AlphaDIA Documentation¶
Open-source DIA search engine built with the alphaX ecosystem. Built with alpharaw and alphatims for raw file acces. Spectral libraries are predicted with peptdeep and managed by alphabase. Quantification is powered by directLFQ.
Features
Empirical library and fully predicted library search
End-to-end transfer learning for custom RT, mobility, and MS2 models
Label free quantification
DIA multiplexing
We support the following vendor and processing modes:
Platform |
Empirical lib |
Predicted lib |
|---|---|---|
Thermo .raw |
✅ |
✅ |
Sciex .wiff |
✅ |
✅ |
Bruker .d |
✅ |
⚠️ |
Predicted libraries with Bruker .d data
Although search is possible, alphaDIA’s feature-free search takes a long time with fully predicted libraries. We are still evaluating how to better support fully predicted libraries.
Manuscript
AlphaDIA enables DIA transfer learning for feature-free proteomics
Georg Wallmann, Patricia Skowronek, Vincenth Brennsteiner, Mikhail Lebedev, Marvin Thielert, Sophia Steigerwald, Mohamed Kotb, Oscar Despard, Tim Heymann, Xie-Xuan Zhou, Maximilian T. Strauss, Constantin Ammar, Sander Willems, Magnus Schwörer, Wen-Feng Zeng & Matthias Mann Nature Biotechnology (2025)
Install alphaDIA on your system to run your own DIA searches.
Introduction to your first DIA search with alphaDIA.