Yasin El Abiead

Hi Chris. So it would have to be high resolution and DDA data. The main idea here was to use environmental sample types for which we have exact coordinates. While most data we have up to this point are from environmental materials such as soil, wild animals would sure be interesting to add as well!

Great, thank you! I assume the data are already on MassIVE then. Then we just have to make sure to get all relevant metadata into redu.gnps2.org/selection/

Thank you for your interest! I have sent you an email and also turned private messages on here on bluesky for others.

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.

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.

Increasing the Scale of the Mass Spectrometry Query Language Compendium with Explainable AI A significant bottleneck in metabolomics data interpretation is the effective use of domain knowledge to assign structural information based on fragmentation patterns. The mass spectrometry query lang...

Increasing the Scale of the Mass Spectrometry Query Language Compendium with Explainable AI #AC pubs.acs.org/doi/10.1021/...

A Perspective on Unintentional Fragments and their Impact on the Dark Metabolome, Untargeted Profiling, Molecular Networking, Public Data, and Repository Scale Analysis. In/post-source fragments (ISFs) arise during electrospray ionization or ion transfer in mass spectrometry when molecular bonds break, generating ions that can complicate data interpretation. Although ISFs have been recognized for decades, their contribution to untargeted metabolomics - particularly in the context of the so-called “dark matter” (unannotated MS or MS/MS spectra) and the “dark metabolome” (unannotated molecules) - remains unsettled. This ongoing debate reflects a central tension: while some caution against overinterpreting unidentified signals lacking biological evidence, others argue that dismissing them too quickly risks overlooking genuine molecular discoveries. These discussions also raise a deeper question: what exactly should be considered part of the metabolome? As metabolomics advances toward large-scale data mining and high-throughput computational analysis, resolving these conceptual and methodological ambiguities has become essential. In this perspective, we propose a refined definition of the “dark metabolome” and present a systematic overview of ISFs and related ion forms, including adducts and multimers. We examine their impact on metabolite annotation, experimental design, statistical analysis, computational workflows, and repository-scale data mining. Finally, we provide practical recommendations - including a set of dos and don’ts for researchers and reviewers - and discuss the broader implications of ISFs for how the field explores unknown molecular space. By embracing a more nuanced understanding of ISFs, metabolomics can achieve greater rigor, reduce misinterpretation, and unlock new opportunities for discovery.

If you’ve been following #metabolomics literature, you’ve probably seen a lot of debate on in-source fragmentation. We’ve put together a manuscript to clarify what it is, how to deal with it, and what it means for discovery in #metabolomics and #exposomics.
doi.org/10.26434/che...

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...

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....

Computationally unmasking each fatty acyl C=C position in complex lipids by routine LC-MS/MS lipidomics - Nature Communications Physiologically relevant omega-positions of double bonds in fatty acyls in complex lipids can now only be identified with specialized instrumentation. Here, the authors present a computational approac...

Nice work, demonstrating determination of omega positions in lipid acyls using only RT prediction! www.nature.com/articles/s41...

The mass spectrometry of microbiome-mediated metabolism of food: challenges and opportunities With the exception of molecules acquired through the lungs, skin absorption, or part of a medication regime, nearly all molecules in our bodies origin…

The interactions between food, microbiome and host that modulate health can be complex. Here, we offer a perspective on how mass spectrometry can be leveraged to address some of these challenges to understand host and microbial metabolism of food. A step closer to personalized health and nutrition.

GNPS2 and associated services will be down for power maintenance tonight and into tomorrow.

Detection of functional clusters (FCs) specific to the phenylalanine (PAL) and p-coumaroyltyramine (THT) pathways. Top left: Network depicting the relationship between transcripts and mass signatures within the PAL FC. Bottom left: Network illustrating the interplay between transcripts and mass signatures within the THT FC. Top right: Heatmap illustrating the expression levels of all transcripts within the PAL and THT FCs. Upper middle right: Heatmap displaying the abundance of all mass signatures present in the PAL and THT FCs. Lower middle right: Correlation matrix highlighting the correlations among transcripts and mass signatures within the PAL FC. Bottom right: Correlation matrix displaying the relationships between transcripts and mass signatures within the THT FC, including Mutual rank and transformed edge weights.

Elucidating #plant #Biosynthetic pathways: @jjjvanderhooft.bsky.social @marnixmedema.bsky.social &co develop #MEANtools, an unsupervised computational workflow that integrates #MultiOmics data to predict #metabolic pathways by linking transcripts to metabolites @plosbiology.org 🧪 plos.io/4odL94g

Excellent news: 𝐒𝐞𝐛𝐚𝐬𝐭𝐢𝐚𝐧 𝐰𝐢𝐥𝐥 𝐫𝐞𝐜𝐞𝐢𝐯𝐞 𝐚𝐧 #𝐄𝐑𝐂 𝐀𝐝𝐯𝐚𝐧𝐜𝐞𝐝 𝐆𝐫𝐚𝐧𝐭!

𝐁𝐢𝐧𝐝𝐢𝐧𝐠𝐒𝐡𝐚𝐝𝐨𝐰𝐬 will develop ML models to predict whether some query molecule has a particular bioactivity or is binding to a certain protein, where the only information we have about the query molecule is its tandem mass spectrum.

Enhancing tandem mass spectrometry-based metabolite annotation with online chemical labeling - Nature Communications To improve annotation in non-targeted metabolomics studies, authors develop a Multiplexed Chemical Metabolomics (MCheM) platform, combining post-column derivatization with integrated data processing. ...

New paper from the group. Together with Chambers Hughes, Giovanni Vitale and our amazing collaborators, we developed a multiplexed chemical metabolomics workflow to assign functional groups in non-targeted LC-MS/MS data:

www.nature.com/articles/s41...

Behind the paper story:
go.nature.com/45ljV4d

🚀 We’ve launched the new MassBank! Now live at massbank.eu & massbank.jp — redesigned with a faster backend, better search, and powerful tools for exploring & sharing mass spectral data. Enjoy the fresh experience! Feedback and ideas welcome, please post them on github.com/MassBank/Mas...

An evaluation methodology for machine learning-based tandem mass spectra similarity prediction - BMC Bioinformatics Background Untargeted tandem mass spectrometry serves as a scalable solution for the organization of small molecules. One of the most prevalent techniques for analyzing the acquired tandem mass spectr...

An evaluation methodology for machine learning-based tandem mass spectra similarity prediction #BMCBioinformatics bmcbioinformatics.biomedcentral.com/articles/10....

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

what is a good European and/or Open alternative to Feedly? I like something that works well on a phone as well as the web

Ideally, with CMLRSS support :)

Combining #rstats and #Python for #MassSpectrometry data analysis is the way to go!

github.com/rformassspec...

supports (for now) #matchms and #spectrum_utils #Python libraries

@metabolights.bsky.social will be in #Metabolomics2025 in Prague!

Visit Posters 3007 C, 3006 C and 3000 C, say hi 👋 & discuss:

💻The most recent MetaboLights developments
🌐 Metabolomics Hub – a global open data consortium 🔗#ELIXIR Implementation Study on ontologies & semantic interoperability

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...

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...

Poster session at #ASMS2025 was as busy as always. Was great to see people agreeing that much remains to be discovered in untargeted #metabolomics. Thank you to all coauthors of the poster and associated paper. www.nature.com/articles/s42...

It’s so nice that an important paper led by yasin - is out. www.nature.com/articles/s41.... This paper is a key milestone as it is the foundation for data science across data repositories through indexing and metadata harmonization of 1.6 million files (although much more now due to updates). 1/n

Hope it is helpful. Also happy to answer questions!

This paper represents a great effort by @roman-bushuiev.bsky.social and his brother @anton-bushuiev.bsky.social. The DreaMS foundation model for mass spectra of small molecules now opens lots of avenues for possible downstream applications. It might be a game changer for computational metabolomics.

Milk phospholipid-coated lipid droplets modulate the infant gut microbiota and metabolome influencing weight gain - Microbiome Background The supramolecular structure and composition of milk fat globules in breast milk is complex. Lipid droplets in formula milk are typically smaller compared to human milk and differ in their ...

The last of my PhD projects is finally out! This was a great collaboration with Danone, looking at supplementing infant formula with a novel milk fat globule. #infant #microbiome #nutrition microbiomejournal.biomedcentral.com/articles/10....

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 changing metabolic landscape of bile acids – keys to metabolism and immune regulation - Nature Reviews Gastroenterology & Hepatology Bile acids have important roles in human metabolism and immune regulation. In this Perspective, Dorrestein and colleagues discuss the technologies and data science-related approaches that are improvin...

Seen at #DDW2025, this Perspective by @pieterdorrestein.bsky.social & co on the changing metabolic landscape of bile acids

www.nature.com/articles/s41...

🔓 link: rdcu.be/ekTBV

#Gastrosky #microsky #microbiome

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...

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...

Please apply for this open position for a senior scientist at our faculty. It is the head of the mass spec center and you will be my close colleague! Application Deadline:8.5.2025
jobs.univie.ac.at/job/Senior-S...