title: Integrated GlycoProteome Analyzer (I-GPA) for Automated Identification and Quantitation of Site-Specific N-Glycosylation.
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.
authors.affiliation: Department of Mass Spectrometry, Korea Basic Science Institute, Ochang, Republic of Korea.|Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea.
authors.forename: Gun Wook
authors.initials: GW
authors.lastname: Park
authors.affiliation: Department of Mass Spectrometry, Korea Basic Science Institute, Ochang, Republic of Korea.
authors.forename: Jin Young
authors.initials: JY
authors.lastname: Kim
authors.affiliation: Department of Mass Spectrometry, Korea Basic Science Institute, Ochang, Republic of Korea.
authors.forename: Heeyoun
authors.initials: H
authors.lastname: Hwang
authors.affiliation: Department of Mass Spectrometry, Korea Basic Science Institute, Ochang, Republic of Korea.
authors.forename: Ju Yeon
authors.initials: JY
authors.lastname: Lee
authors.affiliation: Department of Biomedical Science, Cheongju University, Cheongju, Republic of Korea.
authors.forename: Young Hee
authors.initials: YH
authors.lastname: Ahn
authors.affiliation: Department of Mass Spectrometry, Korea Basic Science Institute, Ochang, Republic of Korea.|Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea.
authors.forename: Hyun Kyoung
authors.initials: HK
authors.lastname: Lee
authors.affiliation: Department of Mass Spectrometry, Korea Basic Science Institute, Ochang, Republic of Korea.|Department of Chemistry, Hannam University, Daejeon, Republic of Korea.
authors.forename: Eun Sun
authors.initials: ES
authors.lastname: Ji
authors.affiliation: Department of Mass Spectrometry, Korea Basic Science Institute, Ochang, Republic of Korea.|Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea.
authors.forename: Kwang Hoe
authors.initials: KH
authors.lastname: Kim
authors.affiliation: Department of Mass Spectrometry, Korea Basic Science Institute, Ochang, Republic of Korea.|Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea.
authors.forename: Hoi Keun
authors.initials: HK
authors.lastname: Jeong
authors.affiliation: Department of Mass Spectrometry, Korea Basic Science Institute, Ochang, Republic of Korea.|Department of Chemistry, Sogang University, Seoul, Republic of Korea.
authors.forename: Ki Na
authors.initials: KN
authors.lastname: Yun
authors.affiliation: Cancer Biomarkers Development Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
authors.forename: Yong-Sam
authors.initials: YS
authors.lastname: Kim
authors.affiliation: Cancer Biomarkers Development Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
authors.forename: Jeong-Heon
authors.initials: JH
authors.lastname: Ko
authors.affiliation: Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea.
authors.forename: Hyun Joo
authors.initials: HJ
authors.lastname: An
authors.affiliation: Department of Food Nutrition, Chungnam National University, Daejeon, Republic of Korea.
authors.forename: Jae Han
authors.initials: JH
authors.lastname: Kim
authors.affiliation: Yonsei Proteome Research Center and Department of Integrated OMICS for Biomedical Science, and Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea.
authors.forename: Young-Ki
authors.initials: YK
authors.lastname: Paik
authors.affiliation: Department of Mass Spectrometry, Korea Basic Science Institute, Ochang, Republic of Korea.|Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea.
authors.forename: Jong Shin
authors.initials: JS
authors.lastname: Yoo
mesh_terms: D000465:Algorithms; D057205:Automation, Laboratory; D001798:Blood Proteins / Q000378:metabolism; D006528:Carcinoma, Hepatocellular / Q000097:blood / Q000378:metabolism; D006020:Glycopeptides / Q000737:chemistry / Q000378:metabolism; D006023:Glycoproteins / Q000737:chemistry / Q000378:metabolism*; D006031:Glycosylation; D006801:Humans; D008113:Liver Neoplasms / Q000097:blood / Q000378:metabolism; D020543:Proteome; D040901:Proteomics / Q000295:instrumentation / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D001798:Blood Proteins; D006020:Glycopeptides; D006023:Glycoproteins; D020543:Proteome