Dataset Information

SBioSITe enables sensitive identification of the cell surface proteome through direct enrichment of biotinylated peptides

ABSTRACT: Background: Cell surface proteins perform critical functions related to immune response, signal transduction, cell-cell interactions, and cell migration. Expression of specific cell surface proteins can determine cell-type identity, and can be altered in diseases including infections, cancer and genetic disorders. Identification of the cell surface proteome remains a challenge despite the development of several enrichment methods exploiting their biochemical and biophysical properties. Methods: We report a novel method for enrichment of proteins localized to the cell surface. We developed surface Biotinylation Site Identification Technology (sBioSITe) by adapting our previously published method for direct identification of biotinylated peptides. The primary amine groups of lysines on cell surface proteins in live PC3 cells in culture were first labeled with biotin with subsequent enrichment of biotinylated peptides with anti-biotin antibodies. The enriched peptides containing biotin were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Biotinylated peptides identified in triplicate were mapped to proteins. Results: By direct detection of biotinylated lysines using sBioSITe, we identified 5,851 peptides biotinylated on the cell surface derived from 1,409 proteins. 533 of these proteins have been previously shown or predicted to be localized to the cell surface, or secreted into the extracellular space. Importantly, several of the identified markers have known associations with prostate cancer and metastasis including CD59, epithelial growth factor receptor (EGFR), 4F2 cell-surface antigen heavy chain (SLC3A2) and Adhesion G protein-coupled receptor E5 (ADGRE5) thus highlighting the robustness of this method. Conclusions: Detection of biotinylation sites on cell surface proteins modified in vitro provides a reliable method for the identification of cell surface proteins. This method is an excellent tool that complements existing methods for the analysis of surface expressed proteins in qualitative as well as comparative studies.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Prostate Gland, Cell Culture

DISEASE(S): Prostate Adenocarcinoma

SUBMITTER: Akhilesh Pandey

LAB HEAD: Akhilesh Pandey, M.D., Ph.D.

PROVIDER: PXD044519 | Pride | 2024-01-26

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	031422_PC3_Biotin_Antibody1.raw	Raw
	031422_PC3_Biotin_Antibody1_All_three.pdResult	Other
	031422_PC3_Biotin_Antibody2.raw	Raw
	031422_PC3_Biotin_Antibody3.raw	Raw
	checksum.txt	Txt

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sBioSITe enables sensitive identification of the cell surface proteome through direct enrichment of biotinylated peptides.

Garapati Kishore K Ding Husheng H Charlesworth M Cristine MC Kim Yohan Y Zenka Roman R Saraswat Mayank M Mun Dong-Gi DG Chavan Sandip S Shingade Ashish A Lucien Fabrice F Zhong Jun J Kandasamy Richard K RK Pandey Akhilesh A

Clinical proteomics 20231205 1

<h4>Background</h4>Cell surface proteins perform critical functions related to immune response, signal transduction, cell-cell interactions, and cell migration. Expression of specific cell surface proteins can determine cell-type identity, and can be altered in diseases including infections, cancer and genetic disorders. Identification of the cell surface proteome remains a challenge despite several enrichment methods exploiting their biochemical and biophysical properties.<h4>Methods</h4>Here, ...[more]

PMID: 38053024

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