Tomáš Pluskal
@pluskal-lab.org
Group Leader at the Institute of Organic Chemistry and Biochemistry (IOCB Prague @iocbprague.bsky.social). Plant biochemistry, metabolomics, genomics, bioML, etc. https://www.pluskal-lab.org
Reposted by Tomáš Pluskal
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
October 26, 2025 at 10:40 PM
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
Reposted by Tomáš Pluskal
We train machine learning models on millions of proteins. But when it comes to making predictions, do we need them to understand all proteins at once? Often, we need an accurate model for the specific protein we are studying or designing. We address this with ProteinTTT arxiv.org/abs/2411.02109 1/🧵
October 23, 2025 at 1:08 PM
We train machine learning models on millions of proteins. But when it comes to making predictions, do we need them to understand all proteins at once? Often, we need an accurate model for the specific protein we are studying or designing. We address this with ProteinTTT arxiv.org/abs/2411.02109 1/🧵
BIG BIG congratulations to our PhD student
@roman-bushuiev.bsky.social for receiving the Google PhD Fellowship 2025 in Health Research! 🎉💰 goo.gle/43wJWw8
@roman-bushuiev.bsky.social for receiving the Google PhD Fellowship 2025 in Health Research! 🎉💰 goo.gle/43wJWw8
October 25, 2025 at 12:44 AM
BIG BIG congratulations to our PhD student
@roman-bushuiev.bsky.social for receiving the Google PhD Fellowship 2025 in Health Research! 🎉💰 goo.gle/43wJWw8
@roman-bushuiev.bsky.social for receiving the Google PhD Fellowship 2025 in Health Research! 🎉💰 goo.gle/43wJWw8
Reposted by Tomáš Pluskal
Je život ve vesmíru vzácný, nebo se naopak může vyskytovat skoro všude?
Odpověď na to hledá projekt #PROTOCELL Kláry Hlouchové a @pluskal-lab.org, který vzniká v @iocbprague.bsky.social. 1/3
#ČeskáCestaDoVesmíru #CzechSpace #CzechSpaceWeek2025 #CzechSpaceWeek #UOCHB #IOCB #IOCBPrague
Odpověď na to hledá projekt #PROTOCELL Kláry Hlouchové a @pluskal-lab.org, který vzniká v @iocbprague.bsky.social. 1/3
#ČeskáCestaDoVesmíru #CzechSpace #CzechSpaceWeek2025 #CzechSpaceWeek #UOCHB #IOCB #IOCBPrague
October 21, 2025 at 6:37 PM
Je život ve vesmíru vzácný, nebo se naopak může vyskytovat skoro všude?
Odpověď na to hledá projekt #PROTOCELL Kláry Hlouchové a @pluskal-lab.org, který vzniká v @iocbprague.bsky.social. 1/3
#ČeskáCestaDoVesmíru #CzechSpace #CzechSpaceWeek2025 #CzechSpaceWeek #UOCHB #IOCB #IOCBPrague
Odpověď na to hledá projekt #PROTOCELL Kláry Hlouchové a @pluskal-lab.org, který vzniká v @iocbprague.bsky.social. 1/3
#ČeskáCestaDoVesmíru #CzechSpace #CzechSpaceWeek2025 #CzechSpaceWeek #UOCHB #IOCB #IOCBPrague
Reposted by Tomáš Pluskal
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...
@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
September 16, 2025 at 2:57 PM
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...
@robinschmid.bsky.social @pluskal-lab.org
www.nature.com/articles/s41...
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.
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
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
September 16, 2025 at 8:25 AM
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.
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! 🤖🧬
August 21, 2025 at 8:22 PM
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! 🤖🧬
Reposted by Tomáš Pluskal
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!
August 1, 2025 at 8:37 AM
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!
Reposted by Tomáš Pluskal
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
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
June 9, 2025 at 8:11 PM
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
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
Reposted by Tomáš Pluskal
🚨 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
📩info.emn@metabolomicssociety.org
🗓️ Submissions now open until June 13!
Two categoried:
👤 Human-Created // 🤖 AI-Generated
🏆Winner @ #MetSoc25 on June 24
Details👉 tinyurl.com/dh37xt78
📩info.emn@metabolomicssociety.org
🎨 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
📩 info.emn@metabolomicssociety.org
#MetaboART #SciArt
@metsoc.bsky.social
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
📩 info.emn@metabolomicssociety.org
#MetaboART #SciArt
@metsoc.bsky.social
June 6, 2025 at 7:41 AM
🚨 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
📩info.emn@metabolomicssociety.org
🗓️ Submissions now open until June 13!
Two categoried:
👤 Human-Created // 🤖 AI-Generated
🏆Winner @ #MetSoc25 on June 24
Details👉 tinyurl.com/dh37xt78
📩info.emn@metabolomicssociety.org
Reposted by Tomáš Pluskal
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
May 30, 2025 at 3:01 PM
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
Reposted by Tomáš Pluskal
⚛️ @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.
May 28, 2025 at 1:43 PM
⚛️ @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.
Reposted by Tomáš Pluskal
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...
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
May 26, 2025 at 1:44 PM
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...
www.nature.com/articles/s41...
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.
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
May 24, 2025 at 8:21 AM
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.
Reposted by Tomáš Pluskal
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...
www.nature.com/articles/s41...
May 13, 2025 at 3:25 PM
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...
www.nature.com/articles/s41...
Reposted by Tomáš Pluskal
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! 👋
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! 👋
May 17, 2025 at 11:27 AM
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! 👋
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! 👋
Reposted by Tomáš Pluskal
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.
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.
May 10, 2025 at 9:14 AM
Reposted by Tomáš Pluskal
🤝 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
See more ► www.uochb.cz/en/open-posi... ⤵️
#openposition #iocbprague #iocb #researchjobs #biosciences
May 6, 2025 at 7:09 PM
🤝 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
See more ► www.uochb.cz/en/open-posi... ⤵️
#openposition #iocbprague #iocb #researchjobs #biosciences
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.
@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.
April 29, 2025 at 9:34 AM
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.
@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.
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
April 11, 2025 at 11:34 AM
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
Reposted by Tomáš Pluskal
#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
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
April 8, 2025 at 1:33 PM
#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
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
Reposted by Tomáš Pluskal
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
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
March 26, 2025 at 9:43 AM
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
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
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...
Registration:
docs.google.com/forms/d/e/1F...
Program:
docs.google.com/document/d/1...
March 11, 2025 at 3:22 PM
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...
Registration:
docs.google.com/forms/d/e/1F...
Program:
docs.google.com/document/d/1...
This is the first paper from our Piper-series, many more to follow. A great effort by multiple lab members!
𝐓𝐞𝐜𝐡𝐧𝐢𝐜𝐚𝐥 𝐀𝐝𝐯𝐚𝐧𝐜𝐞
Computational metabolomics reveals overlooked chemodiversity of alkaloid scaffolds in Piper fimbriulatum
📖 doi.org/10.1111/tpj.70086
📝 Damiani, Smith et al @tomas_pluskal´s lab
🗺️ @iocbprague.bsky.social @czechacademy.bsky.social @CharlesUniPRG
Computational metabolomics reveals overlooked chemodiversity of alkaloid scaffolds in Piper fimbriulatum
📖 doi.org/10.1111/tpj.70086
📝 Damiani, Smith et al @tomas_pluskal´s lab
🗺️ @iocbprague.bsky.social @czechacademy.bsky.social @CharlesUniPRG
doi.org
March 9, 2025 at 4:52 PM
This is the first paper from our Piper-series, many more to follow. A great effort by multiple lab members!