Reposted by Tobias
Exited to share our latest work! Out now in @natcomms.nature.com
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Koina: Democratizing machine learning for proteomics research - Nature Communications
Koina is an open-source, online platform that simplifies access to machine learning models in proteomics, enabling easier integration into analysis tools and helping researchers adopt and reuse ML mod...
www.nature.com
November 11, 2025 at 8:06 PM
Exited to share our latest work! Out now in @natcomms.nature.com
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!
www.nature.com/articles/s41...
Reposted by Tobias
Our new review paper about Pathway-Centric PTM Data Analysis is out this week in #Proteomics!
We cover databases, enrichment tools, software for pathway reconstruction, and full-fledged platforms that help to interpret high-throughput PTM datasets.
Check it out here: doi.org/10.1002/pmic...
We cover databases, enrichment tools, software for pathway reconstruction, and full-fledged platforms that help to interpret high-throughput PTM datasets.
Check it out here: doi.org/10.1002/pmic...
Computational Approaches for Pathway‐Centric Analysis of Protein Post‐Translational Modifications
Protein function is dynamically modulated by post-translational modifications (PTMs). Many different types of PTMs can nowadays be identified and quantified at a large scale using mass spectrometry. ...
doi.org
October 20, 2025 at 7:07 AM
Our new review paper about Pathway-Centric PTM Data Analysis is out this week in #Proteomics!
We cover databases, enrichment tools, software for pathway reconstruction, and full-fledged platforms that help to interpret high-throughput PTM datasets.
Check it out here: doi.org/10.1002/pmic...
We cover databases, enrichment tools, software for pathway reconstruction, and full-fledged platforms that help to interpret high-throughput PTM datasets.
Check it out here: doi.org/10.1002/pmic...
Reposted by Tobias
ELIXIR-NL's @magnuspalmblad.bsky.social co-organized the Computational Proteomics Dagstuhl Seminar 2025, uniting experts in ML/AI for proteomics. Breakouts sparked collaborations, manuscripts, and proposals, making this the most productive seminar yet. #Proteomics #Dagstuhl #Collaboration
September 10, 2025 at 12:02 PM
ELIXIR-NL's @magnuspalmblad.bsky.social co-organized the Computational Proteomics Dagstuhl Seminar 2025, uniting experts in ML/AI for proteomics. Breakouts sparked collaborations, manuscripts, and proposals, making this the most productive seminar yet. #Proteomics #Dagstuhl #Collaboration
Reposted by Tobias
The University of Michigan now blocks the iProX database, which is a part of the PRIDE consortium of mass spec data repositories. All requests to unblock were denied. Any other US universities in a similar situation? There is a lot of valuable MS proteomics data there no longer accessible to us.
September 10, 2025 at 5:44 PM
The University of Michigan now blocks the iProX database, which is a part of the PRIDE consortium of mass spec data repositories. All requests to unblock were denied. Any other US universities in a similar situation? There is a lot of valuable MS proteomics data there no longer accessible to us.
Reposted by Tobias
The “target landscape of clinical kinase drugs” (2017) has just gotten its 900th citation! There is no shame, I believe, to feel proud of having been part of this effort of the Kuster lab to provide such an - apparently very useful - interactive resource to the scientific community.
September 4, 2025 at 12:30 PM
The “target landscape of clinical kinase drugs” (2017) has just gotten its 900th citation! There is no shame, I believe, to feel proud of having been part of this effort of the Kuster lab to provide such an - apparently very useful - interactive resource to the scientific community.
@magnuspalmblad.bsky.social I was bored in the train and moved my simulations of the #Dagstuhl seating problem to an online R session tkschmidt.me/posts/dagstu... Quite amazing what one can do nowadays in the browser via #webr #webasm
Dagstuhl seminar: A Generalization of the Coupon Collector Problem
A private blog concerning my digital and non digital life
tkschmidt.me
August 29, 2025 at 12:51 PM
@magnuspalmblad.bsky.social I was bored in the train and moved my simulations of the #Dagstuhl seating problem to an online R session tkschmidt.me/posts/dagstu... Quite amazing what one can do nowadays in the browser via #webr #webasm
Reposted by Tobias
Looking forward to a week of productive discussions on Computational Proteomics at Schloss Dagstuhl! Has been a fun meeting to plan with @magnuspalmblad.bsky.social and Mathias Wilhelm
August 24, 2025 at 1:14 PM
Looking forward to a week of productive discussions on Computational Proteomics at Schloss Dagstuhl! Has been a fun meeting to plan with @magnuspalmblad.bsky.social and Mathias Wilhelm
Reposted by Tobias
Great presentation! Just FYI: It is a little known fact that the MS1 quantification by CHIMERYS on the MSAID Platform works by deconvoluting isotope envelopes in a similar way as JMod since the inception of the platform a year ago. If you are interested in 9-plex DIA support, feel free to reach out!
The talk by Dr. Kevin McDonnell at #SCP2025 is on YouTube:
JMod: Joint modeling of mass spectra for enhanced multiplexing in the mass and time domains
youtu.be/qgqloCJJa1M?...
JMod: Joint modeling of mass spectra for enhanced multiplexing in the mass and time domains
youtu.be/qgqloCJJa1M?...
JMod: Joint modeling of mass spectra for enhanced multiplexing in the mass and time domains, SCP2025
YouTube video by Nikolai Slavov
youtu.be
June 21, 2025 at 9:19 PM
Great presentation! Just FYI: It is a little known fact that the MS1 quantification by CHIMERYS on the MSAID Platform works by deconvoluting isotope envelopes in a similar way as JMod since the inception of the platform a year ago. If you are interested in 9-plex DIA support, feel free to reach out!
Reposted by Tobias
Another day of #ASMS2025 in Baltimore, and we're back with another poster! Make sure to visit Flo today - he'll present the latest insights from his large-scale decryptM project.
Go #TeamMassSpec!
Go #TeamMassSpec!
June 4, 2025 at 9:28 AM
Another day of #ASMS2025 in Baltimore, and we're back with another poster! Make sure to visit Flo today - he'll present the latest insights from his large-scale decryptM project.
Go #TeamMassSpec!
Go #TeamMassSpec!
Reposted by Tobias
As an "omics" sciences enthusiast, I am excited to share our latest publication in #metabolomics #biomarker discovery 🧪: www.sciencedirect.com/science/arti...
We identified previously unknown metabolites associated with early-onset Parkinson's disease - in both mice and patients. 🐁 🩸
#TeamMassSpec
We identified previously unknown metabolites associated with early-onset Parkinson's disease - in both mice and patients. 🐁 🩸
#TeamMassSpec
Pervasive glycative stress links metabolic imbalance and muscle atrophy in early-onset Parkinson's disease
Parkinson’s disease (PD) is recognized as a systemic condition, with clinical features potentially modifiable by dietary intervention. Diets high in s…
www.sciencedirect.com
June 3, 2025 at 11:56 AM
As an "omics" sciences enthusiast, I am excited to share our latest publication in #metabolomics #biomarker discovery 🧪: www.sciencedirect.com/science/arti...
We identified previously unknown metabolites associated with early-onset Parkinson's disease - in both mice and patients. 🐁 🩸
#TeamMassSpec
We identified previously unknown metabolites associated with early-onset Parkinson's disease - in both mice and patients. 🐁 🩸
#TeamMassSpec
Reposted by Tobias
5/5 All of @msaid-de.bsky.social at #ASMS2025 can be found at www.msaid.de/conferences/.... Two more highlights:
- @martinfrejno.bsky.social's oral TOA pm 04:10 shows a confirmation bias in DIA that inflates data completeness
- Daniel Zolg's oral ThOA pm 03:30 showing our platform
Enjoy!
- @martinfrejno.bsky.social's oral TOA pm 04:10 shows a confirmation bias in DIA that inflates data completeness
- Daniel Zolg's oral ThOA pm 03:30 showing our platform
Enjoy!
ASMS 2025 | MSAID
ASMS 2025 – Find more information about our participation in conferences and events.
www.msaid.de
May 30, 2025 at 2:43 PM
5/5 All of @msaid-de.bsky.social at #ASMS2025 can be found at www.msaid.de/conferences/.... Two more highlights:
- @martinfrejno.bsky.social's oral TOA pm 04:10 shows a confirmation bias in DIA that inflates data completeness
- Daniel Zolg's oral ThOA pm 03:30 showing our platform
Enjoy!
- @martinfrejno.bsky.social's oral TOA pm 04:10 shows a confirmation bias in DIA that inflates data completeness
- Daniel Zolg's oral ThOA pm 03:30 showing our platform
Enjoy!
Reposted by Tobias
4/5 Our newly introduced TimsTOF ✈️ support deserves its own spotlight! Visit @tkschmidt.me on Tuesday at TP 507. We show how Chimerys 5 and Inferys 5 perform on dda-PASEF and dia-PASEF and outperform or match alternatives out-of-the-box.
May 30, 2025 at 2:43 PM
4/5 Our newly introduced TimsTOF ✈️ support deserves its own spotlight! Visit @tkschmidt.me on Tuesday at TP 507. We show how Chimerys 5 and Inferys 5 perform on dda-PASEF and dia-PASEF and outperform or match alternatives out-of-the-box.
Reposted by Tobias
#TeamMassSpec, don't miss my talk about double dipping in DIA data analysis on Tuesday afternoon at #ASMS2025! It's not as savoury as the one below, but will contain a couple of spicy takes. 🙃
May 31, 2025 at 5:04 PM
#TeamMassSpec, don't miss my talk about double dipping in DIA data analysis on Tuesday afternoon at #ASMS2025! It's not as savoury as the one below, but will contain a couple of spicy takes. 🙃
Reposted by Tobias
Woke up in Baltimore for #ASMS2025 and wondering what's on today? Here's a good start:
11:30 - 5:30 pm Waters user meeting -> Intact MS of BIG molecules, upgraded QQQ, maybe a QTOF upgrade?
5:30 - 9:30 pm Evosep user meeting -> Upgraded version of their existing LC
That's lunch/dinner covered ;)
11:30 - 5:30 pm Waters user meeting -> Intact MS of BIG molecules, upgraded QQQ, maybe a QTOF upgrade?
5:30 - 9:30 pm Evosep user meeting -> Upgraded version of their existing LC
That's lunch/dinner covered ;)
May 31, 2025 at 11:16 AM
Woke up in Baltimore for #ASMS2025 and wondering what's on today? Here's a good start:
11:30 - 5:30 pm Waters user meeting -> Intact MS of BIG molecules, upgraded QQQ, maybe a QTOF upgrade?
5:30 - 9:30 pm Evosep user meeting -> Upgraded version of their existing LC
That's lunch/dinner covered ;)
11:30 - 5:30 pm Waters user meeting -> Intact MS of BIG molecules, upgraded QQQ, maybe a QTOF upgrade?
5:30 - 9:30 pm Evosep user meeting -> Upgraded version of their existing LC
That's lunch/dinner covered ;)
Reposted by Tobias
We are working hard on generalizing our peptide property prediction models to more diverse peptide classes! Watch out for my colleague @lizimamisashvili.bsky.social's ASMS talk (TOE am) to input any molecular structure to our models. Next, we need to generalize our model output too.
April 23, 2025 at 8:37 AM
We are working hard on generalizing our peptide property prediction models to more diverse peptide classes! Watch out for my colleague @lizimamisashvili.bsky.social's ASMS talk (TOE am) to input any molecular structure to our models. Next, we need to generalize our model output too.
Reposted by Tobias
One algorithm to rule them all? CHIMERYS bridges the gap — DDA,DIA and PRM — together at last!
With #CHIMERYS, we can now directly compare DDA and DIA data — 🍎 to 🍎 finally made possible.
doi.org/10.1038/s41592-025-02663-w
#KusterLab #WilhelmLab #MSAID #Proteomics
With #CHIMERYS, we can now directly compare DDA and DIA data — 🍎 to 🍎 finally made possible.
doi.org/10.1038/s41592-025-02663-w
#KusterLab #WilhelmLab #MSAID #Proteomics
Unifying the analysis of bottom-up proteomics data with CHIMERYS - Nature Methods
CHIMERYS is a spectrum-centric and data acquisition method-agnostic algorithm for the analysis of MS2 spectra. It is capable of deconvoluting any MS2 spectrum, regardless of whether it was acquired by...
doi.org
April 22, 2025 at 11:44 AM
One algorithm to rule them all? CHIMERYS bridges the gap — DDA,DIA and PRM — together at last!
With #CHIMERYS, we can now directly compare DDA and DIA data — 🍎 to 🍎 finally made possible.
doi.org/10.1038/s41592-025-02663-w
#KusterLab #WilhelmLab #MSAID #Proteomics
With #CHIMERYS, we can now directly compare DDA and DIA data — 🍎 to 🍎 finally made possible.
doi.org/10.1038/s41592-025-02663-w
#KusterLab #WilhelmLab #MSAID #Proteomics
Reposted by Tobias
Backyard proteomics: A case study with the black widow spider https://www.biorxiv.org/content/10.1101/2025.04.11.648442v1
April 12, 2025 at 4:49 AM
Backyard proteomics: A case study with the black widow spider https://www.biorxiv.org/content/10.1101/2025.04.11.648442v1
Reposted by Tobias
Hey #TeamMassSpec, exciting news to end the week! 🔬✨
We are announcing our next seminar!
Join us for the Advanced Mass Spectrometry Seminar with special guest Brendan MacLean, the #PI behind #Skyline — the leading open-source tool for targeted proteomics and metabolomics. 🧪💻
We are announcing our next seminar!
Join us for the Advanced Mass Spectrometry Seminar with special guest Brendan MacLean, the #PI behind #Skyline — the leading open-source tool for targeted proteomics and metabolomics. 🧪💻
March 28, 2025 at 6:45 PM
Hey #TeamMassSpec, exciting news to end the week! 🔬✨
We are announcing our next seminar!
Join us for the Advanced Mass Spectrometry Seminar with special guest Brendan MacLean, the #PI behind #Skyline — the leading open-source tool for targeted proteomics and metabolomics. 🧪💻
We are announcing our next seminar!
Join us for the Advanced Mass Spectrometry Seminar with special guest Brendan MacLean, the #PI behind #Skyline — the leading open-source tool for targeted proteomics and metabolomics. 🧪💻
Reposted by Tobias
The Brixen Proteomics Summer School speaker list has been finalised!. Lots of amazing science to be discussed! Big thanks to @eupaproteomics.bsky.social @msaid-de.bsky.social @thermofishersci.bsky.social @biognosys.bsky.social @ionopticks.bsky.social @evosep.bsky.social for support
March 7, 2025 at 10:21 AM
The Brixen Proteomics Summer School speaker list has been finalised!. Lots of amazing science to be discussed! Big thanks to @eupaproteomics.bsky.social @msaid-de.bsky.social @thermofishersci.bsky.social @biognosys.bsky.social @ionopticks.bsky.social @evosep.bsky.social for support
Reposted by Tobias
Want to know more about how the MSAID Platform can process your #proteomics data from #massSpec raw file to data insight powered by the #cloud? 🌩️
Have a look at our newest publication 🔥
Have a look at our newest publication 🔥
We are thrilled to announce our first publication featuring the MSAID Platform, the all-in-one solution for #proteomics data analysis.
📙 Read the full article here: pubs.acs.org/doi/full/10....
➡️ Try the MSAID Platform for free: platform.msaid.io
#TeamMassSpec #TeamProteomics #MassSpectrometry
📙 Read the full article here: pubs.acs.org/doi/full/10....
➡️ Try the MSAID Platform for free: platform.msaid.io
#TeamMassSpec #TeamProteomics #MassSpectrometry
February 25, 2025 at 1:03 PM
Want to know more about how the MSAID Platform can process your #proteomics data from #massSpec raw file to data insight powered by the #cloud? 🌩️
Have a look at our newest publication 🔥
Have a look at our newest publication 🔥
Reposted by Tobias
The Brixen Summer School is back and is, as usual, building up a strong speaker list. Thank you @eupaproteomics.bsky.social @ukbspr.bsky.social @msaid-de.bsky.social @thermofishersci.bsky.social @biognosys.bsky.social @ionopticks.bsky.social @evosep.bsky.social for support!
February 3, 2025 at 12:04 PM
The Brixen Summer School is back and is, as usual, building up a strong speaker list. Thank you @eupaproteomics.bsky.social @ukbspr.bsky.social @msaid-de.bsky.social @thermofishersci.bsky.social @biognosys.bsky.social @ionopticks.bsky.social @evosep.bsky.social for support!
Reposted by Tobias
The @eubic-ms.org Dev Meeting was amazing! We explored how to automatically extract metadata. I'm super excited to continue this effort 🤗 A huge thanks to the incredible team of this hackathon 🙏
#EuBIC2025
#EuBIC2025
February 7, 2025 at 10:22 AM
The @eubic-ms.org Dev Meeting was amazing! We explored how to automatically extract metadata. I'm super excited to continue this effort 🤗 A huge thanks to the incredible team of this hackathon 🙏
#EuBIC2025
#EuBIC2025
It is surprisingly easy to connect your Bluesky handle with your own domain :)
December 31, 2024 at 8:52 AM
It is surprisingly easy to connect your Bluesky handle with your own domain :)