PXD037870
PXD037870 is an original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
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 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 |
Full Dataset Link List
iProX dataset URI |