PXD037360-3

PXD037360 is an original dataset announced via ProteomeXchange.

Title	Hypothesis-free Illustration on How Phosphorylation Dynamically Impact Protein Turnover
Description	The turnover measurement of proteins and proteoforms has been largely facilitated by the metabolic labeling coupled with mass spectrometry (MS), such as the dynamic Stable isotope labeling by amino acids in cell culture (SILAC) experiments, i.e., the dynamic SILAC or pSILAC approach. Very recent studies including ours have integrated post-translational modification (PTM) proteomic methodology, such as phosphoproteomics, with pSILAC experiments in steady-state systems and revealed the link between protein PTM and turnover on the proteome-scale. In this study, we present a novel pSILAC phosphoproteomic dataset in a dynamic process of cell starvation using data-independent acquisition mass spectrometry (DIA-MS). We further propose a “hypothesis-free”, time series data analysis strategy to interrogate how phosphorylation dynamically impact protein turnover. With this strategy, we discovered complex relationship between phosphorylation and protein turnover that was previously underexplored. Our results further revealed potential biological features including phosphorylation stoichiometry that are associated with the peptideform turnover of phosphorylation. Our data also suggested that phosphoproteomic abundance regulation during starvation tends to be not correlated with turnover diversity, underscoring the importance of studying PTM site-resolved turnover datasets in the future.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:41:16.417.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wenxue Li
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-10-13 06:48:13	ID requested
1	2022-12-01 13:41:21	announced
2	2023-11-14 07:53:39	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 05:41:17	announced	2024-10-22: Updated project metadata.

10.1002/pmic.202100387;

Li W, Salovska B, Fornasiero EF, Liu Y, Toward a hypothesis-free understanding of how phosphorylation dynamically impacts protein turnover. Proteomics, 23(3-4):e2100387(2023) [pubmed]

submitter keyword: Peptidoform,Phosphorylation, Protein turnover, Clustering, DeltaSILAC, DIA-MS, Pulse SILAC, Data analysis, Time course

Yansheng Liu
contact affiliation	Yale Cancer Biology Institute, West Haven, USA.
contact email	yansheng.liu@yale.edu
lab head
Wenxue Li
contact affiliation	Yale University
contact email	wenxue.li@yale.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD037360
     1. Label: PRIDE project
     2. Name: Hypothesis-free Illustration on How Phosphorylation Dynamically Impact Protein Turnover