Structure-centric searching enables global mapping of the public metabolome - @pieterdorrestein.bsky.social @mingxunwang.bsky.social @yelabiead.bsky.social go.nature.com/481Sbmk

Structure-centric searching enables global mapping of the public metabolome - Nature Biotechnology

StructureMASST enables pan-repository MS/MS searches using a chemical name or structure.

go.nature.com

Yet another new function of bile acids -and relevance of the microbiome in regulating the efficacy of medications. #microbiome #IBD. Discovered using #metabolomics repository scale analysis. #opendata Thanks to all the collaborators and Vincent for leading it. www.biorxiv.org/content/10.6...

Welcome to the Bluesky page for the Avalon Lab! Currently located at UC Irvine, we explore marine natural products in pursuit of discovering novel neurotherapeutics. Keep up with our lab through our social media posts! Learn more about the Avalon Lab through the Linktree in our bio :)

Navigating the conjugated metabolome https://www.biorxiv.org/content/10.64898/2026.02.06.704496v1

A searchable metadata network graph for microbiome metabolomics https://www.biorxiv.org/content/10.64898/2026.02.04.703849v1

Synthesis-driven reverse metabolomics reveals 3-hydroxy N-acyl amides as gut microbial molecules https://www.biorxiv.org/content/10.64898/2026.01.07.698252v1

C’est un départ pour le BiSP/Micrhub! Plus de 150 participants pour jaser de bactériologie en français. @vincentlamoureux.bsky.social ouvre le bal avec ses résultats de post doctorat en métabolomique! @micrhub.bsky.social

🚨 Last chance! Submit your abstracts or apply for scholarships by Sept 23 (11:59pm MDT) for the joint Keystone Symposia: Microbiome Metabolism & Metabolites / Human Microbiome. #KSMicroMetab26 #KSMicrobiome26

Yes reach out to Yasin for this project. It will allow a worldwide picture of the environmental metabolome. This can be already published or not yet published data but will need world coordinates.

Yasin El Abiead@yelabiead.bsky.social · 11mo ago

Interested in a co-authorship? We’re building a tool for repository-scale untargeted #metabolomics and #exposomics of #environmental data. To make it the best it can be, we’re looking for people willing to share high-resolution LC-MS/MS (DDA) data from #water, #soil, #sediment, and related samples.

Interested in a co-authorship? We’re building a tool for repository-scale untargeted #metabolomics and #exposomics of #environmental data. To make it the best it can be, we’re looking for people willing to share high-resolution LC-MS/MS (DDA) data from #water, #soil, #sediment, and related samples.

Brilliant! 50 years after reverse spectral matching in GC-MS, a refined reverse search strategy to improve annotation rates. By @shipei-xing.bsky.social @vincentlamoureux.bsky.social Haoqi N. Zhao @yelabiead.bsky.social @mingxunwang.bsky.social @pieterdorrestein.bsky.social doi.org/10.1021/acs....

Reverse Spectral Search Reimagined: A Simple but Overlooked Solution for Chimeric Spectral Annotation

The exponential growth of untargeted metabolomics data, now reaching billions of mass spectra in public repositories, benefits from reannotation strategies for data reuse. While tandem mass spectromet...

doi.org

We just crossed the 800,000 files mark in Pan-ReDU. That's 800,000 public #metabolomics raw data files with harmonized metadata that can be re-analyzed to learn about new molecules and bio-distributions. 🎉 redu.gnps2.org

If you have ever wondered what might happen to short chain fatty acids made by the microbiome. Here is a large class of metabolites and how they link to biology. www.cell.com/cell/fulltex...

The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids

Mass spectrometry data mining tools enabled the creation of an MS/MS spectral library containing hundreds of N-acyl lipids, including conjugates with short-chain fatty acids. This resource enabled the...

cell.com

This methodology is as important as the development of molecular networking and can be used together.Examples of its use by my lab and how it’s used and how we think about using it is in its infancy www.cell.com/cell/fulltex..., www.biorxiv.org/content/10.1..., www.researchsquare.com/article/rs-6...

The underappreciated diversity of bile acid modifications

Using mass spectrometry-based tools to mine public untargeted MS/MS data revealed the vastly underappreciated diversity of bile acids hidden in plain sight and led to the discovery of previously unkno...

cell.com

Nature Methods@natmethods.nature.com · last yr.

The Mass Spectrometry Query Language (MassQL) is an open-source language for instrument-independent searching across mass spectrometry data for complex patterns of interest via concise and expressive queries without the need for programming skills. www.nature.com/articles/s41...

The Mass Spectrometry Query Language (MassQL) is an open-source language for instrument-independent searching across mass spectrometry data for complex patterns of interest via concise and expressive queries without the need for programming skills. www.nature.com/articles/s41...

I am excited to share the latest project I have been working on "A Multi-Organ Murine Metabolomics Atlas Reveals Molecular Dysregulations in Alzheimer’s Disease". 1/n www.biorxiv.org/content/10.1...

A Multi-Organ Murine Metabolomics Atlas Reveals Molecular Dysregulations in Alzheimer’s Disease

The etiology of Alzheimer’s Disease (AD) remains largely unclear but is likely driven by gene-environment interactions. Here, we present a multi-organ untargeted metabolomics dataset (2,271 samples) g...

biorxiv.org

#FeaturedProtocol this week is a #reversemetabolomics protocol, in which a tandem #massspec spectrum is used as a search term to probe public #metabolomic data, enabling discovery of new metabolic associations bit.ly/4hdyQQF

A guide to reverse metabolomics—a framework for big data discovery strategy - Nature Protocols

In this reverse metabolomics protocol, a tandem mass spectrometry spectrum is used as a search term to probe public metabolomic data. Analysis of the metadata connected with these search results enabl...

bit.ly

Human Untargeted Metabolomics in High-Throughput Gut Microbiome Research: Ethanol vs Methanol | Analytical Chemistry pubs.acs.org/doi/10.1021/...

Human Untargeted Metabolomics in High-Throughput Gut Microbiome Research: Ethanol vs Methanol

Untargeted metabolomics is frequently performed on human fecal samples in conjunction with sequencing to unravel the gut microbiome functionality. As sample collection efforts are rapidly expanding, with individuals often collecting specimens at home, metabolomics experiments should adapt to accommodate the safety and needs of bulk off-site collections and improve high throughput. Here, we show that a 95% ethanol, safe to be shipped and handled, extraction part of the Matrix Method pipeline recovers comparable amounts of metabolites as a validated 50% methanol extraction, preserving metabolic profile differences between investigated subjects. Additionally, we show that the fecal metabolome remains relatively stable when stored in 95% ethanol for up to 1 week at room temperature. Finally, we suggest a metabolomics data analysis workflow based on robust centered log ratio transformation, which removes the variance introduced by possible different sample weights and concentrations, allowing for reliable and integration-ready untargeted metabolomics experiments in gut microbiome research.

pubs.acs.org

Excited to share our correspondence in @naturemetabolism.bsky.social, where we address claims that the “dark metabolome” is merely an in‐source fragmentation artifact. www.nature.com/articles/s42... #Metabolomics #TeamMassSpec

Discovery of metabolites prevails amid in-source fragmentation - Nature Metabolism

Nature Metabolism - Discovery of metabolites prevails amid in-source fragmentation

nature.com

A study using an n=1 experiment with single standards at 0V CID reported that 70% of detected ions were in-source fragments (ISFs). www.nature.com/articles/s42... This finding was extrapolated to suggest that ISFs affect all metabolomics experiments to this degree. A counterpoint. rdcu.be/ebFwc 1/n

Check out our new #preprint, a collaborative effort to explore emerging #bile acids (also referred as MCBAs) during early life. Briefly, here we analyzed MCBAs in early life and found distinct age-related trajectories linked to gut #microbiota, #immune modulation & islet #autoimmunity progression.

Was great to see this AMAZING talk by Robert Quinn of @quinn-labs.bsky.social here at UCSD. This talk included a history of the discovery of amine conjugated bile acids, the enzymology behind them, and their impact on health and disease. Some featured papers in his talk shared below:

This is only achieved due to the creativity of people that we get to work and collaborate with. Thanks to all.

Skaggs School of Pharmacy and Pharmaceutical Sciences@ucsdpharmacy.bsky.social · 2y ago

Congratulations to @pieterdorrestein.bsky.social, who was once again named to the prestigious Highly Cited Researchers list! Compiled by Clarivate, the list identifies scholars ranked in the top 1% in their respective fields. Story ➡️ bit.ly/3B3inzF

Ok a third bleetorial or skeetorial of another preprint. www.biorxiv.org/content/10.1... in this case Nina, our exposome expert, Kine, our expert pharmacist, Corinna, the MS/MS guru, wanted to identify medication exposures from untargeted metabolomics data. Why? - aren’t there good medical records?

Empirically establishing drug exposure records directly from untargeted metabolomics data

Despite extensive efforts, extracting information on medication exposure from clinical records remains challenging. To complement this approach, we developed the tandem mass spectrometry (MS/MS) based...

biorxiv.org

Here is a second bleetorial about a paper we recently preprinted. Here @shipei-xing.bsky.social wanted to find a solution to be able to re-use data in the public domain with MS1 data only - LC-MS and imaging mass spectrometry data. www.biorxiv.org/content/10.1...

Annotating full-scan MS data using tandem MS libraries

Full-scan mass spectrometry (MS) data from both liquid chromatography (LC) and MS imaging capture multiple ion forms, including their in-source fragments. Here we leverage such fragments to structural...

biorxiv.org

This will me my fist blueet! Microbial N-Acyl lipids have been shown to regulate glucose, pain etc among other things. Therefore Helena, Vincent and Martijn asked the question - are there more and if so what types? And boy did they find some www.biorxiv.org/content/10.1...

The microbiome diversifies N-acyl lipid pools - including short-chain fatty acid-derived compounds

N -acyl lipids are important mediators of several biological processes including immune function and stress response. To enhance the detection of N -acyl lipids with untargeted mass spectrometry-based...

biorxiv.org