Mathias Wilhelm

TT Professor of Computational Mass Spectrometry at the Technical University of Munich. Focusing on mass spectrometry-based proteomics. @proteomicsdb @msaid_de

[Mathias Wilhelm @wilhelm_compms]

Prosit-MultiFrag, a model predicting spectra for UVPD, ECD, ETciD & EID, is out 🚀
🔗 https://t.co/2ZB15q0AsF
Great collaboration with Shabaz Mohammed & Nikita Levin.

Try it via Koina https://t.co/sbLw1qX3Ao and Oktoberfest: https://t.co/1ugfA4mCUr

#Proteomics #MassSpectrometry

[Mathias Wilhelm @wilhelm_compms]

You want easy access, integration, and reuse of deep learning models?🤖
You want to plug new models into your pipelines without pain?🔌
Koina is your solution🚀https://t.co/xggDwB1gKm
An open and decentralized model hub — built to make ML in proteomics usable🌐
#proteomics #AI

[Mathias Wilhelm @wilhelm_compms]

After a long journey, we’re thrilled to share our new preprint! 🎉
🔬 Prosit-PTM leveraging ProteomeTools-PTM and novel data augmentation to enable zero-shot prediction
👉 Boosts PTM site localization, histone peptide IDs, and even modifications on HLA peptides
#AI #Proteomics

[bioRxiv Bioinfo @biorxiv_bioinfo]

Learning the Unseen: Data-Augmented Deep Learning for PTM Discovery with Prosit-PTM https://t.co/vEcpppkmmt #biorxiv_bioinfo

[bioRxiv Bioinfo @biorxiv_bioinfo]

Learning the Unseen: Data-Augmented Deep Learning for PTM Discovery with Prosit-PTM https://t.co/vEcpppkmmt #biorxiv_bioinfo

[Mathias Wilhelm @wilhelm_compms]

🚀 Join us for a PhD in AI & proteomics!
Work on confidence prediction for fine-tuned AI peptide property models with applications in single-cell proteomics.
🔬 Apply by Nov 30 2025:
👉 https://t.co/JdBTeApGfd

#PhD #AI #Proteomics #MachineLearning #TUM #MarieCurie #Research

[Mathias Wilhelm @wilhelm_compms]

🚨 New paper drop! Prosit-XL by Mostafa from @PROTrEIN_ITN!
🔬 Accurately predicts fragment intensities
🧬 For cleavable & non-cleavable linkers
📈 Boosts PPI discovery
🧠 Smarter rescoring avoids FDR inflation
👉 https://t.co/hGuawUfXC4
#Proteomics #MassSpec #AI #Bioinformatics

[Mathias Wilhelm @wilhelm_compms]

Good things­ take time🎆 This is certainly true for #CHIMERYS . First prototype implemented in 2019 for DDA only. New with full support for DIA and PRM as well. So happy to finally see it published in #naturemethods Great accomplishment by @msaid_de

[MSAID @msaid_de]

🚨 New in @naturemethods
#CHIMERYS has already transformed #proteomics since 2022, powering DDA, DIA & PRM analysis in a single workflow.
Wanna know how CHIMERYS works? 👉 https://t.co/sq8LuPgFud
#TeamMassSpec #NatureMethods #ASMS2025 🧪🔬
1/7

[kusterlab (Inactive) @kusterlab]

#HUPO2024 starts tomorrow and the Terrific TUM Team is ready! Kusterlab, Wilhelmlab (@wilhelm_compms), Leelab (@msleemslab) and BayBioMS (@BayBioMS) have printed their posters and prepared their talks, and we're very excited for the next days. See you in Dresden!

[Mathias Wilhelm @wilhelm_compms]

You have a strong background in bioinformatics🖥️, data science📈, machine learning, and multi omics? You want to do a PhD👩‍🎓facilitating non-clinical safety assessment? If so, come and join our ProteomicsDB team.

https://t.co/PFXK8E45Ln

[Mathias Wilhelm @wilhelm_compms]

📊Never heard about rescoring in proteomics?
Check our latest manuscript on rescoring search engine results in proteomics using machine and deep learning and our perspective on it for users and developers📈
https://t.co/H4Udwh8PZ4

#proteomics #machinelearning #deeplearning

[Maria Martin @martinmariaj]

If you value UniProt, please help us to capture this in this survey!

[Mathias Wilhelm @wilhelm_compms]

#proteomics ⚖️, #datascience 📊 or #programmers 🧑‍💻? We are looking to fill a staff scientist position centered around ProteomicsDB. More details available here: https://t.co/Dp2bT0nn1E

[Mathias Wilhelm @wilhelm_compms]

First paper in 2024 is out. Spectralis for de novo peptide sequencing https://t.co/ZgKoMuI9Eg. Awesome collaboration with @gagneurlab spearheaded by Daniela Klaproth-Andrade.

[The Proteomes That Feed The World @CropProteomics]

Hey, #BSPREUPA2023 folks! We are coming to #BSPREUPA2023 in Newcastle with a poster and a talk! Looking forward to meeting, discussing and doing new collaborations! 🤩 #cropproteomeengine

[Mathias Wilhelm @wilhelm_compms]

@teerap16 @chrashwood Levenshtein 1. Maybe reflections have less penalty?

[MS Lee Lab @msleemslab]

Time flies! Last day at #ASMS2023 we are excited to reveal our final meters of posters by @leelab and @wilhelm_compms, showcasing the Prosit PTM model and its impact on citrullination identification accuracy. Don't miss out on this finale! #TTTT #TUM

[Ralf Gabriels @RalfGabriels]

At #ASMS2023 and want to discuss or learn about #OpenMS and about #MachineLearning?
Join the @OpenMSTeam (Samuel Wein & @JeongKyowon), @sgessulat, @wilhelm_compms, and me at the #BioinformaticsHub for sessions at 10:30 and at 12:30.
Full schedule 👇https://t.co/DLnXi72Qrn

[Matthias Trost 🇪🇺 @TrostLab]

Less than 2 weeks left to register and submit abstracts to the BSPR-EUPA 2023 conference in Newcastle! Deadline May 21st!

register here: https://t.co/DQ60k9It83

#proteomics @EuPAProteomics @UKBspr

[Goh Lab @GohLab]

Prosit Oktoberfest & Koiner for #ML predicted peptide identification #proteomics #aohupo2023 #aoapo2023 #wilhelmlab #ms #maxquant

@wilhelm_compms

[MSAID @msaid_de]

Join us at the #ASMS2023 Conference in Houston in June. Visit our booth #707, where we will be presenting major updates to CHIMERYS, our intelligent search algorithm for proteomics. See you in Texas! https://t.co/eMAtsiM2eX
#TeamMassSpec #TeamProteomics