Lightnews — Scholar-powered news

Reposted by Tomáš Pluskal

Nature Methods @natmethods.nature.com · 22d

MSnLib: a large-scale, open multi-stage fragmentation mass spectral library for 30,000 unique small molecules.
@robinschmid.bsky.social @pluskal-lab.org

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

MSnLib: efficient generation of open multi-stage fragmentation mass spectral libraries - Nature Methods

MSnLib is a large-scale, open MSn spectral library featuring >2.3 million MSn and >357,000 MS2 spectra for 30,008 unique small molecules.

www.nature.com

2 11

Tomáš Pluskal @pluskal-lab.org · 22d

Also, it is a great showcase of our ongoing collaboration with @mzio-gmbh.bsky.social @robinschmid.bsky.social on developing new @mzmine.bsky.social workflows.

Tomáš Pluskal @pluskal-lab.org · 22d

Most importantly, the effort still continues and we hope to reach 200,000 analyzed compounds in a few months, with all the data publicly available with no restrictions. This open resource is super valuable for the whole metabolomics community and especially for ML applications.

1

Tomáš Pluskal @pluskal-lab.org · 22d

I am very proud of the final outcome of this project, mainly driven by Corinna Brungs and supported by numerous labs who donated compounds for analysis.

IOCB Prague @iocbprague.bsky.social · 22d

The @pluskal-lab.org is helping colleagues around the world identify unknown compounds.

A #research article about their vast #massspec library has been published in @natmethods.nature.com with Corinna Brungs & @robinschmidt.bsky.social as the first two authors.

See more ► www.uochb.cz/en/news/732

2 1 18

Tomáš Pluskal @pluskal-lab.org · Aug 21

The first day of our bioML symposium at @iocbprague.bsky.social went very well. It is amazing to see how fast this field is moving forward. Thanks to everyone for the fantastic talks! 🤖🧬

1 7 15

Reposted by Tomáš Pluskal

Kyo Bin Kang @kyobinkang.bsky.social · Aug 1

Yesterday @roman-bushuiev.bsky.social visited our lab. He gave a seminar talk about his recent work on DreaMS (www.nature.com/articles/s41...), and provided a hands-on training to my lab members. Looking forward to what we will discover using this awesome tool!

1 3 11

Tomáš Pluskal @pluskal-lab.org · Jun 27

My pleasure! 🙂

2

Reposted by Tomáš Pluskal

mzio @mzio-gmbh.bsky.social · Jun 9

At #ASMS2025, we presented a next-gen workflow pairing the #timsMetabo MoRE (Mobility Range Enhancement) with #mzmine and #DreaMS

Compared to conventional LC-MS2, the data delivered:

- 84% more detected features
- 5.7× more MS² spectra
- 3× more spectral matches

Read the full poster to learn MoRE

3 12

Reposted by Tomáš Pluskal

EMN Metabolomics Society @emn-metsoc.bsky.social · Jun 6

🚨 MetaboART 🎨 2025 – Deadline Extended:

🗓️ Submissions now open until June 13!

Two categoried:
👤 Human-Created // 🤖 AI-Generated

🏆Winner @ #MetSoc25 on June 24
Details👉 tinyurl.com/dh37xt78
📩[email protected]

EMN Metabolomics Society @emn-metsoc.bsky.social · Apr 1

🎨 MetaboART 2025 is here!

Turn your #metabolomics research into visual art!

The categories:
👤 Human-made //🤖 AI-generated

🗓️ Submit Apr 1–May 31
🏆 Winners @ #MetSoc25 on June 24

Details 👉 tinyurl.com/dh37xt78
📩 [email protected]

#MetaboART #SciArt
@metsoc.bsky.social

7 8

Reposted by Tomáš Pluskal

mzio @mzio-gmbh.bsky.social · Jun 3

#mzmine 4.7 is now available!

This release brings our most significant improvement in memory efficiency to date, unlocking new capabilities for analyzing large-scale datasets.

Join us for a live software demo at our booth today and tomorrow at 12:00/noon during #ASMS2025

6 13

Tomáš Pluskal @pluskal-lab.org · May 30

Today is the registration deadline for our bioML symposium on Aug 21-22. Last chance to secure your spot! More info at tinyurl.com/bioMLPrague25

3 11

Reposted by Tomáš Pluskal

IOCB Prague @iocbprague.bsky.social · May 28

⚛️ @pluskal-lab.org from IOCB Prague, together with his student @roman-bushuiev.bsky.social and colleagues from #CIIRC CTU, Josef Šivic and @anton-bushuiev.bsky.social, have developed a machine learning model called #DreaMS – which accelerates the analysis of previously unknown molecules.

1 5 11

Reposted by Tomáš Pluskal

Roman Bushuiev @roman-bushuiev.bsky.social · May 26

Mass spectrometry is a key method to discover and identify molecules in biological and environmental samples. Yet, >90% of mass spectra remain hard to interpret. In our recent paper, we present DreaMS — a foundation model to interpret mass spectra of small molecules.
www.nature.com/articles/s41...

Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS - Nature Biotechnology

A transformer model is used to construct the DreaMS Atlas—a molecular network of 201 million MS/MS spectra.

www.nature.com

1 10 25

Tomáš Pluskal @pluskal-lab.org · May 24

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.

Nature Biotechnology @natbiotech.nature.com · May 23

Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS - @pluskal-lab.org @iocbprague.bsky.social go.nature.com/4k1n5iC

Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS - Nature Biotechnology

A transformer model is used to construct the DreaMS Atlas—a molecular network of 201 million MS/MS spectra.

go.nature.com

20 52

Reposted by Tomáš Pluskal

Nature Methods @natmethods.nature.com · May 13

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...

1 16 38

Reposted by Tomáš Pluskal

mzio @mzio-gmbh.bsky.social · May 17

Join us for a power-packed software workshop where we’ll be breaking boundaries in multi-vendor MS analysis using #mzmine at #ASMS2015

Led by experts @robinschmid.bsky.social and @ansgarkorf.bsky.social

𝗡𝗼 𝘀𝗶𝗴𝗻–𝘂𝗽 𝗿𝗲𝗾𝘂𝗶𝗿𝗲𝗱, 𝗷𝘂𝘀𝘁 𝗱𝗿𝗼𝗽 𝗯𝘆 𝘁𝗵𝗲 𝗯𝗼𝗼𝘁𝗵 𝗮𝘁 𝟭𝟮 𝗺𝗶𝗱𝗱𝗮𝘆.

See you there! 👋

7 14

Reposted by Tomáš Pluskal

mzio @mzio-gmbh.bsky.social · May 10

Get Ready! Only 3 weeks to go until #ASMS2025!

Our team will be showcasing our latest developments in #mzmine at this year’s conference.

Stop by Booth 210 for live demonstrations and insights into how you can streamline your data processing across multiple vendors, adding speed and confidence.

5 16

Reposted by Tomáš Pluskal

IOCB Prague @iocbprague.bsky.social · May 6

🤝 IOCB Prague is hiring – we are looking for an outstanding Junior Group Leader in Biosciences to join our vibrant scientific community.

See more ► www.uochb.cz/en/open-posi... ⤵️

#openposition #iocbprague #iocb #researchjobs #biosciences

5 8

Tomáš Pluskal @pluskal-lab.org · Apr 29

Also thanks to Mélissa Nothias (LMR Naturals by IFF) for her great keynote lecture!

2

Tomáš Pluskal @pluskal-lab.org · Apr 29

Another year, another @mzmine.bsky.social workshop at
@iocbprague.bsky.social! Both new and advanced users are learning about the latest mzmine features from our amazing instructors @ansgarkorf.bsky.social, Josh Smith,
@titodamiani.bsky.social, and @roman-bushuiev.bsky.social.

1 3 19

Tomáš Pluskal @pluskal-lab.org · Apr 11

Back in July 2023 we organized a small bioML symposium at @iocbprague.bsky.social, and it turned out to be a very pleasant and successful event. This summer we are following up with a great line-up of speakers. Please register for free, deadline May 30. tinyurl.com/bioMLPrague25

8 17

Reposted by Tomáš Pluskal

IOCB Prague @iocbprague.bsky.social · Apr 8

#mzmine

Rapid MALDI-MS/MS-Based Profiling of Lipid A Species from Gram-Negative Bacteria Utilizing Trapped Ion Mobility Spectrometry and mzmine (Rudt, Froning, @robinschmid.bsky.social, @pluskal-lab.org)–AC: doi.org/10.1021/acs....

@iocbprague.bsky.social @mzmine.bsky.social @uni-muenster.de

1 4 14

Reposted by Tomáš Pluskal

Mikrobiologický ústav AV ČR @mbuavcr.bsky.social · Mar 26

We were hosting a MZmine workshop within our INTER-MICRO /Talking microbes/ OP JAK project.

Presenters: Zdeněk Kameník (Laboratory of Antibiotic Resistance and Microbial Metabolomics IMIC);
Tito Damiani and Joshua Smith (Tomáš Pluskal group @iocbprague.bsky.social)

Learning new things #intermicro

2 3 13

Tomáš Pluskal @pluskal-lab.org · Mar 11

We will bring together seasoned mzmine users, newcomers and developers to exchange knowledge, share best practices, and discuss the ways mzmine powers cutting-edge research.

We will also host keynote speakers Dr. Annika Jagels (LifeMine Therapeutics) and Dr. Mélissa Nothias (LMR Naturals by IFF).

Tomáš Pluskal @pluskal-lab.org · Mar 11

Only a few days remain to register for the first official mzmine Community Meeting, taking place on April 28-29 at @iocbprague.bsky.social.

Registration:
docs.google.com/forms/d/e/1F...

Program:
docs.google.com/document/d/1...

1 5 6