Distinct cell surface proteome profiling by biotin labeling and glycoprotein capturing

• Published in: Journal of proteomics Vol. 74; no. 10; pp. 1985 - 1993
• Main Authors: Nagano, Kohji, Shinkawa, Takashi, Kato, Kuniyasu, Inomata, Noriyuki, Yabuki, Nami, Haramura, Masayuki
• Format: Journal Article
• Language: English
• Published: Kidlington Elsevier B.V 06-09-2011; Elsevier
• Subjects: Animals; Biological and medical sciences; biotin; Biotin labeling; Biotinylation - methods; Cell surface profiling; Chromatography, Liquid; Diverse techniques; Fundamental and applied biological sciences. Psychology; Glycocapturing; glycoproteins; Glycoproteins - metabolism; Glycosylation; HCT116 Cells; Humans; Mass spectrometry; membrane proteins; Membrane Proteins - analysis; Mice; Molecular and cellular biology; plasma membrane; proteome; Proteomics - methods; surface proteins; Tandem Mass Spectrometry; Transplantation, Heterologous; Cell surface profiling; Biotin labeling; Mass spectrometry; Glycocapturing; Glycoprotein; Proteome; Biotin; Cell surface
• ISSN: 1874-3919; 1876-7737
• DOI: 10.1016/j.jprot.2011.05.019

We performed here MS-based cell surface proteome profiling of HCT-116 cells by two distinct methods based on biotin labeling and glycoprotein capturing. In total, 742 biotinylated and 219 glycosylated proteins were identified by the biotin labeling and glycoprotein capturing, of which 224 and 138 proteins known to be located on plasma membrane were included, respectively, according to ingenuity pathway analysis. Although 104 plasma membrane proteins were identified by both methods, the rest of 154 were identified only by one. Almost all the identified plasma membrane proteins possessed consensus N-glycosylation sites, and proteins having various numbers of glycosylation sites were identified by both methods. Thus, the discrepancies of the identified proteins obtained from those two methods might not be only due to the number of glycosylation sites, but also to the expression and/or glycosylation level of the cell surface proteins. We also identified 312 N-glycosylated proteins from xenograft samples by glycoprotein capturing of which 135 were known as plasma membrane proteins. Although a number of highly-expressed plasma membrane proteins were common between culture and xenograft cells, some proteins showed culture- or xenograft-specific expression, suggesting that those proteins might contribute to grow in different environment.
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► Cell surface profiling by biotin-labeling and glycoprotein-capturing methods. ► Each method enriched distinct subsets of the cell surface proteome. ► Glycosylation and/or expression level on the cell surface could be monitored. ► Abundant cell surface proteins were similar between culture and xenograft cells. ► Some proteins showed culture- or xenograft-specific expression.