Publications

2026

• Heo, S.*, Zhang, S.*, Mun, D.-G.*, Pandey, A., Bygrave, A. M., Huganir, R. L. Sex and experience dependent regulation of synaptic protein turnover. Proceedings of the National Academy of Sciences. 2026. 123, e2602111123.
• Garapati, K.*, Mun, D.-G.*, Balaya, R. D. A., Saraswat, M., Renuse, S., Trahan, G., Kandasamy, R.K., Deyle, D.R., Pandey, A. Proteomic alterations in patient-derived mesenchymal stem cells and their secretomes in osteogenesis imperfecta. Molecular Genetics and Metabolism Reports. 2026. 48, 101341.
• Mun, D.-G.*, Nishida, H.*, Bhat, F. A., Pasupuleti, R. R., Delanghe, B., and Pandey, A. Multiplexed quantitation of post-translationally modified peptides in single cells using triggered MS/MS combined with super heavy tandem mass tags. Journal of Proteome Research. 2026. 25, 1184.
• Mun, D.-G., Madugundu, A. K., Renuse, S., Nirujogi, R. S., 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., and Pandey, A. A transcriptomic and proteomic map of primary human cell types. Nucleic Acids Research. 2026. 54, gkaf1498.

2025

• Mun, D.-G.*, Jessen, E.*, Tomlinson, J. K., Carlson, D., Budhraja, R., Alva-Ruiz, R., Abdelrahman, A., Watkins, R., Gregory, L., McCabe, C., Wang, C., Graham, R. P., Woods, K., Golkowski, M., Baker, M., Gores, G. J., Ilyas, S. I., Conboy, C., Larson, E. L., Sample, J. W., Ozmert, E. H., Kandasamy, R. K., Borad, M. J., Roberts, L., Andersen, J., Pandey, A., and Smoot, R. L. Multiomics combined with machine learning defines unique molecular subtypes of cholangiocarcinoma and identifies TNK1 as a therapeutic target. Hepatology. 2025.
• Mun, D.-G., Pujari, G. P., Sachdeva, G., Madden, B. J., Charlesworth, M. C., Johnson, K., Archila, L. R., Alexander, M. P., Denic, A., Mullan, A. F., Sharma, V., Larson, N. B., Luehrs, A. C., Rule, A. D., and Pandey, A. Spatial proteomics to discover aging-associated alterations in the renal tubulointerstitium. Clinical Proteomics. 2025. 22, 37.
• Bhat, F. A., Ding, H., Mun, D.-G., Peterson, J. A., Charlesworth, M. C., Kandasamy, R. K., and Pandey, A. Targeted quantitation of phosphotyrosine-containing proteins in T cell receptor signaling using a SureQuant-based targeted mass spectrometry approach. Proteomics. 2025, 25, 40.
• Lee, S., Park, J., Back, S., Poudyal, R. S., Mun, D.-G., Bae, J., Gwak, N., Lee, S.-W., Hwang, D., and Kim, Y. Identification of STN7-associated leaf senescence networks in thylakoid membranes of Arabidopsis. iScience. 2025, 28, 112577.
• Aalam, S. M. M.*, Varela, A. R.*, Khaderi, A.*, Mondesir, R. J.*, Mun, D.-G.*, Ding, A., Lombaert, I. M. A., Coppes, R. P., Emperumal, C. P., Pandey, A., Janus, J. R., and Kannan, N. Establishment of salivary tissue-organoid biorepository: characterizing salivary gland stem/progenitor cells and novel differentiation marker PSMA/FOLH1. npj Regenerative Medicine. 2025, 10, 23.
• Kim, J., Mun, D.-G., Ding, H., Forsberg, E. M., Meyer, S. W., Barsch, A., Pandey, A., and Byeon, S. K. Single cell untargeted lipidomics using liquid chromatography ion mobility-mass spectrometry. Journal of Proteome Research. 2025, 24, 1579.

2024

• Xie, X., Truong, T., Huang, S., Johnston, S. M., Hovanski, S., Robinson, A., Webber, K., Lin, H.-J., Mun, D.-G., Pandey, A., and Kelly, R. Multicolumn nanoflow liquid chromatography with accelerated offline gradient generation for robust and sensitive single-cell proteome profiling. Analytical Chemistry. 2024, 96, 10534.
• Mun, D.-G., Bhat, F. A., Joshi, N. S., Sandoval, L., Ding, H., Jain, A., Peterson, J. A., Kang, T., Pujari, G. P., Tomlinson, J. L., Budhraja, R., Zenka, R. M., Kannan, N., Kipp, B. R., Dasari, S., Gaspar-Maia, A., Smoot, R. L., Kandasamy, R. K., and Pandey, A. Diversity of PTMs and cell signaling revealed by single cell and single organelle mass spectrometry. Communications Biology. 2024, 7, 884.
• Garapati, K., Jain, A., Madden, B. J., Mun, D.-G., Sharma, J., Budhraja, R., and Pandey, A. Defining albumin as a glycoprotein with multiple N-linked glycosylation sites. Journal of Translational Medicine. 2024, 22, 454.
• Jackson, L. E., Tomlinson, J. L., Alva-Ruiz, R., Gregory, L. A., Byeon, S. K., Abdelrahman, A. M., Mun, D.-G., Grant, C. W., Fogarty, Z. C., Wang, C., Roberts, L. R., Graham, R. P., Borad, M. J., Ilyas, S. I., Gores, G. J., Pandey, A., Athreya, A. P., and Smoot, R. L. Metabolome-wide association identifies altered metabolites and metabolic pathways in the serum of patients with cholangiocarcinoma. JHEP Reports. 2024, 6, 101068.
• Bhat, F. A., Mangalaparthi, M., Ding, H., Jain, A., Hsu, J-S., Peterson, J. A., Zenka, R. M., Mun, D.-G., Kandasamy, R. K., and Pandey, A. Exploration of nitrotyrosine-containing proteins and peptides by antibody-based enrichment strategies. Molecular & Cellular Proteomics. 2024, 23, 100733.

2023

• Garapati, K., Ding, H., Charlesworth, C. M., Kim, Y., Zenka, R. M., Saraswat, M., Mun, D.-G., Chavan, S., Shingade, A., Lucien, F., Zhong, J., Kandasamy, R. K., and Pandey, A. sBioSITe enables sensitive identification of the cell surface proteome through direct enrichment of biotinylated peptides. Clinical Proteomics. 2023, 20, 56.
• Mun, D.-G.*, Joshi, N. S.*, Budhraja, R., Sachdeva, G. S., Kang, T., Bhat, F. A., Ding, H., Madden, B. J., Zhong, J., and Pandey, A. Automated sample preparation workflow for tandem mass tag-based proteomics. Journal of the American Society for Mass Spectrometry. 2023, 34, 2087-2092.
• Mun, D.-G., Bhat, F. A., Ding, H., Madden, B. J., Natesampillai, S., Badley, A.D., Johnson, K. L., Kelly, R. T., and Pandey, A. Optimizing single cell proteomics using trapped ion mobility spectrometry for label-free experiments. Analyst. 2023, 148, 3466-3475.
• Mun, D.-G., Budhraja, R., Bhat, F. A., Zenka, R. M., Johnson, K. L., Moghekar, A., and Pandey, A. Four-dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility mass spectrometry using PASEF. Proteomics. 2023, 23, e2200507.
• 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., and Lee, S.-W. Proteogenomic landscape of human pancreatic ductal adenocarcinoma in an Asian population reveals tumor cell-enriched and immune-rich subtypes. Nature Cancer. 2023, 4, 290-307.

2022

• Conboy, C. B., Yonkus, J. A., Buckarma, E. H., Mun, D.-G., Werneburg, N. W., Watkins, R. D., Alva-Ruiz, R., Guo, Y., Wang, J., O’Brien, D., McCabe, C. E., Jessen, E., Graham, R. P., Buijsman, R. C., Vu, D., Man J., Ilyas, S. I., Truty, M. J., Borad, M., Pandey, A., Gores, G. J., and Smoot, R. L. LCK inhibition downregulates YAP activity and is therapeutic in patient-derived models of cholangiocarcinoma. Journal of Hepatology. 2022, 78, 142-152.

2021

• Mun, D.-G., Vanderboom, P. M., Madugundu, A. K., Garapati, K., Chavan, S., Peterson, J. A., Saraswat, M., and Pandey, A. DIA-based proteome profiling of nasopharyngeal swabs from COVID-19 patients. Journal of Proteome Research. 2021, 20, 4165-4175.
• Vanderboom, P. M., Mun, D.-G., Madugundu, A. K., Mangalaparthi, K. K., Saraswat, M., Garapati, K., Chakraborty, R., Ebihara, H., Sun, J., and Pandey, A. Proteomic signature of host response to SARS-CoV-2 infection in the nasopharynx. Molecular & Cellular Proteomics. 2021, 20, 100134.
• 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. R., Krasnoperov, V., Truty, M., Graham, R. P., Gill, P. S., Mukhopadhyay, D., and Pandey, A. Tyrosine phosphoproteomics of patient-derived xenografts reveals Ephrin type-B receptor 4 tyrosine kinase as a therapeutic target in pancreatic cancer. Cancers. 2021, 13, 3404.
• Saraswat, M., Garapati, K., Mun, D.-G., and Pandey, A. Extensive heterogeneity of glycopeptides in plasma revealed by deep glycoproteomic analysis using size-exclusion chromatography. Molecular Omics. 2021, 17, 939-947.
• Wu, X., Wang, Li., Pearson, N. A., Renuse, S., Chen, Ren., Liang, Ye., Mun, D.-G., Madugundu, A. K., Xu, Y., Gill, P. S., and Pandey, A. Quantitative tyrosine phosphoproteome profiling of AXL receptor tyrosine kinase signaling network. Cancers. 2021, 13, 4234.
• Renuse, S., Vanderboom, P. M., Maus, A. D., Kemp, J. V., Gurtner, K. M., Madugundu, A. K., Chavan, S., Peterson, J. A., Madden, B. J., Mangalaparthi, K. K., Mun, D.-G., Singh, S., Kipp, B. R., Dasari, S., Singh, R. J., Grebe, S. K., and Pandey, A. A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens. EBioMedicine. 2021, 69.
• Prakash, A., Taylor, L., Varkey, M., Hoxie, N., Mohammed, Y., Goo, Y. A., Peterman, S., Moghekar, A., Yuan, Y., Glaros, T., Steele, J. R., Faridi, P., Parihari, S., Srivastava, S., Otto, J. J., Nyalwidhe, J. O., Semmes, O. J., Moran, M. F., Madugundu, A., Mun, D.-G., Pandey, A., Mahoney, K. E., Shabanowitz, J., Saxena, S., and Orsburn, B. C. Reinspection of a clinical proteomics tumor analysis consortium (CPTAC) dataset with cloud computing reveals abundant post-translational modifications and protein sequence variants. Cancers. 2021, 13, 5034.

2020

• Mun, D.-G., Renuse, S., Saraswat, M., Madugundu, A., Udainiya, S., Kim, H., Park, S. R., Zhao, H., Nirujogi, R. S., Na, C. H., Kannan, N., Yates J. R., Lee, S.-W., and Pandey, A. PASS-DIA: A data-independent acquisition approach for discovery studies. Analytical Chemistry. 2020, 92, 14466-14475.

2019

• Mun, D.-G.*, Nam, D.*, Kim, H., Pandey, A., and Lee, S.-W. Accurate precursor mass assignment improves peptide identification in data-independent acquisition mass spectrometry. Analytical Chemistry. 2019, 91, 8453-8460.
• Mun, D.-G.*, Bhin, J.*, Kim, S.*, Kim, H.*, Jung, J.*, Jang, Y., Park J.-M., Kim, H., Lee, H., Bae, J., Back S., Kim, S.-J., Kim, J., Park, H., Li, H., Hwang, K.-B., Park, Y., Yook, J., Kim, B., Kwon, S.Y., Ryu, S.Y., Park, D.Y., Jeon, T.Y., Kim, D.H., Lee, J.-H., Han, S.-U., Song, K.S., Park, D., Park, J.W., Yu, M.-H., Lee, H., Kim, K.P., Yang, E.K., Kim, H.K., Paek, E., Lee, S., Lee, S.-W., and Hwang, D. Proteogenomic characterization of human early onset gastric cancer. Cancer Cell. 2019, 35, 111-124.

2018

• Park, J. W., Kim, M.-S., Voon, D. C., Kim, S.-J., Bae, J., Mun, D.-G., Ko, S.-I., Kim, H. K., Lee, S.-W., and Kim, D.-Y. 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. 2018, 57, 947-954.
• Madar, I. H., Lee, W, Wang, X, Ko, S.-I., Kim, H., Mun, D.-G., Zhang, B., and Lee, S.-W. Comprehensive and sensitive proteogenomics data analysis strategy based on complementary multi-stage database search. International Journal of Mass Spectrometry. 2018, 427, 11-19.

2017

• Madar, I. H., Ko, S.-I., Kim, H., Mun, D.-G., Kim, S., Smith, R., and Lee, S.-W. Multiplexed post-experimental monoisotopic mass refinement (mPE-MMR) to increase sensitivity and accuracy in peptide identifications from tandem mass spectra of co-fragmentation. Analytical Chemistry. 2017, 89, 1244-1253.

2016

• Lee, H., Mun, D.-G., So, J. E., Bae, J., Kim, H., Masselon, C., and Lee, S.-W. Efficient exploitation of separation space in two-dimensional liquid chromatography system for comprehensive and efficient proteomic analyses. Analytical Chemistry. 2016, 88, 11734-11741.
• Lee, S. J., Choi, T. S., Lee, J. W., Lee, H. J., Mun, D.-G., Akashi, S., Lee, S.-W., Lim, M. H., and Kim, H. Structure and assembly mechanisms of toxic human islet amyloid polypeptide oligomers associated with copper. Chemical Science. 2016, 7, 5398-5406.

2015

• Park, J.-M.*, Park, J.-H.*, Mun, D.-G.*, Bae, J., Jung, J. H., Back, S., Lee, H., Kim, H., Jung, H.-J., Kim, H. K., Lee, H., Kim, K. P., Hwang, D., and Lee, S.-W. Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks. Scientific Reports. 2015, 5, 18189.
• Lee, H., Mun, D.-G., Bae, J., Kim, H., Oh, S. Y., Park, Y. S., Lee, J.-H., and Lee, S.-W. A simple dual online ultra-high pressure liquid chromatography system (sDO-UHPLC) for high throughput proteome analysis. Analyst. 2015, 140, 5700-5706.

2014

• Park, H., Bae, J., Kim, H., Kim, S., Kim, H., Mun, D.-G., Lee, W., Joh, Y., Chae, S., Lee, S., Kim, H. K., Hwang, D., Paek, E., and Lee, S.-W. Compact variant-rich customized sequence database and a fast and sensitive database search for efficient proteogenomics analysis. Proteomics. 2014, 14, 2742-2749.
• Li, H., Hwang, K.-B., Mun, D.-G., Kim, H., Lee, H., Lee, S.-W., and Paek, E. Estimating influence of co-fragmentation on peptide quantification and identification in iTRAQ experiments by simulating multiplexed spectra. Journal of Proteome Research. 2014, 13, 3488-3497.
• Kim, S.-J., Chae, S., Kim, H., Mun, D.-G., Back, S., Choi, H. Y., Park, K. S., Hwang, D., Choi, S. H., and Lee, S.-W. A protein profile of visceral adipose tissues linked to early pathogenesis of type 2 diabetes mellitus. Molecular & Cellular Proteomics. 2014, 13, 811-822.
• Madar, I. H., Back, S., Mun, D.-G., Kim, H., Jung, J. H., Kim, K. P., and Lee, S.-W. Reduction of ambiguity in phosphorylation-site localization in large-scale phosphopeptide profiling by data filter using unique mass class information. Bulletin of The Korean Chemical Society. 2014, 35, 845-850.

2013

• Yi, J.-S.*, Mun, D.-G.*, Lee, H., Park, J.-S., Lee, J.-W., Lee, J.-S., Kim, S.-J., Cho, B. R., Lee, S.-W., and Ko, Y.-G. PTRF/Cavin-1 is essential for multidrug resistance in cancer cells. Journal of Proteome Research. 2013, 12, 605-614.

2012

• Lee, J. H., Hyung, S.-W., Mun, D.-G., Jung, H.-J., Kim, H., Lee, H., Kim, S.-J., Park, K. S., Moore, R. J., Smith, R. D., and Lee, S.-W. Fully automated multifunctional ultrahigh pressure liquid chromatography system for advanced proteome analyses. Journal of Proteome Research. 2012, 11, 4373-4381.

2011

• Hyung, S.-W., Kim, M.-S., Mun, D.-G., Lee, H., and Lee, S.-W. 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. 2011, 136, 2100-2105.

2010

• Jung, H.-J., Purvine, S. O., Kim, H., Petyuk, V. A., Hyung, S.-W., Monroe, M. E., Mun, D.-G., Kim, K.-C., Park, J.-M., Kim, S.-J., Tolic, N., Slysz, G. W., Moore, R. J., Zhao, R., Adkins, J. N., Anderson, G. A., Lee, H., Camp II, D. G., Yu, M.-H., Smith, R. D., and Lee, S.-W. Integrated post-experiment monoisotopic mass refinement: An integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data. Analytical Chemistry. 2010, 82, 8510-8518.