PXD037870-2

PXD037870 is an original dataset announced via ProteomeXchange.

Title	Evaluation of library-free strategies for phosphoproteomics and ubiquitinomics data-independent acquisition data
Description	Phosphoproteomics 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.
HostingRepository	iProX
AnnounceDate	2023-05-17
AnnouncementXML	Submission_2023-06-01_05:19:16.675.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chuanqi Zhong
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-11-01 00:36:20	ID requested
1	2023-02-20 21:54:44	announced
⏵ 2	2023-06-01 05:19:17	announced	2023-06-01: Update publication information.

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]

submitter keyword: Data-Independent Acquisition, Phosphoproteomics, Ubiquitinomics

Chuanqi Zhong
contact affiliation	Xiamen University
contact email	zhongcq@xmu.edu.cn
lab head
Chuanqi Zhong
contact affiliation	Xiamen University
contact email	zhongcq@xmu.edu.cn
dataset submitter

iProX dataset URI