DDA-BERT
DDA-BERT is a computational platform designed for data-dependent acquisition (DDA) proteomics analysis. It features a simple, installation-free graphical user interface (GUI) and can also run in command-line mode. Compatible with Windows and Linux environments, it is powered by the ultra-fast Sage engine—a specialized proteomics search engine for peptide identification. DDA-BERT rescores peptide identifications using a pre-trained Transformer-based model trained on 3,706 DDA files and over 95 million peptide-spectrum matches (PSMs). It demonstrates superior performance across various sample types and mass spectrometry platforms—from trace samples to mouse proteomics. Results are output in CSV format as a comprehensive summary table that is easy to manipulate and interpret, facilitating further biological insights and downstream applications.
This software is currently under development, and we welcome you to try it out. If you have any feedback or suggestions, please let us know. Email address: guotiannan@westlake.edu.cn
This software is currently under development, and we welcome you to try it out. If you have any feedback or suggestions, please let us know. Email address: guotiannan@westlake.edu.cn