Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks

Jong Moon Park, Ji Hwan Park, Dong Gi Mun, Jingi Bae, Jae Hun Jung, Seunghoon Back, Hangyeore Lee, Hokeun Kim, Hee Jung Jung, Hark Kyun Kim, Hookeun Lee, Kwang Pyo Kim, Daehee Hwang, Sang-Won Lee

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Abstract

Multi-dimensional proteomic analyses provide different layers of protein information, including protein abundance and post-translational modifications. Here, we report an integrated analysis of protein expression, phosphorylation, and N-glycosylation by serial enrichments of phosphorylation and N-glycosylation (SEPG) from the same tissue samples. On average, the SEPG identified 142,106 unmodified peptides of 8,625 protein groups, 18,846 phosphopeptides (15,647 phosphosites), and 4,019 N-glycopeptides (2,634 N-glycosites) in tumor and adjacent normal tissues from three gastric cancer patients. The combined analysis of these data showed that the integrated analysis additively improved the coverages of gastric cancer-related protein networks; phosphoproteome and N-glycoproteome captured predominantly low abundant signal proteins, and membranous or secreted proteins, respectively, while global proteome provided abundances for general population of the proteome. Therefore, our results demonstrate that the SEPG can serve as an effective approach for multi-dimensional proteome analyses, and the holistic profiles of protein expression and PTMs enabled improved interpretation of disease-related networks by providing complementary information.

Original languageEnglish
Article number18189
JournalScientific Reports
Volume5
DOIs
Publication statusPublished - 2015 Dec 11

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Park, J. M., Park, J. H., Mun, D. G., Bae, J., Jung, J. H., Back, S., Lee, H., Kim, H., Jung, H. J., Kim, H. K., Lee, H., Kim, K. P., Hwang, D., & Lee, S-W. (2015). Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks. Scientific Reports, 5, [18189]. https://doi.org/10.1038/srep18189