PXD075483-1

PXD075483 is an original dataset announced via ProteomeXchange.

Title	Carafe2 enables high quality in silico spectral library generation for timsTOF data-independent acquisition proteomics
Description	Carafe (https://github.com/Noble-Lab/Carafe) is a software tool that uses deep learning models to generate high-quality, experiment-specific in silico libraries by training directly on DIA data. In this study, we extend Carafe to generate libraries for timsTOF DIA data, which involves fine-tuning retention time, fragment ion intensity, and ion mobility prediction models using timsTOF DIA data. Carafe2 operates directly on native timsTOF raw data (Bruker .d directories) without the need for data conversion.
HostingRepository	PanoramaPublic
AnnounceDate	2026-03-31
AnnouncementXML	Submission_2026-03-31_12:31:41.109.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Bo Wen
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932;
ModificationList	Phospho; Carbamidomethyl
Instrument	timsTOF Ultra 2

Revision	Datetime	Status	ChangeLog Entry
0	2026-03-10 21:44:22	ID requested
⏵ 1	2026-03-31 12:31:41	announced

Carafe2 enables high quality in silico spectral library generation for timsTOF data-independent acquisition proteomics. Bo Wen, J. Sebastian Paez, Chris Hsu, Daniele Canzani, Alexis Taylor Chang, Nicholas Shulman, Brendan X. MacLean, Matthew D. Berg, Judit Villen, William Fondrie, Lindsay Pino, Michael J. MacCoss, William Stafford Noble. bioRxiv 2026.03.27.714846

doi: https://doi.org/10.64898/2026.03.27.714846

submitter keyword: Carafe, Carafe2, DIA, deep learning, timsTOF, spectral library

Michael MacCoss
contact affiliation	University of Washington
contact email	maccoss@uw.edu
lab head
Bo Wen
contact affiliation	University of Washington
contact email	bwen1@uw.edu
dataset submitter

Panorama Public dataset URI