PXD058753-1

PXD058753 is an original dataset announced via ProteomeXchange.

Title	Global analysis of protein turnover dynamics in single cells
Description	Single-cell proteomics (SCP) has advanced significantly, yet it remains largely unidimensional, focusing primarily on protein abundances. This limitation hinders our understanding of the dynamic processes occurring within individual cells, particularly protein turnover, which is crucial for cellular function and regulation. In this study, we employed a pulsed stable isotope labeling by amino acids in cell culture (SILAC) approach to simultaneously evaluate protein abundance and turnover in single cells (SC-pSILAC). Using state-of-the-art SCP workflow, we demonstrated that two SILAC labels are detectable from ~4000 proteins in single HeLa cells recapitulating known biology. We investigated drug effects using protein synthesis and degradation inhibitors on global and specific protein turnover in single cells and performed a large-scale time-series SC-pSILAC analysis of undirected differentiation of human induced pluripotent stem cells (iPSC) encompassing six sampling times over two months and analyzed >1000 cells. Abundance measurements highlighted cell-specific markers of stem cells and various organ-specific cell types. Protein turnover dynamics highlighted differentiation-specific co-regulation of core members of protein complexes with core histone turnover discriminating dividing and non-dividing cells with potential in stem cell and cancer research. Lastly, correlating the abundance of individual proteins from cells displaying a wide range of diameters show that histones and some proteins involved in the cell cycle do not scale with cell size confirming previous observations in yeast. Our study represents the most comprehensive SCP analysis to date, offering new insights into cellular diversity and pioneering functional post-translational measurements beyond protein abundance. This method not only distinguishes SCP from other single-cell omics approaches and enhances its scientific relevance in biological research in a multidimensional manner but also showcase the discovery potential of SCP in fundamental biology.
HostingRepository	PRIDE
AnnounceDate	2025-03-28
AnnouncementXML	Submission_2025-03-28_14:37:30.631.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Maico Yannic Lechner
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-10 21:33:56	ID requested
⏵ 1	2025-03-28 14:37:31	announced

Dataset with its publication pending

submitter keyword: histone turnover,LC-MS,hFF cells, Single Cel Proteomics , pulsed SILAC

Jesper Velgaard
contact affiliation	Novo Nordisk Foundation Center for Protein Research
contact email	jesper.olsen@cpr.ku.dk
lab head
Maico Yannic Lechner
contact affiliation	NNF CPR
contact email	maico.lechner@cpr.ku.dk
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/03/PXD058753

PRIDE project URI

• PRIDE
  1. PXD058753
     1. Label: PRIDE project
     2. Name: Global analysis of protein turnover dynamics in single cells