Indeed - we have an entire workshop next week dedicated to FDR estimation in mass spectrometry-based proteomics, with most of the leading researchers in the field attending: www.lorentzcenter.nl/trustworthin...
DDLS Research School Postdoc Program opens in January 2026. 🧪🖥️
@lukaskall.bsky.social, Director of the program, explains how the initiative is designed to identify talent and support researchers who want to build long-term careers in Sweden. ↓
www.scilifelab.se/news/intervi...
Organelles do NOT have a single uniform pH.
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
RAW data repository is unfortunately in maintenance mode :(
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...
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...
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
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.
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
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
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!
Do you know if the talks are recorded? I couldn’t be there and I have the feeling I’m missing a lot ^^
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!
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
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!
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.
#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. 🙃
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 ;)
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.
The UVEN device taught me that high power LED can become very hot and desolder themself 🤓
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
Backyard proteomics: A case study with the black widow spider https://www.biorxiv.org/content/10.1101/2025.04.11.648442v1
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. 🧪💻
Lecture of @kusterlab.bsky.social about bioanalytics in general :)
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
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 🔥
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!
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
I like cinnamon (mint) but we use internally only Ubuntu. Most special drivers (looking at you cuda) would probably work also on Mint.
