DIA Site Localization



Spectrum library searching is a powerful alternative to database searching for data-dependent acquisition experiments but has been historically limited to identifying previously observed peptides in libraries. Scribe is a new library search engine that leverages deep learning fragmentation prediction software such as Prosit. Rather than relying on highly curated DDA libraries, this approach predicts fragmentation and retention times for every peptide in a FASTA database. Scribe provides a new approach to quantification that considers data from multiple charge states simultaneously and attempts to detect and remove interference.

The Scribe project has been merged into EncyclopeDIA, a joint open source project with the same goals. You can now access the latest version of Scribe in encyclopedia-2.12.30 or higher.


Searle BC, Shannon AE, Wilburn DB. Scribe: Next Generation Library Searching for DDA Experiments. J Proteome Res. 2023 Feb 3;22(2):482-490. Publication