Announcement

We’re excited to share the publication of alphaDIA in Nature Biotechnology. alphaDIA is a modern, open-source search engine that brings deep learning directly to raw mass spectrometry data for data-independent acquisition (DIA) proteomics. Figure: Wallmann et al, 2025, Nature Biotech. A search engine for modern DIA proteomics Mass spectrometry-based proteomics continues to generate increasingly complex datasets, especially with new, high-speed time-of-flight (TOF) detectors and advanced acquisition modes. alphaDIA addresses this complexity head-on through a feature-free processing approach, applying machine learning directly on the raw signal instead of relying on peak detection or data reduction. This enables robust analysis even for highly noisy TOF data, ensuring that all information contributes to peptide identification. ...

Launching alphapept: Open and Modern Tools for Proteomics We are pleased to announce the release of alphapept ecosystem, an open-source ecosystem of proteomics tools designed to accelerate mass spectrometry research and improve accessibility to advanced analysis methods. alphapept bundles tools developed in the Mann Labs at the Max Planck Institute for Biochemistry and the Insitute for Protein Research, Copenhagen into a unified ecosystem in which the individual tools can interact seamlessly with one another. Taken together, it aims to provide a comprehensive suite of open source tools for the analysis of modern proteomics data ...