Carafe2 enables high quality <i>in silico</i> spectral library generation for timsTOF data-independent acquisition proteomics
libraries generated by Carafe2 for peptide detection on several different types of timsTOF DIA datasets by comparing with the libraries generated with DDA-trained AlphaPeptDeep models, DIA-NN built-in models, and empirical spectral libraries generated from DDA experiments.
Authors
- Judit Villén (ORCID: https://orcid.org/0000-0002-1005-1739)
- William E. Fondrie (ORCID: https://orcid.org/0000-0002-1554-3716)
- Lindsay K. Pino (ORCID: https://orcid.org/0000-0003-1857-7222)
- Brendan MacLean (ORCID: https://orcid.org/0000-0002-9575-0255)
- Daniele Canzani (ORCID: https://orcid.org/0000-0002-9390-0571)
- Nicholas Shulman (ORCID: https://orcid.org/0000-0003-1674-0794)
- William Stafford Noble (ORCID: https://orcid.org/0000-0001-7283-4715)
- Chris Hsu (ORCID: https://orcid.org/0000-0002-0846-6126)
- Matthew D. Berg (ORCID: https://orcid.org/0000-0002-7924-9241)
- Bo Wen
- J. Sebastian Paez
- Michael J. MacCoss
- Alexis Taylor Chang
Institutions
- University of Washington (US)
- TRIA Bioscience (United States) (US)
Publication Details
- Journal
- bioRxiv (Cold Spring Harbor Laboratory)
- Published
- 2026-03-31
- DOI
- https://doi.org/10.64898/2026.03.27.714846
- Primary Topic
- Advanced Proteomics Techniques and Applications
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Science Foundation
- National Institutes of Health
- Intelligence Advanced Research Projects Activity
- Army Research Office