Dong-Gi Mun,^1,21 Jinhyuk Bhin,^2,3,21 Sangok Kim,^4,21 Hyunwoo Kim,^5,6,21 Jae Hun Jung,^7,21 Yeonjoo Jung,⁴ Ye Eun Jang,⁴ Jong Moon Park,⁸ Hokeun Kim,¹ Yeonhwa Jung,⁴ Hangyeore Lee,¹ Jingi Bae,¹ Seunghoon Back,¹ Su-Jin Kim,¹ Jieun Kim,⁴ Heejin Park,⁵ Honglan Li,⁹ Kyu-Baek Hwang,⁹ Young Soo Park,¹⁰ Jeong Hwan Yook,¹¹ Byung Sik Kim,¹¹ Sun Young Kwon,¹² Seung Wan Ryu,¹² Do Youn Park,¹³ Tae Yong Jeon,¹⁴ Dae Hwan Kim,¹⁴ Jae-Hyuck Lee,¹⁵ Sang-Uk Han,¹⁶ Kyu Sang Song,¹⁷ Dongmin Park,¹⁸ Jun Won Park,¹⁸ Henry Rodriguez,¹⁹ Jaesang Kim,⁴ Hookeun Lee,⁸ Kwang Pyo Kim,⁷ Eun Gyeong Yang,^20,* Hark Kyun Kim,^{18, *} Eunok Paek,^5,* Sanghyuk Lee,^4,* Sang-Won Lee,^1,* and Daehee Hwang<sup>2,22,*

1</sup> Department of Chemistry, Center for Proteogenome Research, Korea University, Seoul 136-701, Republic of Korea
² Department of New Biology and Center for Plant Aging Research, Institute for Basic Science, DGIST, Daegu 711-873, Republic of Korea
³ Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
⁴ Department of Life Science and Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 120-750, Republic of Korea
⁵ Department of Computer Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea
⁶ Research Data Hub Center, Korea Institute of Science and Technology Information, Daejeon 34141, Republic of Korea
⁷ Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yong-in 446-701, Republic of Korea
⁸ Gachon Institute of Pharmaceutical Sciences, Gachon College of Pharmacy, Gachon University, Incheon 406-799, Republic of Korea
⁹ School of Computer Science and Engineering, Soongsil University, Seoul 156-743, Republic of Korea
¹⁰ Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-873, Republic of Korea
¹¹ Department of Surgery, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-873, Republic of Korea
¹² Department of Surgery, Keimyung University School of Medicine, Daegu 700-712, Republic of Korea
¹³ Department of Pathology, Pusan National University School of Medicine, Busan 602-739, Republic of Korea
¹⁴ Department of Surgery, Pusan National University School of Medicine, Busan 602-739, Republic of Korea
¹⁵ Department of Pathology, Chonnam National University Medical School, Gwangju 501-746, Republic of Korea
¹⁶ Department of Surgery, Ajou University School of Medicine, Suwon 443-380 Republic of Korea
¹⁷ Department of Pathology, School of Medicine, Chungnam National University, Daejeon 301-747 Republic of Korea
¹⁸ National Cancer Center, Goyang 410-769, Republic of Korea
¹⁹ Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
²⁰ Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea
²¹ These authors contributed equally
²² Lead Contact

^*Correspondence : Eun Gyeong Yang, Hark Kyun Kim, Eunok Paek, Sanghyuk Lee, Sang-Won Lee, Daehee Hwang

We report proteogenomic analysis of diffuse gastric cancers (GCs) in young populations. Phosphoproteome data elucidated signaling pathways associated with somatic mutations based on mutation-phosphorylation correlations. Moreover, correlations between mRNA and protein abundances provided potential oncogenes and tumor suppressors associated with patient survival. Furthermore, integrated clustering of mRNA, protein, phosphorylation, and N-glycosylation data identified four subtypes of diffuse GCs. Distinguishing these subtypes was possible by proteomic data. Four subtypes were associated with proliferation, immune response, metabolism, and invasion, respectively; and associations of the subtypes with immune- and invasion-related pathways were identified mainly by phosphorylation and N-glycosylation data. Therefore, our proteogenomic analysis provides additional information beyond genomic analyses, which can improve understanding of cancer biology and patient stratification in diffuse GCs.