|Lab||큐바이오 정밀의학 연구실|
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.
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.
- 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.