pr2c00672_si_001.pdf (25.92 MB)
Scribe: Next Generation Library Searching for DDA Experiments
journal contribution
posted on 2023-01-25, 13:42 authored by Brian C. Searle, Ariana E. Shannon, Damien Beau WilburnSpectrum
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.
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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