white meats and fish are generally associated with positive health outcomes, red and especially processed meats have been associated with colorectal cancer and other diseases. The contribution of these foods to the development or prevention of chronic diseases is still not fully elucidated. One of the main problems is the difficulty in properly evaluating meat intake, as the existing self-reporting tools for dietary assessment may be imprecise and therefore affected by systematic and random errors. Dietary biomarkers measured in biological fluids have been proposed as possible objective measurements of the actual intake of specific foods and as a support for classical assessment methods. Good biomarkers for meat intake should reflect total dietary intake of meat, independent of source or processing and should be able to differentiate meat consumption from that of other protein-rich foods; alternatively, meat intake biomarkers should be specific to each of the different meat sources (e.g., red vs. white; fish, bird, or mammal) and/or cooking methods. In this paper, we present a systematic investigation of the scientific literature while providing a comprehensive overview of the possible biomarker(s) for the intake of different types of meat, including fish and shellfish, and processed and heated meats according to published guidelines for biomarker reviews (BFIrev). The most promising biomarkers are further validated for their usefulness for dietary assessment by published validation criteria.