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Min-Sik Kim

Associate Professor


Min-Sik Kim received his M.Sc. with Dr. Sang-Won Lee from Korea University and Ph. D. with Dr. Akhilesh Pandey from Johns Hopkins University School of Medicine. During his postdoctoral research he map, for the first time, a draft map of the human proteome. Before starting his lab of QBIO and Precision Medicine at DGIST, he was an assistant professor in Kyung Hee University between 2016 and 2018.
Office E6-611
Tel +82-53-785-1630
E-mail mkim@dgist.ac.kr
Lab 큐바이오 정밀의학 연구실


Dr. Min-Sik Kim is currently an assistant professor of the Department of New Biology at Daegu Gyeongbuk Institute of Science and Technology (DGIST). He received his master degree with Dr. Sang-Won Lee at Korea University and doctor degree with Dr. Akhilesh Pandey at Johns Hopkins University School of Medicine. During his postdoctoral research with Dr. Pandey, he constructed, for the first time, a draft map of the human proteome which is a landmark paper published in Nature in 2014 (see the paper). In recognition of the outstanding research contribution, he received the 'Albert Lehninger Award,' a prestigious award at the Johns Hopkins University. Dr. Kim is interested in understanding how a biological system rearranges its molecular landscape upon perturbation in altered states such as cancer. Especially, he seeks for developing technologies to integrate multi-omics data including genomics, transcriptomics, proteomics, PTM-omics and metabolomics. 


When he opened his laboratory in the Department of Applied Chemistry, Kyung Hee University, he started proteogenomic analysis at the sequence levels to discover novel, unannotated protein-coding regions in the human genome. At the same time, he began to collaborate with clinical doctors in several hospitals such as Samsung Hospital, Seoul National Hospital, Kyung Hee Hospital and etc towards precision medicine by expending applications of mass spectrometry based proteomic technologies. Currently, he began his new laboratory of QBIO and Precision Medicine at DGIST which focuses on detailed understanding of biological systems using quantitative biological mass spectrometry.​

Research Summary

In-Depth Proteomics 


Advance in mass spectrometry has enabled to explore a proteome in a daily basis. Nonetheless, in-depth proteome analysis in a given time is still challenging due to the complexity of the proteome. I have contributed to optimizing methodologies to increase the rate of protein identifications and proved that alternative fragmentation method by combining CID to ETD improves site localization of phosphorylation. We are interested in developing newer methodologies towards in-depth and ultra high throughput proteomic analysis for cancer.






Proteogenomics Analysis


Mass spectrometry combined with bioinformatic tools is a promising technology to identify novel genomic regions that are yet to be annotated as protein-coding. Using this combined approach, I have contributed to identify hundreds of novel protein-coding genes from several publications including the Nature paper. Multi-Omic analysis method by combining transcriptome to proteome of a single donor has proven its uniqueness to annotate the current human genome and this combined information can be used towards precision medicine. Currently, we currently focus on analyzing multi-omics data to understand cancer proteogenomes of multiple cancers.




Global PTM Analysis to Study Signal Transduction using Mass Spectometry

Mass spectrometry became an essential tool to study post-translational modifications in a high-throughput fashion. I have constantly sought to establish analytical workflows to study these modifications using mass spectrometry. For example, I have used TiO2 and IMAC to enrich abundant phosphorylation in an unbiased manner as well as anti-tyrosine phosphorylation antibodies to enrich low abundant tyrosine phosphorylation. In addition, I have established antibody-based enrichment for ubuiquitination. We are developing newer PTM enrichment methodologies to discover new biological networks of cancers.​




Selected Publications

  • Lee, S.-E., Song, J.-G., Bösl, K., Müller, A. C., Vitko, D., Bennett, K. L., Superti-Furga, G, Pandey, A., Kandasamy, R. K.* and Kim, M.-S.* (2018) Proteogenomic analysis to identify missing proteins from haploid cell lines. Proteomics. 18(8):e1700386.
  • Kim, M.-S., Zhong, J. and Pandey, A. (2015). Common errors in mass spectrometry-based analysis of post-translational modifications. Proteomics. 16, 700-714.
  • Kim, M.-S., Pinto, S. M., Getnet, D., Nirujogi, R. S., Manda, S. S., Chaerkady, R., Madugundu, A. K., Kelkar, D. S., Isserlin, R., Jain, S., Thomas, J. K., Muthusamy, B., Leal-Rojas, P., Kumar, P., Sahasrabuddhe, N. A., Balakrishnan, L., Advani, J., George, B., Renuse, S., Selvan, L. D. N., Patil, A. H., Nanjappa, V., Radhakrishnan, A., Prasad, S., Subbannayya, T., Raju, R., Kumar, M., Sreenivasamurthy, S. K., Marimuthu, A., Sathe, G. J., Chavan, S., Datta, K. K., Subbannayya, Y., Sahu, A., Yelamanchi, S. D., Jayaram, S., Rajagopalan, P., Sharma, J., Murthy, K. R., Syed, N., Goel, R., Khan, A. A., Ahmad, S., Dey, G., Mudgal, K., Chatterjee, A., Huang, T. C., Zhong, J., Wu, X., Shaw, P. G., Freed, D., Zahari, M. S., Mukherjee, K. K., Shankar, S., Mahadevan, A., Lam, H., Mitchell, C. J., Shankar, S. K., Satishchandra, P., Schroeder, J. T., Sirdeshmukh, R., Maitra, A., Leach, S. D., Drake, C. G., Halushka, M. K., Prasad, T. S. K., Hruban, R. H., Kerr, C. L., Bader, G. D., Iacobuzio-Donahue, C. A., Gowda, H. and Pandey, A. (2014). A draft map of the human proteome. Nature. 509, 575-581.
  • Kim, M.-S., Zhong, Y., Yachida, S., Rajeshkumar, N. V., Abel, M., Marimuthu, A., Mudgal, K., Hruban, R. H., Tyner, J. W., Maitra, A., Iacobuzio-Donahue, C. A. and Pandey, A. (2014). Heterogeneity of pancreatic cancer metastases in a single patient revealed by quantitative proteomics. Molecular and Cellular Proteomics. 13, 2803-2811.
  • Haeusler, A. R., Donnelly, C. J., Periz, G., Simko, E. A., Shaw, P. G., Kim, M.-S., Maragakis, N. J., Troncoso, J. C., Pandey, A., Sattler, R., Rothstein, J. D. and Wang, J. (2014). C9orf72 nucleotide repeat structures initiate molecular cascades of disease. Nature. 507, 195-200.
  • 030. Martin, I., Kim, J. W., Lee, B. D., Kang, H. C., Xu, J. C., Jia, H., Stankowski, J., Kim, M.-S., Zhong, J., Kumar, M., Andrabi, S. A., Xiong, Y., Dickson, D. W., Wszolek, Z. W., Pandey, A., Dawson, T. M. and Dawson, V. L. (2014). Ribosomal protein s15 phosphorylation mediates LRRK2 neurodegeneration in Parkinson's disease. Cell. 157, 472-485.
  • Kim, M.-S., Kuppireddy, S. V., Sakamuri, S., Singal, M., Getnet, D., Harsha, H. C., Goel, R., Balakrishnan, L., Jacob, H. K. C., Kashyap, M. K., Tankala, S. G., Maitra, A., Iacobuzio-Donahue, C. A., Jaffee, E., Goggins, M. G., Velculescu, V. E., Hruban, R. H. and Pandey, A. (2012). Rapid characterization of candidate biomarkers for pancreatic cancer using cell microarrays (CMAs). Journal of Proteome Research. 11, 5556-5563.
  • Kim, M.-S. and Pandey, A. (2012). Electron transfer dissociation mass spectrometry in proteomics. Proteomics. 12, 530-542.
  • Kim, M.-S., Zhong, J., Kandasamy, K., Delanghe, B. and Pandey, A. (2011). Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides. Proteomics. 11, 2568-2572.
  • Bae, T. J.+, Kim, M.-S.+, Kim, J. W., Kim, B. W., Choo, H. J., Lee, J. W., Kim, K. B., Lee, C. S., Kim, J. H., Chang, S. Y., Kang, C. Y., Lee, S. W., Ko, Y. G. (2004). Lipid raft proteome reveals ATP synthase complex in the cell surface. Proteomics. 4(11):3536-3548.