AquOmixLab

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

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

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

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...

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

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/...

Huge congrats to Sylvia Bonilla 🏆 on winning the Kilham Memorial Lecture Award from SIL! Her vital work on toxic cyanobacteria across Latin America is attracting high interest from researchers across Europe and worldwide. 🔬🌍

@cyanoaction.bsky.social @ictc13.bsky.social

🧪📣 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.

Save the date for an exciting #HABs Session at #SETACMaastricht 👇

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....

Great work by @helenamrusso.bsky.social and Wilhan Nunes on the CMMC @microbialcmmc.bsky.social analysis dashboard in @gnps2.bsky.social . It is very exciting to explore results in new ways ! #teammassspec

Implementing the MCheM setup is pretty easy, and all reagents and hardware components are commercially available and relatively cheap.
MCheM data analysis is supported in @mzmine.bsky.social @gnps2.bsky.social and SIRIUS (@brightgiant.bsky.social) and free for academic researchers.

Thanks so much to everybody who made this interdisciplinary project possible. And epically the editor and the three reviewers at @natcomms.nature.com for their throughout positive feedback.

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

#WeekendRead

DreaMS — a self-supervised transformer model trained on 700M+ unannotated MS/MS spectra. It learns rich molecular representations directly from raw spectral data.

Curious? 🔗bit.ly/43BDjYV

#metabolomics #AI #machinelearning #deeplearning #annotation

🧵(4/6)

🌟 There will be additional talks by our #local "#heroes" in the #Bavarian #TeamMassSpec community!

A great mixture between all the pillars of our team, #Proteomics, #Metabolomics, #Bioinformatics, and applied #MassSpec techniques for a vast diversity of biological questions.

jerry from tom and jerry is reading a book while laying on a lounge chair ALT: jerry from tom and jerry is reading a book while laying on a lounge chair

Just out: Latest selection of novel methods for #metabolomics and #lipidomics

biomed.news/bims-metlip/...

A collaboration with @biomednews.bsky.social

Our new paper in Molecular Ecology:
Omics to Study and Manage Aquatic Environments: A Snapshot From the AquaEcOmics Meeting (Evian-les-Bains, 2025). onlinelibrary.wiley.com/doi/10.1111/...
#omics #water #ecology #metabarcoding #metagenomics #metabolomics #biodiversity

Distilled rule of thumb for optimal Cosine cutoffs at various n matching MS2 fragments in #metabolomics ID:

Cosine > 0.90 - 0.05*MMP

Aligns well with ~80% at 3 matched fragments I learned before.

From Fig4a here www.nature.com/articles/s41...

[ASAP] Advanced Computational Approaches for Unraveling Transformation Pathways of Organic Micropollutants in Aquatic Environments: Insights from the Photodegradation of Ciprofloxacin Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00088

(JASMS) [ASAP] Advanced Computational Approaches for Unraveling Transformation Pathways of Organic Micropollutants in Aquatic Environments: Insights from the Photodegradation of Ciprofloxacin: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00088 (RSS) #MassSpecRSS #JASMS

Our new paper on the aroma of #Spirulina is out now in IJMS! A #sensomics approach to find out what makes it smell so unique. Congrats to Katerina Paraskevopoulou, M. Steinhaus, and V. Mall! A great collab between LSB at TUM and NCSR Demokritos. @mdpiopenaccess.bsky.social
doi.org/10.3390/ijms...

This article reviews #metabolomics data #preprocessing methods, discusses their pros and cons, and emphasizes that the choice of method depends on the biological hypothesis, #dataset characteristics, and the selected statistical data analysis method. @uicdom.bsky.social

#MostRead: buff.ly/tQpaQns

SingleFrag: a deep learning tool for MS/MS fragment and spectral prediction and metabolite annotation Abstract. Metabolite and small molecule identification via tandem mass spectrometry (MS/MS) involves matching experimental spectra with prerecorded spectra

New paper out in Briefings in Bioinformatics

📰SingleFrag: a deep learning tool for MS/MS fragment and spectral prediction and metabolite annotation academic.oup.com/bib/article/...

Announcing the 2025 Simons Early Career Investigators in Aquatic Microbial Ecology and Evolution The Simons Foundation and Simons Foundation International have named six scientists as 2025 Simons Early Career Investigators in Aquatic Microbial Ecology and Evolution. The two-year awards are intend...

Congratulations to our six new 2025 Simons Early Career Investigators in Aquatic Microbial Ecology and Evolution! See full list: www.simonsfoundation.org/2025/07/01/a... #science @systemsecology.bsky.social @daniel-petras.bsky.social @kendraturkkubo.bsky.social