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PXD056793

PXD056793 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleCarafe enables high quality in silico spectral library generation for data-independent acquisition proteomics
DescriptionData-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.
HostingRepositoryPanoramaPublic
AnnounceDate2024-10-19
AnnouncementXMLSubmission_2024-10-19_21:13:39.864.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterChris Hsu
SpeciesList scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932;
ModificationListPhospho; Carbamidomethyl
InstrumentOrbitrap Fusion Lumos; Orbitrap Exploris 480; Orbitrap Astral
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-10-14 16:31:51ID requested
12024-10-19 21:13:40announced
Publication List
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.
Keyword List
submitter keyword: spectral library generation, Carafe, deep learning, DIA
Contact List
Michael MacCoss
contact affiliationUniversity of Washington
contact emailmaccoss@uw.edu
lab head
Chris Hsu
contact affiliationUniversity of Washington
contact emailchrhsu@uw.edu
dataset submitter
Full Dataset Link List
Panorama Public dataset URI