Tri Kaloudis

Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data www.biorxiv.org/content/10.6...

It’s finally out! Together with @embopress.org and
@reviewcommons.org, we conducted a structured side-by-side comparison of human peer review and our AI scientific review (see thread 👇👇👇🔥).

Complete Data Analysis Workflow for Quantitative DIA Mass Spectrometry Using Nextflow pubs.acs.org/doi/10....

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#proteomics #prot-paper

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

A special opportunity for lovers of mass spectrometry proteomics to join a like-minded team at PTI.

Join a collaborative initiative to enable direct protein analysis at unprecedented scale, in partnership with leading instrument developers, academics, and industry leaders.

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Great opportunity to work with Hanna Mazur-Marzec's group at the University of Gdansk.👇
Position for an Associate Professor in the research and teaching staff group at the #Phycology Laboratory, Department of Marine #Biology and #Biotechnology.
More info: euraxess.ec.europa.eu/jobs/403757

🔥 We’re hiring! A rare opportunity to rethink neurodegeneration:
🟦 Develop creative, rigorous approaches to data interpretation toward mechanistic insights.

Join our team at PTI to study neurodegenerative disease using direct protein analysis at single-cell resolution.

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Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data https://www.biorxiv.org/content/10.64898/2026.01.24.701521v1

Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data Microbial metabolites play a critical role in regulating ecosystems, including the human body and its microbiota. However, understanding the physiologically relevant role of these molecules, especially through liquid chromatography tandem mass spectrometry (LC-MS/MS)-based untargeted metabolomics, poses significant challenges and often requires manual parsing of a large amount of literature, databases, and webpages. To address this gap, we established the Collaborative Microbial Metabolite Center knowledgebase (CMMC-KB), a platform that fosters collaborative efforts within the scientific community to curate knowledge about microbial metabolites. The CMMC-KB aims to collect comprehensive information about microbial molecules originating from microbial biosynthesis, drug metabolism, exposure-related molecules, food, host-derived molecules, and, whenever available, their known activities. Molecules from other sources, including host-produced, dietary, and pharmaceutical compounds, are also included. By enabling direct integration of this knowledgebase with downstream analytical tools, including molecular networking, we can deepen insights into microbiota and their metabolites, ultimately advancing our understanding of microbial ecosystems.

(BioRxiv All) Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data: Microbial metabolites play a critical role in regulating ecosystems, including the human body and its microbiota. However, understanding the physiologically relevant… #BioRxiv #MassSpecRSS

Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data https://www.biorxiv.org/content/10.64898/2026.01.24.701521v1

Vibe Coding Omics Data Analysis Applications Building custom data analysis platforms has traditionally required extensive software engineering expertise, limiting access for many researchers. Here, I demonstrate that modern large language models...

Well, I don’t know what to say here. Discuss…

@cashwood.proteaglyco.com

pubs.acs.org/doi/10.1021/...

Nice piece of #CompMS.

Ionization efficiency prediction of electrospray ionization mass spectrometry analytes based on molecular fingerprints and cumulative neutral losses - Journal of Cheminformatics Quantification is a challenge for non-targeted analysis (NTA) with liquid chromatography–high resolution mass spectrometry (LC–HRMS), due to the lack of analytical standards. Quantification via struct...

Ionization efficiency prediction of electrospray ionization mass spectrometry analytes based on molecular fingerprints and cumulative neutral losses #JCherminform link.springer.com/article/10.1...

A Perspective on Unintentional Fragments and Their Impact on the Dark Metabolome, Untargeted Profiling, Molecular Networking, Public Data, and Repository Scale Analysis In/postsource 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 do nots 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.

The existence of unintentional fragmentation (often referred to as in-source fragments) in untargeted #metabolomics data can cause uncertainty among newcomers to the field and skepticism among data consumers such as medical experts or biologists.

pubs.acs.org/doi/10.1021/...

This is an important paper to read for people that are trying to understand metabolomics data. Ions detected (features) are not molecules and molecules will generate many ion forms. Be aware of MS ion forms - understand and leverage them. Dark metabolome has a lot of discovery potential.

The abstract submission deadline for #SETACMaastricht is around the corner! Submit your abstract by 26 November to showcase your research live in Maastricht next May and connect with environmental experts from around the world. 🌍 Don't miss the deadline and submit today! 👉https://lnkd.in/ec-V3n5j

SETAC staff posing with Voodoo Doughnut bags

Nothing says “hello, Portland” like Voodoo Doughnuts! 🍩 SETAC staff are here, prepping for your arrival at #SETACPortland. Safe travels, and see you all very soon!

Available to read now via Open Access:
pubs.rsc.org/en/content/a...
Fast, general-purpose metabolome analysis by mixed-mode liquid chromatography–mass spectrometry
Nicola Zamboni et al @nzamboni.bsky.social @alaaothman.bsky.social @ethz.ch
#MassSpec

We are super excited that our new paper on microfluidic-based LC-MS/MS fractionation in combination with bioluminescence bioreporters readouts, for compound-resolved bioactivity metabolomics, was just published: pubs.acs.org/doi/10.1021/...

Call for Abstracts: Share Your Science at SETAC Maastricht

📢 #Abstract submission for #SETACMaastricht is open! Join us in May and share your latest #research with a vibrant community of #environmental scientists and professionals. 🌿🧪 Submit your abstract by 26 November and take part in shaping a bold scientific programme!
🔗 lnkd.in/e9rXdwdQhttp...

BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)

Web-based multi-omics suite by Jianguo Xia lab

ExpressAnalyst➡️Transcriptomics/Proteomics
MetaboAnalyst➡️Metabolomics

OmicsNet, OmicsAnalyst➡️Mutiomics integration
omicsnet.ca
www.omicsanalyst.ca

+miRNet mGWAS-Explorer MicrobiomeAnalyst

#NatureProtocols 2024
www.nature.com/articles/s41...

Abstract submission is now open (till 26 November). Join us in an exciting #HABs Session #SETACMaastricht 👇
Session description: setac.secure-platform.com/meetings/gal...
#SETAC #SETACEurope #SETAC2026
@setac.bsky.social @setac-glb.bsky.social

Computational Mass Spectrometry-Based Reassessment of European Amanita sect. Phalloideae Cyclopeptidome An advanced metabolomic workflow featuring expert knowledge-tailored mass spectral queries and multi-informative molecular networking was applied to French DNA-barcoded collections of Amanita species ...

Thrilled to share with you a recent work from our group: Computational Mass Spectrometry-Based Reassessment of European Amanita sect. Phalloideae Cyclopeptidome | Journal of Natural Products pubs.acs.org/doi/10.1021/... Please have a look to the associated MassQL compendium.

A week with Judita Koreiviene, Jurate Karosiene and their Algology (Phycology) lab at the Natural Research Center in #Vilnius. We had fun setting up the HPLC method for #microcystins and organizing an HPLC seminar. A new collaboration has started and exciting results are coming soon....

Last week we had the pleasure to host Constantina Varnava, PhD candidate of Iro Tsipa's group at the University of #Cyprus. We had fun analyzing MS datasets for #microbial #metabolites.

The #IFHAB Workshop 16-17 October at Hamilton #Ontario. #Freshwater #HABs. Still time to register. www.ifhabworkshop.com

Impact of Salinity on Cell Surface Chemistry of Cyanobacteria From Freshwater, Marine and Alkaline Environments: A Hidden Phosphorus Engine The study examines the impact of salinity on surface properties of freshwater Synechocystis sp. PCC6803, marine Synechococcus sp. PCC8806 and alkaliphilic Spirulina platensis. The differences in memb...

Impact of Salinity on Cell Surface Chemistry of Cyanobacteria From Freshwater, Marine and Alkaline Environments: A Hidden Phosphorus Engine enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

Aaand it's out! Meet MITE - the natural product tailoring enzyme database, just published in @narjournal.bsky.social! MITE DB captures the substrate- and reaction-specificity of tailoring enzymes, allowing to capture this information in a human- and machine-readable way! doi.org/10.1093/nar/...

🧪📣 Save the date for SETAC Europe 2016 @setac.bsky.social #SETACMaastricht !
Our Session title: "Integrating #Genomics, #Metabolomics, and Control Strategies to Address Harmful Algal and #Cyanobacterial Blooms", Chaired by Petra Visser, Dail Laughinghouse, @anastasiahiskia.bsky.social.