Scribe: Next Generation
Library Searching for DDA
Posted on 2023-01-25 - 13:42
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. Here we present Scribe, a new library search engine designed to leverage 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 embeds Percolator for false discovery rate correction and an interference tolerant, label-free quantification integrator for an end-to-end proteomics workflow. By leveraging expected relative fragmentation and retention time values, we find that library searching with Scribe can outperform traditional database searching tools both in terms of sensitivity and quantitative precision. Scribe and its graphical interface are easy to use, freely accessible, and fully open source.
CITE THIS COLLECTION
Searle, Brian C.; Shannon, Ariana E.; Wilburn, Damien Beau (2023): Scribe: Next Generation Library Searching for DDA Experiments. ACS Publications. Collection. https://doi.org/10.1021/acs.jproteome.2c00672
Select your citation style and then place your mouse over the citation text to select it.
Read the peer-reviewed publication
Brian C. Searle
Ariana E. Shannon
Damien Beau Wilburn
fully open sourcefree quantification integratorapproach predicts fragmentationretention time valuesscribe embeds percolatorend proteomics workflowretention timesquantitative precisionpresent scribepowerful alternativelibrary searchinginterference toleranthistorically limitedgraphical interfacefreely accessiblefasta databaseevery peptidedatabase searching