Integrated GlycoProteome Analyzer (I-GPA) for Automated Identification and Quantitation of Site-Specific N-Glycosylation

Gun Wook Park, Jin Young Kim, Heeyoun Hwang, Ju Yeon Lee, Young Hee Ahn, Hyun Kyoung Lee, Eun Sun Ji, Kwang Hoe Kim, Hoi Keun Jeong, Ki Na Yun, Yong Sam Kim, Jeong Heon Ko, Hyun Joo An, Jae Han Kim, Young Ki Paik, Jong Shin Yoo

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40 Citations (Scopus)

Abstract

Human glycoproteins exhibit enormous heterogeneity at each N-glycosite, but few studies have attempted to globally characterize the site-specific structural features. We have developed Integrated GlycoProteome Analyzer (I-GPA) including mapping system for complex N-glycoproteomes, which combines methods for tandem mass spectrometry with a database search and algorithmic suite. Using an N-glycopeptide database that we constructed, we created novel scoring algorithms with decoy glycopeptides, where 95 N-glycopeptides from standard α1-acid glycoprotein were identified with 0% false positives, giving the same results as manual validation. Additionally automated label-free quantitation method was first developed that utilizes the combined intensity of top three isotope peaks at three highest MS spectral points. The efficiency of I-GPA was demonstrated by automatically identifying 619 site-specific N-glycopeptides with FDR ≤ 1%, and simultaneously quantifying 598 N-glycopeptides, from human plasma samples that are known to contain highly glycosylated proteins. Thus, I-GPA platform could make a major breakthrough in high-throughput mapping of complex N-glycoproteomes, which can be applied to biomarker discovery and ongoing global human proteome project.

Original languageEnglish
Article number21175
JournalScientific reports
Volume6
DOIs
Publication statusPublished - 2016 Feb 17

All Science Journal Classification (ASJC) codes

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    Park, G. W., Kim, J. Y., Hwang, H., Lee, J. Y., Ahn, Y. H., Lee, H. K., Ji, E. S., Kim, K. H., Jeong, H. K., Yun, K. N., Kim, Y. S., Ko, J. H., An, H. J., Kim, J. H., Paik, Y. K., & Yoo, J. S. (2016). Integrated GlycoProteome Analyzer (I-GPA) for Automated Identification and Quantitation of Site-Specific N-Glycosylation. Scientific reports, 6, [21175]. https://doi.org/10.1038/srep21175