title: Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks.
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.
authors.affiliation: Department of Pharmaceutics, College of Pharmacy, Gachon University, Incheon 406-799, Republic of Korea.
authors.forename: Jong-Moon
authors.initials: JM
authors.lastname: Park
authors.affiliation: Department of Chemical Engineering, POSTECH, Pohang 790-784, Republic of Korea.
authors.forename: Ji-Hwan
authors.initials: JH
authors.lastname: Park
authors.affiliation: Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, Republic of Korea.
authors.forename: Dong-Gi
authors.initials: DG
authors.lastname: Mun
authors.affiliation: Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, Republic of Korea.
authors.forename: Jingi
authors.initials: J
authors.lastname: Bae
authors.affiliation: Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yong-in 446-701, Republic of Korea.
authors.forename: Jae Hun
authors.initials: JH
authors.lastname: Jung
authors.affiliation: Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, Republic of Korea.
authors.forename: Seunghoon
authors.initials: S
authors.lastname: Back
authors.affiliation: Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, Republic of Korea.
authors.forename: Hangyeore
authors.initials: H
authors.lastname: Lee
authors.affiliation: Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, Republic of Korea.
authors.forename: Hokeun
authors.initials: H
authors.lastname: Kim
authors.affiliation: Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea.
authors.forename: Hee-Jung
authors.initials: HJ
authors.lastname: Jung
authors.affiliation: National Cancer Center, Goyang 410-769, Republic of Korea.
authors.forename: Hark Kyun
authors.initials: HK
authors.lastname: Kim
authors.affiliation: Department of Pharmaceutics, College of Pharmacy, Gachon University, Incheon 406-799, Republic of Korea.
authors.forename: Hookeun
authors.initials: H
authors.lastname: Lee
authors.affiliation: Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yong-in 446-701, Republic of Korea.
authors.forename: Kwang Pyo
authors.initials: KP
authors.lastname: Kim
authors.affiliation: Department of Chemical Engineering, POSTECH, Pohang 790-784, Republic of Korea.|Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea.
authors.forename: Daehee
authors.initials: D
authors.lastname: Hwang
authors.affiliation: Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul 136-701, Republic of Korea.
authors.forename: Sang-Won
authors.initials: SW
authors.lastname: Lee
mesh_terms: D000328:Adult; D016000:Cluster Analysis; D005260:Female; D006023:Glycoproteins / Q000378:metabolism*; D006801:Humans; D008297:Male; D008875:Middle Aged; D008954:Models, Biological; D010750:Phosphoproteins / Q000378:metabolism*; D025941:Protein Interaction Mapping / Q000379:methods; D060066:Protein Interaction Maps; D020543:Proteome; D040901:Proteomics / Q000379:methods; D013274:Stomach Neoplasms / Q000175:diagnosis / Q000378:metabolism
chemical_list: D006023:Glycoproteins; D010750:Phosphoproteins; D020543:Proteome