PXD056793-1

PXD056793 is an original dataset announced via ProteomeXchange.

Title	Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics
Description	Data-independent acquisition (DIA)-based mass spectrometry is becoming an increasingly popular mass spectrometry acquisition strategy for carrying out quantitative proteomics experiments. Most of the popular DIA search engines make use of in silico generated spectral libraries. However, the generation of high-quality spectral libraries for DIA data analysis remains a challenge, particularly because most such libraries are generated directly from data-dependent acquisition (DDA) data or are from in silico prediction using models trained on DDA data. In this study, we developed Carafe, a tool that generates high-quality experiment-specific in silico spectral libraries by training deep learning models directly on DIA data. We demonstrate the performance of Carafe on a wide range of DIA datasets, where we observe improved fragment ion intensity prediction and peptide detection relative to existing pretrained DDA models.
HostingRepository	PanoramaPublic
AnnounceDate	2024-10-19
AnnouncementXML	Submission_2024-10-19_21:13:39.864.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Chris Hsu
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932;
ModificationList	Phospho; Carbamidomethyl
Instrument	Orbitrap Fusion Lumos; Orbitrap Exploris 480; Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-14 16:31:51	ID requested
⏵ 1	2024-10-19 21:13:40	announced

Wen, Bo, Chris Hsu, Wen-Feng Zeng, Michael Riffle, Alexis Chang, Miranda Mudge, Brook L. Nunn, et al. “Carafe Enables High Quality in Silico Spectral Library Generation for Data-Independent Acquisition Proteomics.” bioRxiv, 2024.10.15.618504.

submitter keyword: spectral library generation, Carafe, deep learning, DIA

Michael MacCoss
contact affiliation	University of Washington
contact email	maccoss@uw.edu
lab head
Chris Hsu
contact affiliation	University of Washington
contact email	chrhsu@uw.edu
dataset submitter

Panorama Public dataset URI