Marc-Emmanuel Dumas

@marcedumas.bsky.social

Biochemist and engineer. Chair/Head of Systems Medicine @Imperial 🇬🇧 Research Director @CNRS🇫🇷 Adjunct Professor @McGill 🇨🇦 human #metabolome #microbiome #holobiont in #cardiometabolic diseases and #environmental ecosystems too #OneHealth

Reposting this from April 1, 2007 in honor of Craig Venter. I did this as an April Fool's joke - sharing it as a PDF. I got stressed when I found out Craig had seen it and knew it was by me. But he loved it and said it was OK to share it more widely. So then I posted it on the web.

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Researchers, including MDR's @marcedumas.bsky.social, have discovered that chemicals produced by gut bacteria could act as an early warning system for future heart disease, potentially allowing doctors to identify at-risk individuals years before symptoms appear ⬇️ www.imperial.ac.uk/news/article...

Gut microbes may reveal heart disease risk years before symptoms

Scientists have discovered that chemicals produced by gut bacteria could act as an early warning system for future heart disease, potentially allowin...

imperial.ac.uk

METLIN 960K is now out: >960,000 compounds with empirically acquired MS/MS spectra from authentic standards. A step toward more reliable, reproducible small-molecule identification. doi.org/10.1021/acs....

METLIN 960 K: An Empirical Tandem Mass Spectrometry Data Resource

METLIN 960 K represents the largest collection of experimentally acquired small-molecule MS/MS spectra currently available. We introduce a reengineered publicaly accessible METLIN platform integrating high-resolution tandem mass spectrometry (MS/MS) data for over 960,000 empirically validated molecular standards. This scale was enabled by a high-throughput experimental framework integrating acoustic droplet ejection with high-throughput LC–MS/MS acquisition, allowing systematic empirical generation of MS/MS spectra from authentic standards. In addition to scale, METLIN 960 K provides a uniquely standardized MS/MS data set, with spectra acquired under controlled and consistent conditions across ionization modes and collision energies, enabling reproducible spectral comparison and machine-learning applications. Each compound is characterized by MS/MS spectra acquired in both positive and negative ionization modes across four collision energies (0, 10, 20, and 40 eV), enabling comprehensive fragmentation coverage and improved structural annotation. Designed as a reference library for XCMS-METLIN and compatible with machine-learning workflows, METLIN 960 K supports high-fidelity spectral matching, neutral loss analysis, and filtering of misannotations, including annotation of in-source fragments and biologically synchronized ranking of candidate metabolites. The platform also provides empirically derived MRM transitions on all standards (via METLIN-MRM), supporting quantitative method development across a chemically diverse range of metabolites, natural products, lipids, peptides, pharmaceuticals, and toxicants. A redesigned interface enables efficient querying by exact mass, formula, or structure with direct access to curated spectra and metadata. Two additional resources enhance identification: (1) METLIN Core, a high-frequency-use subset for rapid searching, and (2) > 1.02 million additional structures without MS/MS data for hypothesis generation. Derived exclusively from authentic standards, METLIN 960 K (https://metlin.scripps.edu) provides the largest publicly available empirical MS/MS database, delivering high-confidence annotation for both untargeted and targeted mass spectrometry workflows.

doi.org

Great collaboration that took us to places we definitely were not anticipating! Thank you Zoe and congratulations to you too! 🎉 ♥️

Zoe Hall@zoehall-icl.bsky.social · 5mo ago

In our new paper with @louisefets.bsky.social we show with #MSI that drugs can accumulate heterogeneously in #ovarian #cancer and may explain why treatments work well in some patients and not others. Huge congrats to Carmen Ramirez Moncayo, Louise and all authors! bit.ly/4byaY9W