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PXD037870

PXD037870 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleEvaluation of library-free strategies for phosphoproteomics and ubiquitinomics data-independent acquisition data
DescriptionPhosphoproteomics and ubiquitinomics data-independent acquisition MS data is generally analyzed using a DDA spectral library. Performance of different library-free strategies of analyzing phosphoproteomics and ubiquitinomics DIA MS data are not evaluated. In this study, we assess three library-free approaches including DIA-Umpire, DIA-MSFragger and in silico-predicted library for analysis of phosphoproteomics SWATH, DIA and diaPASEF data as well as ubiquitinomics diaPASEF data. In silico-predicted library based on DIA-NN performs best among three library-free methods, but identify less or equal phosphopeptides compared to a DDA spectral library. Furthermore, the common phosphopeptides by the predicted library and DDA library are about 50%. This case is also observed for phospho-diaPASEF data. For ubiquitinomics diaPASEF data, in silico-predicted library detects about 50% more K-GG peptides than a project-specific DDA spectral library. Our results demonstrate that the predicted library, although performs best in library-free methods, requires improvement for phospho DIA MS data and displays substantial advantages for ubiquitinomics diaPASEF MS data.
HostingRepositoryiProX
AnnounceDate2023-05-17
AnnouncementXMLSubmission_2023-06-01_05:19:16.675.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterChuanqi Zhong
SpeciesList scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationListphosphorylated residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-11-01 00:36:20ID requested
12023-02-20 21:54:44announced
22023-06-01 05:19:17announced2023-06-01: Update publication information.
Publication List
Wen C, Wu X, Lin G, Yan W, Gan G, Xu X, Chen XY, Chen X, Liu X, Fu G, Zhong CQ, Evaluation of DDA Library-Free Strategies for Phosphoproteomics and Ubiquitinomics Data-Independent Acquisition Data. J Proteome Res, 22(7):2232-2245(2023) [pubmed]
Keyword List
submitter keyword: Data-Independent Acquisition, Phosphoproteomics, Ubiquitinomics
Contact List
Chuanqi Zhong
contact affiliationXiamen University
contact emailzhongcq@xmu.edu.cn
lab head
Chuanqi Zhong
contact affiliationXiamen University
contact emailzhongcq@xmu.edu.cn
dataset submitter
Full Dataset Link List
iProX dataset URI