PXD053647 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Deciphering the mechanisms of macrophage polarization through comprehensive analysis of protein glycosylation in cells and on the surface |
Description | In this work, we conducted an in-depth characterization of protein glycosylation including total glycoproteins and surface ones across different macrophage phenotypes using mass spectrometry (MS)-based proteomics. The global analysis of glycoproteins was performed using the boronic acid-conjugated dendrimer beads-based enrichment method. The N-glycoproteome was found to undergo more pronounced changes in M1 macrophages compared to M2 macrophages. To examine the alterations of surface glycoproteins, we employed enzymatic and chemical reactions to label surface glycoproteins. The remodeling of the glycoproteome in macrophage polarization is primarily driven by changes in protein expression and sugar donors rather than changes in the protein glycosylation machinery. Comparative analysis of cell-surface glycoproteins between M1 and M2 macrophages reveals phenotype-specific N-glycosylation patterns. Moreover, we identified potential targets for suppressing M2 macrophages, including CD36, FLT1, Siglec11, THSD7A, and SLC12A2. Finally, we characterized the site-specific changes of cell-surface glycoproteins between M1 and M2 macrophages related to their local protein structures and adjacent residues. The dramatic alterations in N-glycosylation sites were located within crucial protein domains, including the immunoglobulin (Ig)-like domain, fibronectin type III domain, and growth factor domain. Global and site-specific analysis of protein glycosylation and surface glycoproteins advance our understanding of different types of macrophages and provide valuable and unprecedented information for future functional and mechanistic investigations of human macrophages, leading to a better understanding of cancer immunity and the development of immunotherapy. |
HostingRepository | PRIDE |
AnnounceDate | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_06:52:51.621.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD053647 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Xing Xu |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | (18)O label at both C-terminal oxygens; monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Orbitrap Exploris 480 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2024-07-04 15:29:40 | ID requested | |
1 | 2024-08-08 02:47:56 | announced | |
⏵ 2 | 2024-10-22 06:52:52 | announced | 2024-10-22: Updated project metadata. |
Publication List
Keyword List
submitter keyword: Glycoproteomics, proteomics, tumor-associated macrophages, M1 macrophage, M2 macrophage, surfaceome, macrophage polarization |
Contact List
Xing Xu, Kejun Yin, and Ronghu Wu |
contact affiliation | School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA |
contact email | ronghu.wu@chemistry.gatech.edu |
lab head | |
Xing Xu |
contact affiliation | Georgia Institute of Technology |
contact email | xingxu@gatech.edu |
dataset submitter | |
Full Dataset Link List
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/2024/08/PXD053647 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD053647
- Label: PRIDE project
- Name: Deciphering the mechanisms of macrophage polarization through comprehensive analysis of protein glycosylation in cells and on the surface