Seoul National University Biological Sciences Website

Publications

Systems Mass Spectrometry Lab

2025

Yujung Chang†, Yongwoo Na†, Hyeonjoo Im†, Hyun Soo Shim, Chunggu Kim, Garam Yang, GyeungYun Kim, Hyeok Ju Park, Hee Young Kim, Seung Eun Lee, Wonwoong Lee, Yoon Ha, Sungho Park, Jieun Kim, Won-Young Cho, Woong Sun, Jong-Seo Kim* and Junsang Yoo* (2025). NDST3-induced epigenetic reprogramming reverses neurodegeneration in Parkinson’s disease. Advanced Science, (), under revision.

Hyunyoung Kim†, Sanghee Shin†, Jeongho Han, Kangseok Yun, Jong-Seo Kim* and Hyungju Park* (2025). Serpina1e mediates the exercise-induced enhancement of hippocampal memory. Nature Communications, (), revision under review.

Myeong-Gyun Kang†, Sanghee Shin†, Dong-Gi Jang, Ohyeon Kwon, Song-Yi Lee, Pratyush Kumar Mishra, Minkyo Jung, Ji Young Mun, Jung-Min Kee*, Jong-Seo Kim*, and Hyun-Woo Rhee* (2025). Intracristal space proteome mapping using super-resolution proximity labeling with isotope-coded probes. Nature Communications, 16(1), Article number: 7757.

Yongwoo Na†, Yeon Choi†, Thi Thanh My Nguyen, Hoang-Anh Pham-Bui, Jeesoo Kim, V. Narry Kim, Mihye Lee* and Jong-Seo Kim* (2025). Gene expression dynamics before and after zygotic genome activation in Drosophila early embryogenesis. iScience, 28(9), 113272.

Su Jin Ham†, Sunhoe Bang†, Daihn Woo, Jae-Yoon Jo, Takwon Yoo, Eunju Yoon, Yeonju Kyoung, Daehyun Baek, Jong-Seo Kim*, and Jongkyeong Chung* (2025). Mitochondrial fumarate inhibits Parkin-mediated mitophagy. Molecular Cell, 85(12), 2287-2302.

Chae Soo Yeon†, Se-Young Jang†, Jinhui Kim, Sehyun Hwang, Disha Malani, Olli Kallioniemi, Seung Gyu Yun*, Jong-Seo Kim*, and Hugh Kim* (2025). Mechanisms of chemotherapy failure in refractory/relapsed acute myeloid leukemia: The role of cytarabine resistance and mitochondrial metabolism. Cell Death & Disease, 16(1), Article number: 331.

JinA Lim†, Namseok Lee†, Seonmin Ju†, Jeesoo Kim, Subin Mun, Moonhyeon Jeon, Yong-ki Lee, Seok-Hoon Lee, Jayoung Ku, Sujin Kim, Sangsu Bae, Jong-Seo Kim* and Yoosik Kim* (2025). Cellular dsRNA interactome reveals the regulatory map of exogenous RNA sensing. Communications Biology, 8(1), Article number: 389.

Hyesung Jo, Seonmin Ju, Jiyun Beon, Minhye Kim, Se-Young Jang, Seung Pil Pack, Chang Yun Son, Jong-Seo Kim, and Seung Soo Oh* (2025). Aptamer-guided deoxyoxanosine positioning for epitope- and moiety-selective conjugation to non-engineered proteins. Journal of the American Chemical Society, 147(11), 9328–9340.

2024

Seonhwa Lee†, Dong-Gi Jang†, Yeon Ju Kyoung, Jeesoo Kim, Eui-Soon Kim, Ilseon Hwang, Jong-Chan Youn*, Jong-Seo Kim* and In-Cheol Kim* (2024). Proteome-wide characterization and pathophysiology correlation in three non-ischemic cardiomyopathies. Korean Circulation Journal, 54(8), 468-481.

Yeon Choi†, Buyeon Um†, Yongwoo Na, Jeesoo Kim, Jong-Seo Kim*, and V. Narry Kim* (2024). Time-resolved profiling of RNA binding proteins throughout the mRNA life cycle. Molecular Cell, 84(9), 1764-1782.

Sanghee Shin†, Song-Yi Lee†, Myeong-Gyun Kang, Dong-Gi Jang, Jeesoo Kim, Hyun-Woo Rhee* and Jong-Seo Kim* (2024). Super-resolution proximity labeling with enhanced direct identification of biotinylation sites. Communications Biology, 7(1), Article number: 554.

Ara Lee†, Gihyun Sung†, Sanghee Shin, Song-Yi Lee, Jaehwan Sim, Truong Thi My Nhung, Tran Diem Nghi, Sang Ki Park, Ponnusamy Pon Sathieshkumar, Imkyeung Kang, Ji Young Mun, Jong-Seo Kim*, Hyun-Woo Rhee*, Kyeng Min Park*, and Kimoon Kim* (2024). OrthoID: profiling dynamic proteomes through time and space using mutually orthogonal chemical tools. Nature Communications, 15(1), Article number: 1851.

Isaac Park†, Kwang-eun Kim†, Jeesoo Kim†, Ae-Kyeong Kim, Subin Bae, Minkyo Jung, Jinhyuk Choi, Pratyush Kumar Mishra, Taek-Min Kim, Chulhwan Kwak, Myeong-Gyun Kang, Chang-Mo Yoo, Ji Young Mun, Kwang-Hyeon Liu, Kyu-Sun Lee*, Jong-Seo Kim*, JaeMyoung Suh*, and Hyun-Woo Rhee* (2024). Mitochondrial matrix RTN4IP1/OPA10 is an oxidoreductase for coenzyme Q synthesis. Nature Chemical Biology, 20(2), 221–233.

2023

Yun-Bin Lee, Minkyo Jung, Jeesoo Kim, Afandi Charels, Wanda Christ, Myeong-Gyun Kang, Chulhwan Kwak, Jonas Klingström, Anna Smed Sörenson, Jong-Seo Kim*, Ji-Young Mun*, and Hyun-Woo Rhee* (2023). Super-resolution proximity labeling reveals antiviral protein network and its structural changes against SARS-CoV-2 viral proteins. Cell Reports, 42(8), 112835.

Thi Thanh My Nguyen†, Choijamts Munkhzul†, Jeesoo Kim, Yeonju Kyoung, Michele Vianney, Sanghee Shin, Seonmin Ju, Pham Bui Hoang Anh, Junhyung Kim, Jong-Seo Kim*, and Mihye Lee* (2023). In vivo profiling of the Zucchini proximal proteome in Drosophila ovary. Development, 150(4), dev201220.

2021

Jong Woo Bae, Sangtae Kim, V. Narry Kim*, and Jong-Seo Kim* (2021). Photoactivatable ribonucleosides mark base-specific RNA-binding sites. Nature Communications, 12(), Article number: 6026.

Kwang-eun Kim†, Isaac Park†, Jeesoo Kim, Myeong-Gyun Kang, Won Gun Choi, Hyemi Shin, Jong-Seo Kim*, Hyun-Woo Rhee* and Jae Myoung Suh* (2021). Dynamic tracking and identification of tissue-specific secretory proteins in the circulation of live mice. Nature Communications, 12(), Article number: 5204.

Yongwoo Na, Hyunjoon Kim, Yeon Choi, Sanghee Shin, Jae Hun Jung, S. Chul Kwon, V. Narry Kim*, and Jong-Seo Kim* (2021). FAX-RIC enables robust profiling of dynamic RNP complex formation in multicellular organisms in vivo. Nucleic Acids Research, 49(5), e28.

Chuna Kim†, Sanghyun Sung†, Jong-Seo Kim†, Hyunji Lee, Yoonseok Jung, Sanghee Shin, Eunkyeong Kim, Jenny J. Seo, Jun Kim, Daeun Kim, Hiroyuki Niida, V. Narry Kim, Daechan Park* and Junho Lee* (2021). Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells. Nature Communications, 12(), Article number: 1097.

Sungyul Lee, Young-suk Lee, Yeon Choi, Ahyeon Son, Youngran Park, Kyung Min Lee, Jeesoo Kim, Jong-Seo Kim, V Narry Kim* (2021). The SARS-CoV-2 RNA interactome. Molecular Cell, 81(13), 2838-2850. e6.

2020

Jihyun Lee†, Jae Hun Jung†, Jeesoo Kim, Won-Ki Baek, Jinseol Rhee, Tae-Hwan Kim, Sang-Hyon Kim, Kwang Pyo Kim*, Chang-Nam Son*, and Jong-Seo Kim* (2020). Proteomic analysis of human synovial fluid reveals potential diagnostic biomarkers for ankylosing spondylitis. Clinical Proteomics, 17(), 20.

Jong Woo Bae, Sung-Chul Kwon, Yongwoo Na, V. Narry Kim* and Jong-Seo Kim* (2020). Chemical RNA digestion enables robust RNA-binding site mapping at single amino acid-resolution. Nature Structural & Molecular Biology, 27(7), 678–682.

Chulhwan Kwak†, Sanghee Shin†, Jong-Seok Park†, Minkyo Jung, Truong Thi My Nhung, Myeong-Gyun Kang, Chaiheon Lee, Tae-Hyuk Kwon, Sang Ki Park*, Ji Young Mun*, Jong-Seo Kim*, and Hyun-Woo Rhee* (2020). Contact-ID, a tool for profiling organelle contact site, reveals regulatory proteins of mitochondrial-associated membrane formation. Proc Natl Acad Sci USA, 117(22), 12109-12120.

Sanghee Shin, Ji Hye Hong, Yongwoo Na, Mihye Lee, Wei-Jun Qian, V. Narry Kim, and Jong-Seo Kim* (2020). Development of Multiplexed Immuno-N-Terminomics to Reveal the Landscape of Proteolytic Processing in Early Embryogenesis of Drosophila melanogaster. Analytical Chemistry, 92(7), 4926-4934.

Yeon Choi†, Kyowon Jeong†, Sanghee Shin†, Joon Won Lee†, Young-suk Lee, Sangtae Kim, Sun Ah Kim, Jaehun Jung, Kwang Pyo Kim, V. Narry Kim* and Jong-Seo Kim* (2020). MS1-level proteome quantification platform allowing maximally increased multiplexity for SILAC and in vitro chemical labeling. Analytical Chemistry, 92(7), 4980-4989.

Jinuk Kim, Wonhee Han, Taeyong Park, Eun Jin Kim, Injin Bang, Hyun Sik Lee, Yejing Jeong, Kyeonghwan Roh, Jeesoo Kim, Jong-Seo Kim, Chanhee Kang, Chaok Seok, Jin-Kwan Han, Hee-Jung Choi* (2020). Sclerostin inhibits Wnt signaling through tandem interaction with two LRP6 ectodomains. Nature Communications, 11(), Article number: 5357.

2019

Jaehun Jung, Kyowon Jeong, Yeon Choi, Sun Ah Kim, Hyunjoon Kim, Joon Won Lee, V. Narry Kim, Kwang Pyo Kim and Jong-Seo Kim* (2019). Deuterium-Free, Three-Plexed Peptide Diethylation for Highly Accurate Quantitative Proteomics. Journal of Proteome Research, 18(3), 1078-1087.

Eunkyong Ko†, Jong-Seo Kim†, Jong Woo Bae, Jeesoo Kim, Sung-Gyoo Park, and Guhung Jung* (2019). SERPINA3 is a key modulator of HNRNP-K transcriptional activity against oxidative stress in HCC. Redox Biology, (), Jun;24:101217.

2017

Song-Yi Lee, Myeong-Gyun Kang, Sanghee Shin, Chulhwan Kwak, Taejoon Kwon, Jeong Kon Seo*, Jong-Seo Kim*, and Hyun-Woo Rhee* (2017). Architecture Mapping of the Inner Mitochondrial Membrane Proteome by Chemical Tools in Live Cells. Journal of the American Chemical Society, 139(10), 3651–3662.

2013

Jong-Seo Kim, Ziyu Dai, Uma K. Aryal, Ronald J. Moore, David G. Camp II, Scott E. Baker, Richard D. Smith, and Wei-Jun Qian* (2013). Resin-assisted enrichment of N-terminal peptides for characterizing proteolytic processing. Analytical Chemistry, 85(14), 6826–32.

Jong-Seo Kim, Matthew E. Monroe, David G. Camp II, Richard D. Smith, and Wei-Jun Qian* (2013). In-source fragmentation and the sources of partially tryptic peptides in shotgun proteomics. Journal of Proteome Research, 12(2), 910-6.

2012

Jong-Seo Kim*, Jin-Su Song, Yongju Kim, Seung Bum Park, Hie-Joon Kim* (2012). De novo analysis of protein N-terminal sequence utilizing MALDI signal enhancing derivatization with Br signature. Anal Bioanal Chem, 402(5), 1911-9.

2011

Jong-Seo Kim*, Mansup Shin, Jin-Su Song, Songhie An, Hie-Joon Kim* (2011). C-terminal de novo sequencing of peptides using oxazolone-based derivatization with bromine signature. Anal Biochem, 419(2), 211-6.

Jong-Seo Kim, Thomas L. Fillmore, Tao Liu, Errol Robinson, Mahmud Hossain, Boyd L. Champion, Ronald J. Moore, Camp David G. II, Richard D. Smith, Wei Jun Qian* (2011). 18O-labeled proteome reference as global internal standards for targeted quantification by selected reaction monitoring-mass spectrometry. Mol Cell Proteomics, 10(12), M110.007302.

Jong-Seo Kim*, Si-Uk Song, Hie-Joon Kim* (2011). Simultaneous identification of tyrosine phosphorylation and sulfation sites utilizing tyrosine-specific bromination. J Am Soc Mass Spectrom, 22(11), 1916-25.

Jong-Seo Kim, Jisoo Kim, Jung Min Oh, Hie-Joon Kim* (2011). Tandem mass spectrometric method for definitive localization of phosphorylation sites using bromine signature. Anal Biochem, 414(2), 294-6.

2009

Jong-Seo Kim, Enshi Cui, Hie-Joon Kim* (2009). Picolinamidination of phosphopeptides for MALDI-TOF-TOF mass spectrometric sequencing with enhanced sensitivity. J Am Soc Mass Spectrom, 20(9), 1751-8.

2008

Jong-Seo Kim, Ji-Hyun Kim, Hie-Joon Kim* (2008). Matrix-assisted laser desorption/ionization signal enhancement of peptides by picolinamidination of amino groups. Rapid Commun Mass Spectrom, 22(4), 495-502.

2005

Jong-Seo Kim, Ji-Young Kim, Hie-Joon Kim* (2005). Suppression of matrix clusters and enhancement of peptide signals in MALDI-TOF mass spectrometry using nitrilotriacetic acid. Analytical Chemistry, 15(77), 7483-8.

2001

Jong-Seo Kim, Hie-Joon Kim* (2001). Matrix-assisted laser desorption/ionization time-of-flight mass spectrometric observation of a peptide triplet induced by thermal cleavage of cystine. Rapid Commun Mass Spectrom, 15(23), 2296-300.