PXD034553

PXD034553 is an original dataset announced via ProteomeXchange.

Title	High-Coverage Four-Dimensional Data-Independent Acquisition Proteomics and Phosphoproteomics Enabled by Deep Learning-Driven Multi-Dimensional Prediction
Description	Here, a workflow of 4D DIA proteomics by using the predicted multi-dimensional in silico library was established. A deep learning model Deep4D that could high-accurately predict the CCS and RT of both the unmodified and phosphorylated peptides was developed, which is the model based on self-attention14 that completely avoid the use of recurrent neural network (RNN) or LSTM. Deep4D exhibited higher accuracy in the prediction of CCS and RT of peptides than the current models based on deep learning. By using Deep4D and MS/MS prediction tool, an integrated in silico library containing CCS, RT, and fragment ion intensities of millions of peptides for 4D DIA proteomics was established based on the SwissProt H. sapiens database, which enables the deeper peptide and proteome coverage for human samples compared to using sample-specific experimental library. We further demonstrate that the introduction of in silico prediction library can greatly complement the experimental library of directly obtained phosphorylated peptides, resulting in a greater increase in the identification of phosphorylated peptides and phosphorylated proteins.
HostingRepository	iProX
AnnounceDate	2023-04-19
AnnouncementXML	Submission_2023-12-06_20:18:56.682.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Moran Chen
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Mus musculus; NCBI TaxID: 10090; scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932;
ModificationList	phosphorylated residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-15 23:32:46	ID requested
1	2022-06-15 23:33:03	announced
2	2022-06-15 23:49:18	announced	2022-06-16: Update information.
⏵ 3	2023-12-06 20:18:58	announced	2022-06-16: Update information. 2023-12-07: Update publication.

Chen M, Zhu P, Wan Q, Ruan X, Wu P, Hao Y, Zhang Z, Sun J, Nie W, Chen S, . Anal Chem, 95(19):7495-7502(2023) [pubmed]

submitter keyword: 4D proteomics, DIA, Phosphoproteomic, ion mobility

Suming Chen
contact affiliation	The Institute for Advanced Studies, Wuhan University
contact email	chensm@iccas.ac.cn
lab head
Moran Chen
contact affiliation	The Institute for Advanced Studies, Wuhan University
contact email	1019524103@qq.com
dataset submitter

iProX dataset URI