2026

113. Mun, D.-G., Madugundu, A. K., Renuse, S., Nirujogi, S. R., Na C. H., Kim, M.-S., Saraswat, M., Singh, S., Ramarajan, M. G., Tiwary, S., Cox, J., Prakash, A., Halushka, M. K., Burns, K. H., Kandasamy, R. K., Pandey, A. A transcriptomic and proteomic map of primary human cell types. Nucleic Acids Research, 2026. 54. Accepted. [Journal link]

2025

112. Kang, M. H.¶, Lee, J.¶, Kim, J.¶, Mohammad, H. B., Park, J., Jung, H. J., Kim, S., Lee, H., Yang, S. W., Kwak, J. M., Kim, M.-S.*, Lee, J.-C.*, and Lim, P. O.* The chloroplast-targeted long noncoding RNA CHLORELLA mediates chloroplast functional transition across leaf ageing via anterograde signaling. Nature Plants. Accepted. [Journal link]

• 동아사이언스 : 식물 잎 노화 '시작 스위치' 찾았다

111. Karuppiah, C., Kim, S., Lee, S. Y., Lee, G., Ahmed, I., Jhung, S. H., Baek, S.-Y., Yim, Y.-H., Alam, R., Kim, M.-S., Lee, H. J. Synergistic NH2-MIL-101(Fe)/thermally reduced graphene oxide composite integrated voltammetric sensor for carcinogenic chrysene in particulate matter. Sensors and Actuators B: Chemical. Accepted. [Journal link]

110. Lee, J. Y., Yang, J., Kim, J. Y., Do, Y., Kim, M.-S., Kye, D. E., Min, G., Jeon, I. S., Kim, E. G., Choi, J. K., Choi, M., Lee, H., Yang, B. Bronchoalveolar lavage proteomics in exacerbation of bronchiectasis. BMC Pulmonary Medicine. 2025 Oct 1. 25. 441. [Journal link]

109. Song, K. J., Kim, M., Heo, Y. J., Cho, K. C., Oh, J. W., Kim, D. H., Hwa, C., Do, Y., Choi, S., Hwang, H. S., Kim, K., Kim, K., Na, S., Paek, E., An, J. Y., Jang, S. J., Kim, M.-S.*, Kim, K. P.* Assessing Long-Term Stored Tissues for Multi-Omics Data Quality and Proteogenomics Suitability. Journal of Proteome Research. Accepted. [Journal link]

108. Alam, R., Mahmood, R. A., Yanto, D. H. Y., Kim, M.-S., Kim, S. Direct Detection of Textile Dyes in Environmental Samples by LDI and MALDI FT-ICR MS. Analytical Chemistry. Accepted. [Journal link]

107. Alam, R., Lee, J.-H., Shin, D.-Y., Choi, I.-K., Kim, S., Lim, H.*, Kim, M.-S.* Recent Advances in Single-Cell Metabolomics Using Mass Spectrometry: Emerging Challenges and Future Perspectives. Applied Spectroscopy Reviews. Accepted. [Journal link]

106. Pham, V. D., Lee, J.-H., Shin, D.-Y., Vu, H. M., Jung, J., Kashyap, M. K., Lee, S. H., Kim, M.-S.* On the ocean of biomarkers for the precise diagnosis and prognosis of lung diseases. Proteomics-Clinical Applications. Accepted. [Journal link]

2024

105. Song, K. J.¶, Choi, S.¶, Kim, K.¶, Hwang, H. S.¶, Chang, E., Park, J. S., Shim, S. B., Choi, S., Heo, Y. J., An, W. J., Yang, D. Y., Cho, K.-C., Ji, W., Choi, C. M., Lee, J. C., Kim, H.-R., Yoo, J., Ahn, H.-S., Lee, G.-H., Hwa, C., Kim, S., Kim, K., Kim, M.-S., Paek, E., Na, S.*, Jang, S. J.*, An, J.-Y.*, Kim, K. P.* Proteogenomic Analysis Reveals Non-small Cell Lung Cancer Subtypes Predicting Chromosome Instability, and Tumor Microenvironment. Nature Communications. 2024. 15, 10164. [Journal link]

104. Vu, H. M.¶, Shiwakoti, S.¶, Ko, J.-Y., Bang, G., Lee, E., Kim, E., Park, S.-H., Park, E.-H., Kim, C.W., Kim, J.Y., Sim, H.-H., Chang, K., Kim, M.-S.*, Oak, M.-H.* Niclosamide attenuates calcification in human heart valvular interstitial cells through inhibition of the AMPK/mTOR signaling pathway. Biochemical Pharmacology. 2024. 230(3). 116614. [Journal link]

103. Rao, R., Gulfishan, M., Kim, M.-S., Kashyap, M. K. Deciphering Cancer Complexity: Integrative Proteogenomics and Proteomics Approaches for Biomarker Discovery. Methods Mol Biol. 2025;2859:211-237. [Journal link]

102. Chung, H.-J.¶, Nguyen, T. N. C.¶, Lee, J. W.¶, Huh, Y., Ko, S., Lim, H., Seo, H., Ha, Y.-G., Chang, J. H., Woo, J.-S., Song, J.-J., Kim, S.-W., Lee, J. S., Mo, J.-S., Park, B., Min, K.-W., Yoon, J.-H.*, Kim, M.-S.*, Jung, J.*, Jeong, N. Y.* Targeting the Hippo pathway in Schwann cells ameliorates peripheral nerve degeneration via a polypharmacological mechanism. Neurotherapeutics. 2024. 21(6). e00458. [Journal link]

101. Chang, E., Kim, S.-J., Hwang, H. S., Song, K. J., Kim, K., Kim, M.-S., Jang, S. J., You, S., Kim, K. P., An, J. Y. Pan-cancer proteogenomic landscape of whole-genome doubling reveals putative therapeutic targets in various cancer types. Clinical and Translational Medicine. 2024 Aug;14(8):e1796. [PubMed link]

100. Vu, H. M.¶, Lee, J. Y.¶, Kim, Y., Park, S., Izaguirre, F., Lee, J., Lee, J.-H., Jo, M., Woo, H. R., Kim, J. Y.*, Lim, P. O.*, Kim, M.-S.* Exploring the feasibility of a single protoplast proteomic analysis. Journal of Analytical Science and Technology. 2024. 15, 45. [Journal link]

099. Lim, H.*, Lee, S., J. S. Jin, Kim, M.-S.* High-throughput quantitative analysis of amino acids in freeze-dried drops using time-of-flight secondary ion mass spectrometry. Analytical Chemistry. 2024 Mar 5;96(9):3717-3721. [PubMed link]

098. Vu, H. M., Huh, S., Lee, J. H., Lee, S. H.*, Kim, M.-S.* (2024) Parallel accumulation-serial fragmentation method for in-depth proteomic analysis of bronchoalveolar lavage fluid collected from patients with non-small cell lung cancer. Proteomics-Clinical Applications. 2024 Mar;18(2):e2300053. [PubMed link]

097. Salman, M., Lee, J. W., Lee, S. H., Lee, M. H., Pham, V. D., Kim, M.-S., Cho, D., Lee, H. J. (2024) A comparative study of ammonia solubility in imidazolium-based ionic liquids with different structural compositions. Heliyon. 2024 Jan 6;10(2):e24305. [PubMed link]

2023

096. Park, G.¶, Jang, E. W.¶, Kim, S.¶, Gonzales, E. L., Ji, J., Choi, S., Kim, Y., Park, J. H., Mohammad, H. B., Bang, G., Kang, M., Kim, S., Jeon, S. J., Kim, J. Y., Kim, K. P., Shin, C. Y.*, An, J.-Y.*, Kim, M.-S.*, Lee, Y.-S.* (2023) Dysregulation of the Wnt/β-catenin signaling pathway via Rnf146 upregulation in a VPA-induced mouse model of autism spectrum disorder. Experimental & Molecular Medicine. 2023 Aug;55(8):1783-1794. [Journal link]

• TV Chosun: 자폐 환자 4년새 40% 급증…"약물 부작용과 연결고리 발견"

• Biz Chosun: 발프로산 약물 부작용이 자폐 일으키는 기전 찾았다

• 연합뉴스: 자폐 스펙트럼 장애 극복을 향해

095. Lee, S., Vu, H. M., Lee, J. H., Lim, H.*, Kim, M.-S.* (2023) Advances in Mass Spectrometry-based Single Cell Analysis. Biology (Basel) 2023, 12(3), 395. [Journal link]

094. Vu, H. M., Mohammad, H. B., Nguyen, T. N. C., Lee, J. H., Do, Y., Sung, J. Y., Lee, S. H.*, Kim, M.-S.* (2023) Quantitative proteomic analysis of bronchoalveolar lavage fluids from patients with small cell lung cancers. Proteomics-Clinical Applications. 2023 Feb 21;e2300011. [PubMed link] 

• 조선일보: 폐암 조기진단 잠재적 바이오마커 찾았다

• 서울경제: 진행 빠른 '소세포폐암' 조기진단 길 열렸다

093. Hyeon, D. Y., Nam, D., Han, Y., Kim, D. K., Kim, G., Kim, D., Bae, J., Back, S., Mun, D.-G., Madar, I. H., Lee, H., Kim, S.-J., Kim, H., Hyun, S., Kim, C. R., Choi, S. A., Kim, Y. R., Jeong, J., Jeon, S., Choo, Y. W., Lee, K. B., Kwon W., Choi, S., Goo, T., Park, T., Suh, Y.-A., Kim, H., Ku, J.-L., Kim, M.-S., Paek, E., Park, D., Jung, K., Baek, S. H., Jang, J.-Y., Hwang, D., Lee, S.-W. (2022) Proteogenomic landscape of human pancreatic ductal adenocarcinoma in an Asian population reveals tumor cell-enriched and immune-rich subtypes. Nature Cancer. 2023 Feb;4(2):290-307. [PubMed link]

092. Jang, E. W.¶, Park, J. H.¶, Park, G., Bang, G., Na, C. H., Kim, J. Y., Kim, K.-Y., Kim, K. P., Shin, C. Y., An, J.-Y., Lee, Y.-S., Kim, M.-S.* (2022) Cntnap2-dependent molecular networks in autism spectrum disorder revealed through an integrative multi-omics analysis. Molecular Psychiatry. 2023 Feb;28(2):810-821. [Journal link]

• Spectrum News: Multi-omics study captures CNTNAP2’s far-ranging effects

• 브릭: 자폐스펙트럼장애의 근본적 치료 가능한‘단서’찾았다!

• 국민일보 : 디지스트 연구진 자폐스펙트럼장애 치료 단서 찾았다

2022

091. Nguyen, T. N. C., Lee, J. H., Kim, N., Choi, J. R., Vu, H. M., Kim, M.-S.* (2022) Comparative sample preparation methods for a label-free proteomic analysis. Mass Spectrometry Letters. 13(4). 184-188. 

090. Chun, Y. L.¶, Eom, W.¶, Lee, J. H.¶, Nguyen, T. N. C., Park, K.-H., Chung, H.-J., Seo H., Huh, Y., Kim, S. H., Yeo, S. G., Park, W., Bang, G., Kim, J. Y., Kim, M.-S.*, Jeong, N. Y.*, Jung, J.* (2022) Investigation of the Hydrogen Sulfide Signaling Pathway in Schwann Cells During Peripheral Nerve Degeneration: Multi-omics Approaches. Antioxidants (Basel). 19;11(8):1606. [PubMed link]

089. Magnusson, R.¶, Rundquist, O.¶, Kim, M. J., Hellberg, S., Na, C.H., Benson, M., Gomez-Cabrero, D., Kockum, I., Tegnér, J.N., Piehl, F., Jagodic, M., Mellergård, J., Altafini, C., Ernerudh, J., Jenmalm, M. C., Nestor, C. E., Kim, M.-S. and Gustafsson, M. (2022) RNA-sequencing and mass-spectrometry proteomic time-series analysis of T-cell differentiation identified multiple splice variants models that predicted validated protein biomarkers in inflammatory diseases. Frontiers in Molecular Biosciences. 9:916128. [PubMed link]

088. Mohammad, H. B., Park, J. H., Lee, J. H., Vu, H. M., Lee, J.-Y., Jeong, W.-H., Kim, M.-S.* (2022) Comprehensive identification of VX-adducted plasma proteins using high-resolution mass spectrometry. Bulletin of the Korean Chemical Society. 43:1217-1222. [Journal link]

087. Kim, M. J.¶, Lim, H.¶, Kim, M., Choi, Y., Nguyen, T. N. C., Park, S. C., Kim, K. P., Jung, J., Kim, M.-S.* (2022) Lipid N-formylation occurs during fixation with formalin. Mass Spectrometry Letters, 13(2), 35-40. [Journal link] 

086. Jeong, Y. S., Huh, S., Kim, J. C., Park, J. Y., Lee, CE, Kim, M.-S., Koo, JH.*, Bae, Y.-S.* (2022) 2-Undecanone derived from Pseudomonas aeruginosa modulates neutrophil activity. BMB Reports. 2022;55(8): 395-400. [PubMed link] 

085. Park, G., Jeon, S. J., Ko, I. O., Park, J. H., Lee, K. C., Kim, M.-S., Shin, C. Y., Kim, H., Lee, Y. S. (2022) Decreased in vivo glutamate/GABA ratio correlates with the social behavior deficit in a mouse model of autism spectrum disorder. Molecular Brain. 15(1):19. [PubMed link] 

2021

084. Lee, J. H.¶, Jang, E. W.¶, Park, J. H., Mohammad, H. B., Lee, J.-Y., Jeong, W.-H., Kim, M.-S.* (2021) Identification of Organophosphate Modifications by High-resolution Mass Spectrometry. Bulletin of the Korean Chemical Society. 43 (3), 444-449. [Journal link] 

083. Cha, S.-J., Kim, M.-S., Na, C. H., Jacobs-Lorena, M. (2021) Plasmodium sporozoite phospholipid scramblase interacts with mammalian carbamoyl-phosphate synthetase 1 to infect hepatocytes. Nature Communications. 12(1):6773. [PubMed link] 

082. Supianto, M., Lee, S. H., Jhung, S. H., Mohammad, H. B., Vu, H. M., Kim, M.-S., Song, W.-Y., Kim, T.-Y., Lee, H. J. (2021) Fluorescent Paper Strip Immunoassay with Carbon Nanodots@Silica for Determination of Human Serum Amyloid A1. Microchimica Acta. 188(11):386. [PubMed link] 

081. Na, A. Y., Paudel, S., Choi, S. Y., Lee, J. H., Kim, M.-S., Bae, J.-S., Lee, S. (2021) Global Lysine Acetylome Analysis of LPS-Stimulated HepG2 Cells Identifies Hyperacetylation of PKM2 as a Metabolic Regulator in Sepsis. International Journal of Molecular Sciences. 22(16), 8529. [PubMed link] 

080. Renuse, S., Madamsetty, V.S., Mun, D.G., Madugundu, A.K., Singh, S., Udainiya, S., Mangalaparthi, K.K., Kim, M.-S., Liu, R., Kumar, S. Ram, Krasnoperov, V., Truty, M., Graham, R.P., Gill, P.S., Mukhopadhyay, D. and Pandey. A. (2021) Tyrosine phosphoproteomics of patient-derived xenografts reveals ephrin type-B receptor 4 tyrosine kinase as a therapeutic target in pancreatic cancer. Cancers. 13(14), 3404. [PubMed link] 

079. Hur, J. W.¶, Kim, M.-S.¶, Oh, S.-Y., Kang, H. Y., Bae, J., Kim, H., Lee, H., Lee, S.-W.* and Park, D.-H.* (2021) Label-free quantitative proteome profiling of cerebrospinal fluid from a rat stroke model with stem cell therapy. Cell Transplantation. 30:9636897211023474. [PubMed link] 

078. Park, J.-H., Ryu, S. J., Kim, B. J., Cho, H.-J. , Park, C. H., Choi, H. J. C., Jang, E.-J., Yang, E. J., Hwang, J.-A., Woo, S.-H., Lee, J. H., Park, J. H., Choi, K. M., Kwon, Y.-Y., Lee, C. K., Park, J. T. , Cho, S. C., Lee, Y. I., Lee, S. B., Han, J. A., Cho, K. A., Kim, M.-S.*, Hwang, D.*, Lee, Y.-S.*, and Park, S. C.* (2021) Disruption of nucleocytoplasmic trafficking as a cellular senescence driver. Experimental & Molecular Medicine. 53, 1092–1108. [PubMed link] 

077. Kim, S., Jang, E. W., Park, J. H., Kim, M.-S.*, Kim, J.-G.* and Kang, L.-W.* (2021) Combined analysis of the time-resolved transcriptome and proteome of plant pathogen Xanthomonas oryzae pv. oryzae. Frontiers in Microbiology. 12, 664857. [PubMed link] 

2020

076. Kim, H. K., Bae, J., Lee, S. H., Hwang, S,-H., Kim, M.-S., Kim, M. J., Jun, S., Cervantes, C. L., Jung, Y.-S., Back, S., Lee, H., Lee, S.-E., Dougherty, P. M., Lee, S.-W., Park, J.-I., Abdi, S. (2020) Blockers of Wnt3a, Wnt10a, or β-Catenin Prevent Chemotherapy-Induced Neuropathic Pain In Vivo. Neurotherapeutics. Jan;18(1):601-614. [PubMed link]

075. Huh, S., Hwang, D.*, Kim, M.-S.* (2020) Statistical modeling for enhancing discovery power of citrullination from tandem mass spectrometry data. Analytical Chemistry. Oct 6;92(19):12975-12986. [PubMed link]

074. Huh, S., Kim, M.-S.* (2020) A user-friendly visualization tool for a multi-omics data. Proteomics. Nov;20(21-22):e2000136. [PubMed link]

073. Ntwali P.V M, Heo CE, Han JU, Chae SY, Kim M, Vu, H. M., Kim, M.-S.* and Kim, H.* (2020) Mass spectrometry-based proteomics of single cells and organoids: The new generation of cancer research. Trends in Analytical Chemistry. [Journal Link]

2019

072. Hwang, J., Vu, H. M., Kim, M.-S., Lim, H. H. (2019) Plasma membrane localization of MLC1 regulates cellular morphology and motility. Mol Brain. 12(1):116. [PubMed link]. (Funding: NRF-2017M3C7A1027472) 

071.  Nguyen, Q. T. C., Lee, S. J., Choi, S. W., Na, Y. J., Song, M. R., Hoang, Q. T. N., Sim, S. Y., Kim, M.-S., Kim, J. I., Soh, M. S., Kim, S. Y. (2019) Arabidopsis Raf-Like Kinase Raf10 Is a Regulatory Component of Core ABA Signaling. Mol Cells. 42(9):646-660. [PubMed link]

070. Sim, S. Y., Choi, Y. R., Lee, J. H., Lim, J. M., Lee, S.-E., Kim, K. P., Kim, J. Y., Lee, S. H., and Kim, M.-S.* (2019) In-depth proteomic analysis of human bronchoalveolar lavage fluid towards the biomarker discovery for lung cancers. Proteomics-Clinical applications. 13(5):e1900028. [PubMed link] (Funding: No. 2019R1C1C1006262, NRF-2017M3C7A1027472) 

• 경희 News: 폐암 치료 위한 새로운 단백질 분석 방법 개발

069. Bae, J., Kim, S.-J., Lee, S.-E., Kwon, W., Kim, H., Han, Y., Jang, J.-Y., Kim, M.-S.* and Lee, S.-W.* (2019) Comprehensive proteome and phosphoproteome profiling shows negligible influence of RNAlater on protein abundance and phosphorylation. Clinical Proteomics. 16:18. [PubMed link] (Funding: NRF-2017M3C9A5031397, NRF-2017M3C7A1027472 , No. 2019R1C1C1006262)

068. Madugundu, A. K., Na, C. H., Nirujogi, R. S., Renuse, S., Kim, K. P., Burns, K. H., Wilks, C., Langmead, B., Ellis, S. E., Collado-Torres, L., Halushka, M. K.,  Kim, M.-S. and Pandey, A.* (2019) Integrated transcriptomic and proteomic analysis of primary human umbilical vein endothelial cells. Proteomics. 19(15):e1800315.  [PubMed link].  (Funding: NRF‐2017M3C7A1027472 , NRF‐2017M3C9A5031597)

067.  Mohammad, H. B., Lee, S.-E., Kim, M.-S.* (2019) Refining a pathogen's genome to know the enemy better for the winning battles. Proteomics. 19(9):e1900005. [PubMed link]. (Funding: NRF‐2017M3C7A1027472)

2018

066.  Yu, J., Kim, H. M., Kim, K. P., Son, Y., Kim, M.-S.*, Park, K.-S.* (2018) Ceramide kinase regulates the migration of bone marrow-derived mesenchymal stem cells. Biochemical and Biophysical Research Communications. 508(2):361-367.  [PubMed link] (Funding: HI16C1002)

065. Wu, X., Zahari, M. S., Renuse, S., Sahasrabuddhe, N., Chaerkady, R., Kim, M.-S., Fackler, M. J., Stampfer, M., Gabrielson, E., Sukumar, S. and Pandey, A. Quantitative phosphoproteomic analysis reveals reciprocal activation of receptor tyrosine kinases between cancer epithelial cells and stromal fibroblasts. Clinical Proteomics. 15:21. [PubMed link].  

064. Shefa, U., Kim, D., Kim, M.-S., Jeong, N. Y. and Jung, J. (2018) Roles of gasotransmitters in synaptic plasticity and neuropsychiatric conditions. Neural Plasticity. 2018:1824713. [PubMed link].  

063. Park, J. W.¶, Kim, M.-S.¶, Voon, M. C., Kim, S.-J., Bae, J., Mun, D.-G., Ko, S.-I., Kim, H. K., Lee, S.-W. and Kim, D. Y. (2018) Multi-omics analysis identifies pathways and genes involved in diffuse-type gastric carcinogenesis induced by E-cadherin, p53, and Smad4 loss in mice. Molecular Carcinogenesis. 57(7):947-954. *Co-first authorship. [PubMed link] (Funding: NRF‐2017M3C9A5031597, NRF‐2017M3C7A1027472)

062. 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. *Co-correspondence authorship. [PubMed link]  (Funding: NRF‐2016K1A3A1A47921601, NRF‐2017M3C7A1027472)

061. Jang, E. W. and Kim, M.-S.* (2018) SILAC expands its territory to the pathogenic yeast, Candida albicans.  Proteomics. 18. 5-6. e1700458. [PubMed link]  (Funding: KHU, GRRC)

060. Shefa, U., Kim, M.-S., Jeong, N. Y. and Jung, J. (2018) Antioxidant and cell-signaling functions of hydrogen sulfide in the central nervous system. Oxidative Medicine and Cellular Longevity. 2018, 1873962, 17. [PubMed link] 

059. Wang, Z., Kim, M.-S., Martinez Ferrando, I., Koleske, A. J., Pandey, A.,  and Cole, P. A. (2018). Analysis of Cellular Tyrosine Phosphorylation via Chemical Rescue of Conditionally Active Abl Kinase. Biochemistry. 57. 1390-1398. [PubMed link]  (Funding: NRF-2016K1A3A1A47921601)

2017

058. Na, C. H., Barbhuiya, M. A., Kim, M. -S., Verbruggen, S., Eacker, S. M., Pletnikova, O., Troncoso, J. C., Halushka, M. K., Menschaert, G., Overall, C. M. and Pandey. A. (2017). Discovery of non-canonical translation initiation sites through mass spectrometric analysis of protein N-termini. Genome Research. 28. 25-36.  [PubMed link]  (Funding: 2016K1A3A1A47921601)

057. McCall, M. N., Kim, M.-S., Adil, M., Patil, A. H., Lu, Y., Mitchell, C. J., Leal-Rojas, P., Xu, J., Kumar, M., Dawson, V. L., Dawson, T. M., Baras, A. S., Rosenberg, A. Z., Arking, D. E., Burns, K. H., Pandey, A. and Halushka, M. K. (2017). Toward the human cellular microRNAome. Genome Research. 27, 1769-1781. [PubMed link] 

056. Cutler, J. A., Tahir, R., Sreenivasamurthy, S. K., Mitchell, C., Renuse, S., Nirujogi, R. S., Patil, A. H., Heydarian, M., Wong, X., Wu, X., Huang, T. C., Kim, M.-S., Reddy, K. L., Pandey, A. (2017). Differential signaling through p190 and p210 BCR-ABL fusion proteins revealed by interactome and phosphoproteome analysis. Leukemia. 31. 1513-1524. [PubMed link]

055. Lee, S., Panthi, S., Jo, H. W., Cho, J., Kim, M.-S., Jeong, N. Y., Song, I. O., Jung, J., Huh, Y. (2017). Anatomical distributional defects in mutant genes associated with dominant intermediate Charcot-Marie-Tooth disease type C in an adenovirus-mediated mouse model. Neural Regeneration Research. 12. 486-492. [PubMed link]  

054. Oh, J. W., Kim, S. K., Cho, K. C., Kim, M.-S., Suh, C. S., Lee, J. R., Kim, K. P. (2017). Proteomic analysis of human follicular fluid in poor ovarian responders during in vitro fertilization. Proteomics. 17. 6. [PubMed link]  

053. Nirujogi, R. S., Muthusamy, B., Kim, M.-S., Sathe, G. J., Lakshmi, P. T., Kovbasnjuk, O. N., Prasad, T. S., Wade, M., Jabbour, R. E. (2017). Secretome analysis of diarrhea-inducing strains of Escherichia coli. Proteomics. 17. 6. [PubMed link]

052. Shefa, U., Yeo, S. G., Kim, M.-S., Song, I. O., Jung, J., Jeong, N. Y., Huh, Y. (2017). Role of Gasotransmitters in Oxidative Stresses, Neuroinflammation, and Neuronal Repair. BioMed Research International. 2017:1689341.  [PubMed link]

2016

051. Asiimwe, N., Yeo, S. G., Kim, M.-S., Jung, J., Jeong, N. Y. (2016). Nitric Oxide: Exploring the Contextual Link with Alzheimer's Disease. Oxidative Medicine and Cellular Longevity. 2016:7205747.[PubMed link]

050. Cha, S.-J., Kim, M.-S., Pandey, A., Jacobs-Lorena, M.  (2016). Identification of GAPDH on the surface of Plasmodium sporozoites as a new candidate for targeting malaria liver invasion.  Journal of Experimental Medicine. 213. 2099-2112. [PubMed link]

049. Mitchell, C. J., Kim, M.-S., Na, C. H. and Pandey, A. (2016). PyQuant: a versatile framework for analysis of quantitative mass spectrometry data. Molecular & Cellular Proteomics, mcp. O115. 056879. [PubMed link]

048. Mitchell, C. J., Kim, M.-S., Zhong, J., Nirujogi, R. S., Bose, A. K. and Pandey, A. (2016). Unbiased identification of substrates of protein tyrosine phosphatase ptp-3 in C. elegans. Molecular Oncology. [PubMed link]

047. Jhaveri, D. T., Kim, M.-S., Thompson, E. D., Huang, L., Sharma, R., Klein, A. P., Zheng, L., Le, D. T., Laheru, D. A., Pandey, A., Jaffee, E. M. and Anders, R. A. (2016). Using quantitative seroproteomics to identify antibody biomarkers in pancreatic cancer. Cancer Immunology Research. 4, 225-233. [PubMed link]

2015

046. Kim, M.-S. (2015). Proteomics equipped with multiplexing toward ultra high throughput. Proteomics 15, 183-184. [PubMed link]

045. Kim, M.-S., Zhong, J. and Pandey, A. (2015). Common errors in mass spectrometry-based analysis of post-translational modifications. Proteomics. 16, 700-714. [PubMed link]

044. Mitchell, C. J.¶, Getnet, D.¶, Kim, M.-S.¶, Manda, S. S., Kumar, P., Huang, T. C., Pinto, S., Nirujogi, R. S., Iwasaki, M., Shaw, P., Wu, X., Zhong, J., Chaerkady, R., Marimuthu, A., Muthusamy, B., Sahasrabuddhe, N. A., Raju, R., Bowman, C., Danilova, L., Cutler, J., Kelkar, D. S., Drake, C. G., Prasad, T. S. K., Marchionni, L., Marukami, P. N., Scott, A. F., Shi, L., Thierry-Mieg, J., Thierry-Mieg, T., Irizarry, R., Cope, L., Ishihama, Y., Wang, C., Gowda, H. and Pandey, A. (2015). A multi-Omic analysis of human naive CD4+ T cells. BMC Systems Biology. 9, 75. [PubMed link]

043. Wu, X., Zahari, M. S., Ma, B., Liu, R., Renuse, S., Sahasrabuddhe N. A., Chen, L., Chaerkady, R., Kim, M.-S., Zhong, J., Jelinek, C., Bharbuiya, M. A., Leal-Rojas, P., Yang, Yi., Kashyap, M. K., Marimuthu, A., Ling, M., Fackler, M. J., Merino, V., Zhang, Z., Zahnow, C. A., Gabrielson, E., Stearns, V., Roa, J. C., Sukumar, S., Gill, P. S. and Pandey, A. (2015). Global phosphotyrosine survey in triple-negative breast cancer reveals activation of multiple tyrosine kinase signaling pathways. Oncotarget. 6, 29143-29160. [PubMed link]

042. Wu, X., Zahari, M. S., Renuse, S., Nirujogi, R. S., Kim, M.-S., Manda, S. S., Stearns, V., Gabrielson, E., Sukumar, S. and Pandey, A. (2015) Phosphoproteomic analysis identifies FAK2 as a potential therapeutic target for tamoxifen resistance in breast cancer. Molecular and Cellular Proteomics. 14, 2887-2900. [PubMed link]

041. Ewing, A. D., Gacita, A., Wood, L. D., Ma, F., Xing, D., Kim, M.-S., Manda, S. S., Abril, G., Pereira, G., Makohon-Moore, A., Looijenga, L. H., Gillis, A. J., Hruban, R. H., Anders, R. A., Romans, K. E., Pandey, A., Iacobuzio-Donahue, C. A., Vogelstein, B., Kinzler, K. W., Kazazian, H. H. Jr. and Solyom, S. (2015). Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution. Genome Research. 25, 1536-1545. [PubMed link]

040. Zahari, M. S., Wu, X., Blair, B. G., Pinto, S. M., Nirujogi, R. S., Jelinek, C. A., Malhotra, R., Kim, M.-S., Park, B. H. and Pandey, A. (2015). Activating mutations in PIK3CA lead to widespread modulation of the tyrosine phosphoproteome. Journal of Proteome Research. 14, 3882-3891. [PubMed link]

039. Zahari, M. S., Wu, X., Pinto, S. M., Nirujogi, R. S., Kim, M.-S., Fetics, B., Philip, M., Barnes, S. R., Godfrey, B., Gabrielson, E., Nevo, E. and Pandey, A. (2015). Phosphoproteomic profiling of tumor tissues identifies HSP27 Ser82 phosphorylation as a robust marker of early ischemia. Scientific Reports. 5, 13660. [PubMed link]

038. Zhang, X., Belkina, N., Jacob, H. K., Maity, T., Biswas, R., Venugopalan, A., Shaw, P. G., Kim, M.-S., Chaerkady, R., Pandey, A. and Guha U. (2015). Identifying novel targets of oncogenic EGF receptor signaling in lung cancer through global phosphoproteomics. Proteomics. 15, 340-355. [PubMed link]

037. Nirujogi, R. S., Wright, J. D., Manda, S. S., Zhong, J., Na, C. H., Meyerhoff, M., Benton, M. B., Jabbour, R., Willis, K., Kim, M.-S., Pandey, A. and Sekowski, J. W. (2015) Phosphoproteomic analysis reveals compensatory effects in the piriform cortex of VX nerve agent exposed rats. Proteomics. 15, 487-499. [PubMed link]

2014

036. 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. [PubMed link]

• BBC News: 'First drafts' of human protein catalogue published

• Chemical & Engineering News: Human Proteome Map Assembled

• ThermoFisher Scientific: Putting the Human Proteome on the Map: The JHU Team

035. Wu, X., Renuse, S., Sahasrabuddhe, N. A., Zahari, M. S., Chaerkady, R., Kim, M.-S., Nirujogi, R. S., Mohseni, M., Kumar, P., Raju, R., Zhong, J., Yang, J., Neiswinger, J., Jeong, J. S., Newman, R., Powers, M. A., Somani, B. L., Gabrielson, E., Sukumar, S., Stearns, V., Qian, J., Zhu, H., Vogelstein, B., Park, B. H. and Pandey, A. (2014). Activation of diverse signaling pathways by oncogenic PIK3CA mutations. Nature Communications. 5, 4961. [PubMed link]

034. Tong, Z, Kim, M.-S., Pandey, A. and Espenshade, P. J. (2014). Identification of candidate substrates for the golgi Tul1 E3 ligase using quantitative diGly proteomics in yeast. Molecular and Cellular Proteomics. 13, 2871-2882. [PubMed link]

033. 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. [PubMed link]

032. Kelkar, D. S., Provost. E., Chaerkady, R., Muthusamy, B., Manda, S. S., Subbannayya, T., Selvan, L. D. N., Wang, C. H., Datta, K. K., Woo, S., Dwivedi, S. B., Renuse, S., Getnet, D., Huang, T. C., Kim, M.-S., Pinto, S. M., Mitchell, C. J., Madugundu, A. K., Kumar, P., Sharma, J. Advani, J., Dey, G., Balakrishnan, L., Syed, N., Nanjappa, V., Subbannayya, Y., Goel, R., Prasad, T. S. K., Bafna, V., Sirdeshmukh, R., Gowda, H., Wang, C., Leach, S. D. and Pandey, A. (2014). Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis. Molecular and Cellular Proteomics. 13, 3184-3198. [PubMed link]

031. 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. [PubMed link]

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. [PubMed link]

029. Sahasrabuddhe, N. A., Huang, T. C., Ahmad, S., Kim, M.-S., Yang, Y., Ghosh, B., Leach, S. D., Gowda, H., Somani, B. L., Chaerkady, R. and Pandey, A. (2014). Regulation of PPAR-alpha pathway by Dicer revealed through proteomic analysis. Journal of Proteomics. 108, 306-315. [PubMed link]

028. Thomas, J. K.¶, Kim, M.-S.¶, Balakrishnan, L., Nanjappa, V., Raju, R., Marimuthu, A., Radhakrishnan, A., Muthusamy, B., Khan, A. A., Sakamuri, S., Tankala, S. G., Singal, M., Nair, B., Sirdeshmukh, R., Chatterjee, A., Prasad, T. S. K., Maitra, A., Gowda, H., Hruban, R. H. and Pandey, A. (2014). Pancreatic Cancer Database: An integrative resource for pancreatic cancer. Cancer Biology and Therapy. 15, 963-7. [PubMed link]

027. Chi, Z., Byrne, S. T., Dolinko, A., Harraz, M. M., Kim, M.-S., Umanah, G., Zhong, J., Chen, R., Zhang, J., Xu, J., Chen, L., Pandey, A., Dawson, T. M. and Dawson. V. L. (2014). Botch is a γ-Glutamyl cyclotransferase that deglycinates and antagonizes notch. Cell Reports. 7, 681-688. [PubMed link]

026. Pinto, S. M., Manda, S. S., Kim, M.-S., Taylor, K., Selvan, L. D. N., Balakrishnan, L., Subbannayya, T., Yan, F., Prasad, T. S. K., Gowda, H., Lee, C., Hancock, W. S. and Pandey, A. (2014). Functional annotation of proteome encoded by human chromosome 22. Journal of Proteome Research. 13, 2749-2760. [PubMed link]

025. Manda, S. S., Nirujogi, R. S., Pinto, S., Kim, M.-S., Datta, K., Sirdeshmukh, R., Prasad, T. S. K., Thongboonkerd, V., Pandey, A. and Gowda, H. (2014). Identification and characterization of proteins encoded by chromosome 12 as part of Chromosome-centric Human Proteome Project. Journal of Proteome Research. 13, 3166-3177. [PubMed link]

024. Ahn, J. M., Kim, M.-S., Kim, Y. I., Jeong, S. K., Lee, H. J., Lee, S.H., Paik, Y. K., Pandey, A. and Cho, J. Y. (2014). Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues. Journal of Proteome Research. 3, 137-146 [PubMed link]

023. Dwivedi, S. B., Muthusamy, B., Kumar, P., Kim, M.-S., Nirujogi, R. S., Getnet, D., Ahiakonu, P., Dey, G., Nair, B., Gowda, H., Prasad, T. S. K., Kumar, N., Pandey, A. and Okulate, M. (2014). Brain proteomics of Anopheles gambiae. OMICS: A Journal of Integrative Biology. 18, 421-437. [PubMed link]

022. Heydarian, M., Luperchio, T. R., Cutler, J., Mitchell, C. J., Kim, M.-S., Pandey, A., Sollner-Webb, B. and Reddy, K. (2014). Prediction of gene activity in early B cell development based on an integrative multi-Omics Analysis. Journal of Proteomics and Bioinformatics. 7, 50-63. [PubMed link]

2013

021. Taylor, M. S., Ruch, T. R., Hsiao, P. Y., Hwang, Y., Zhang, P., Dai, L., Huang, C. R., Berndsen, C. E., Kim, M.-S., Pandey, A., Wolberger, C., Marmorstein, R., Machamer, C., Boeke, J. D. and Cole, P. A. (2013). Architectural organization of the metabolic regulatory enzyme ghrelin O-acyltransferase. Journal of Biological Chemistry. 288, 32211-28 [PubMed link]

020. Hansen, A. M., Chaerkady, R., Sharma, J., Diaz-Mejia, J. J., Tyagi, N., Renuse, S., Jacob, H. K. C., Pinto, S. M., Sahasrabuddhe, N. A., Kim, M.-S., Delange, B., Srinivasan, N., Emili, A., Kaper, J. and Pandey, A. (2013). The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence. PLoS Pathogens. 9, e1003403. [PubMed link]

019. Patel, K., Scrimieri, F., Ghosh, S., Zhong, J., Kim, M.-S., Ren, Y. R., Morgan, R. A., Iacobuzio-Donahue, C. A., Pandey, A. and Kern, S. E. (2013). FAM190A deficiency creates a cell division defect. The American Journal of Pathology. 183, 296-303. [PubMed link]

2012

018. van Bodegom, D., Zhong, J., Kopp, N., Dutta, C., Kim, M.-S., Bird, L., Weigert, O., Tyner, J., Pandey, A., Yoda, A. and Weinstock, D. M. (2012). Differences in signaling through the B-cell leukemia oncoprotein CRLF2 in response to TSLP and through mutant JAK2. Blood. 120, 2853-2863. [PubMed link]

017. Do Vale, L. H., Gomez-Mendoza, D. P., Kim, M.-S., Pandey, A., Ricart, C. A., Ximenes-Filho, E. and Sousa, M. V. (2012). Secretome analysis of the fungus Trichoderma harzianum grown on cellulose. Proteomics. 12, 2716-2728. [PubMed link]

016. 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. [PubMed link]

015. Zhong, J.¶, Kim, M.-S., Chaerkady, R., Wu, X., Huang, T. C., Getnet, D., Mitchell, C. J., Palapetta, S. M., Sharma, J., O'Meally, R. N., Cole, R. N., Yoda, A., Moritz, A., Loriaux, M. M., Rush, J., Weinstock, D. M., Tyner, J. W. and Pandey, A. (2012). TSLP signaling network revealed by SILAC-based phosphoproteomics. Molecular and Cellular Proteomics. 11, M112.017764. [PubMed link]

014. Huang, T. C., Sahasrabuddhe, N. A., Kim, M.-S., Getnet, D., Yang, Y., Peterson, J. M., Ghosh, B., Chaerkady, R., Leach, S. D., Marchionni, L., Wong, G. W. and Pandey A. (2012).Regulation of lipid metabolism by Dicer revealed through SILAC Mice. Journal of Proteome Research. 11, 2193-2205. [PubMed link]

013. Kim, M.-S. and Pandey, A. (2012). Electron transfer dissociation mass spectrometry in proteomics. Proteomics. 12, 530-542. [PubMed link]

2011

012. Chaerkady, R., Kelkar, D. S., Muthusamy, B., Kandasamy, K., Dwivedi, S. B., Sahasrabuddhe, N. A., Kim, M.-S., Renuse, S., Pinto, S. M., Sharma, R., Pawar, H., Sekhar, N. R., Mohanty, A. K., Getnet, D., Yang, Y., Zhong, J., Dash, A. P., MacCallum, R. M., Delanghe, B., Mlambo, G., Kumar, A., Prasad, T. S. K., Okulate, M., Kumar, N. and Pandey, A. (2011). A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry. Genome Research. 21, 1872-1881. [PubMed link]

011. 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. [PubMed link]

006. Hyung SW, Kim, M.-S., Mun DG, Lee H, Lee SW. (2011). The effect and potential of using a temperature controlled separation column with ultra-high pressure microcapillary liquid chromatography/tandem mass spectrometry on proteomic analysis. Analyst. 21;136(10):2100-2015. [PubMed link]

2010

010. Chen, H., Pimienta, G., Gu, Y., Sun, X., Hu, J., Kim, M.-S., Chaerkady, R., Gucek, M., Cole, R. N., Sukumar, S. and Pandey, A. (2010). Proteomic characterization of Her2/neu-overexpressing breast cancer cells. Proteomics. 10, 3800-3810. [PubMed link]

009. Kashyap, M. K., Harsha, H. C., Renuse, S., Pawar, H., Sahasrabuddhe, N. A., Kim, M.-S., Marimuthu, A., Keerthikumar, S., Muthusamy, B., Kandasamy, K., Subbannayya, Y., Prasad, T. S. K., Mahmood, R., Chaerkady, R., Meltzer, S. J., Kumar, R. V., Rustgi, A. K. and Pandey, A. (2010). SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome. Cancer Biology and Therapy. 10, 796-810. [PubMed link]

008. Kim, M.-S., Kandasamy, K., Chaerkady, R. and Pandey, A. (2010). Assessment of resolution parameters for CID-based shotgun proteomic experiments on the LTQ-Orbitrap mass spectrometer. Journal of The American Society for Mass Spectrometry. 21, 1606-1611. [PubMed link]

005. Kim, B. W., Lee, C. S., Yi, J. S., Lee, J. H., Lee, J. W., Choo, H. J., Jung, S. Y., Kim, M.-S., Lee, S. W., Lee, M. S., Yoon, G., Ko, Y. G. (2010). Lipid raft proteome reveals that oxidative phosphorylation system is associated with the plasma membrane. Expert Rev Proteomics. 27(6):849-866. [PubMed link]

2008

007. Chaerkady, R., Thuluvath, P. J., Kim, M.-S., Nalli, A., Vivekanandan, P., Simmers, J., Torbenson, M. and Pandey, A. (2008). 18O labeling for a quantitative proteomic analysis of glycoproteins in hepatocellular carcinoma. Clinical Proteomics. 4, 137-155. [PubMed link]

2004

004. Lee, Y. H., Kim, M.-S., Choie, W. S., Min, H. K., Lee, S. W. (2004). Highly informative proteome analysis by combining improved N-terminal sulfonation for de novo peptide sequencing and online capillary reverse-phase liquid chromatography/tandem mass spectrometry. Proteomics. 2004 Jun;4(6):1684-1694. [PubMed link]

003. 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. [PubMed link]

002. Park, S. J., Park, D. H., Sul, S. H., Oh, S. W. F., Park, I. S., Chung, D. S., Kim, H. J., Kim, M.-S., Lee, S. W.,.. (2004) Investigation of angiotensin glycosylation by MALDI-TOF and ESI tandem mass spectrometry. Bulletin of the Korean Chemical Society. 25 (12), 1791-1800 [PubMed link]

001. Kim, M.-S., Choie, W. S., Shin, Y. S., Yu, M. H. and Lee, S. W. (2004) Development of ultra-high pressure capillary reverse-phase liquid chromatography/tandem mass spectrometry for high-sensitive and high-throughput proteomics. Bulletin of the Korean Chemical Society. 25 (12), 1833-1839 [PubMed link]