we are happy to share that our latest work has been published in Nature Methods!
https://www.nature.com/articles/s41592-026-03042-9

Instead of optimizing around a single fragmentation method, the field is moving toward a flexible, multi-fragmentation ecosystem and making advanced techniques more accessible and practical. In this work, we introduce Prosit-MultiFrag, a first-of-its-kind model that predicts spectra across multiple fragmentation strategies, including UVPD, ECD, ETciD, and EID. Our results demonstrate improved identification performance and richer structural information, highlighting the power of combining fragmentation methods within a unified pipeline. Happy reading!

We’ve integrated the model into Koina
https://koina.proteomicsdb.org/docs#post-/Prosit_2025_intensity_MultiFrag/infer
so you can directly generate predictions, and it can also be used for rescoring via Oktoberfest
https://github.com/wilhelm-lab/oktoberfest