Publications

  • Zacharias, A. O.; Cornelius, S.; Chowdhury, S. M*. Selective Labeling of Tyrosine Residues in Proteins: Insights from PTAD Labeling and Tandem Mass Spectrometry Analysis – Mol. Omics, 2024, Accepted Manuscript
  • Westfall A.K.; Gopalan S. S.;  Kay, J. C.; Tippetts, T. T.; Cervantes, M. B.;  Lackey, K.;  Chowdhury, S. M.; Pellegrino, M. W.; Castoe, T. A. Single-cell resolution of intestinal regeneration in pythons without crypts illuminates conserved vertebrate regenerative mechanisms, Proceedings of the National Academy of Sciences 2024 Vol. 121 Issue 43 Pages e2405463121, DOI: doi:10.1073/pnas.2405463121
  • Mehta, A.; Kamal A. H. M.;  Cornelius, S.;  Chowdhury, S. M. Protein-Protein Interaction Network Mapping by Affinity Purification Cross-Linking Mass Spectrometry (AP-XL-MS) based Proteomics. Methods Mol Biol. 2023;2690:255-267. DOI: 10.1007/978-1-0716-3327-4_22
  • Zacharias, Adway.; Chowdhury, Saiful M (2023). Developing an efficient Tyrosine Reactive Crosslinker (TRCL) for protein crosslinking. Preprint DOI 10.26434/chemrxiv-2023-sx3sw
  • Kamal, A. H. M., Chakrabarty, J. K., & Chowdhury, S. M. (2023). Lipopolysaccharide and Statin Mediated Immune-responsive Protein Networks in Macrophages Revealed Through Affinity Purification Spacer-Arm Controlled Cross-linking (AP-SPACC) Proteomics. Molecular Omics. 2023 Jan 16;19(1):48-59. https://doi.org/10.1039/D2MO00224H
  • Christine E Psaltis Matthews, Lynn A Fussner, Michael Yaeger, Jim J Aloor, Sky W Reece, Brita J Kilburg-Basnyat, Sanjay Varikuti, Bin Luo, Morgan Inks, Selin Sergin, Cameron A Schmidt, P Darrell Neufer, Edward Ross Pennington, Kelsey H Fisher-Wellman, Saiful M Chowdhury, Michael B Fessler, Jenifer I Fenton, Ethan J Anderson, Saame Raza Shaikh, Kymberly M Gowdy (2023). The prohibitin complex regulates macrophage fatty acid composition, plasma membrane packing, and lipid raft-mediated inflammatory signaling. Prostaglandins Leukot Essent Fatty Acids 2023 Mar;190:102540. doi: 10.1016/j.plefa.2023.102540. Epub 2023 Jan 19.
  • Shahinuzzaman ADA, Kamal AHM, Chakrabarty, J. K., Rahman, A., & Chowdhury, S. M. (2022). Identification of Inflammatory Proteomics Networks of Toll-like Receptor 4 through Immunoprecipitation-Based Chemical Cross-Linking Proteomics.. Proteomes. 2022 Sep 1;10(3):31. doi: 10.3390/proteomes10030031.. https://doi.org/10.3390/proteomes10030031
  • Fang, Z., Wanigasekara MSK, Yepremyan, A., Lam, B., Thapa, P., Foss, Jr, F. W., & Chowdhury, S. M. (2022). Mass Spectrometry-Cleavable Protein N-Terminal Tagging Strategy for System-Level Protease Activity Profiling. Journal of the American Society for Mass Spectrometry, 33(1), 189–197. https://doi.org/10.1021/jasms.1c00350
  • Westfall, A. K., Perry, B. W., Kamal AHM, Hales, N. R., Kay, J. C., Sapkota, M., Schield, D. R., Pellegrino, M. W., Secor, S. M., Chowdhury, S. M., & Castoe, T. A. (2022). Identification of an integrated stress and growth response signaling switch that directs vertebrate intestinal regeneration. BMC Genomics, 23(1), 6. https://doi.org/10.1186/s12864-021-08226-5
  • Fang, Z., & Chowdhury, S. M. (2021). Dual-Stage Neutral Loss Tandem Mass Spectrometric Strategy for Confident Identification of Protein Prenylation. Analytical Chemistry, 93(39), 13169–13176. https://doi.org/10.1021/acs.analchem.1c01617
  • Zacharias, A. O., Fang, Z., Rahman, A., Talukder, A., Cornelius, S., & Chowdhury, S. M. (2021). Affinity and chemical enrichment strategies for mapping low-abundance protein modifications and protein-interaction networks. Journal of Separation Science, 44(1), 310–322. https://doi.org/10.1002/jssc.202000930
  • Chakrabarty, J. K., Bugarin, A., & Chowdhury, S. M. (2020). Evaluating the performance of an ETD-cleavable cross-linking strategy for elucidating protein structures. Journal of Proteomics, 225, 103846. https://doi.org/10.1016/j.jprot.2020.103846
  • Shahinuzzaman ADA, Chakrabarty, J. K., Fang, Z., Smith, D., Kamal AHM, & Chowdhury, S. M. (2020). Improved in-solution trypsin digestion method for methanol-chloroform precipitated cellular proteomics sample. Journal of Separation Science, 43(11), 2125–2132. https://doi.org/10.1002/jssc.201901273
  • Ricci, C. A., Kamal, A. H., Chakrabarty, J. K., Ledbetter, B. E., Chowdhury, S. M., & Mydlarz, L. D. (2020). The cell-surface protein composition of a coral symbiont, Breviolum psygmophilum, reveals a mechanism for host specificity and displays dynamic regulation during temperature stress. Marine Biology, 167(66). https://doi.org/10.1007/s00227-020-03680-3
  • Chakrabarty, J. K., Sadananda, S. C., Bhat, A., Naik, A. J., Ostwal, D. V., & Chowdhury, S. M. (2020). High Confidence Identification of Cross-Linked Peptides by an Enrichment-Based Dual Cleavable Cross-Linking Technology and Data Analysis tool Cleave-XL. Journal of the American Society for Mass Spectrometry, 31(2), 173–182. https://doi.org/10.1021/jasms.9b00111
  • Ricci, C. A., Kamal AHM, Chakrabarty, J. K., Fuess, L. E., Mann, W. T., Jinks, L. R., Brinkhuis, V., Chowdhury, S. M., & Mydlarz, L. D. (2019). Proteomic Investigation of a Diseased Gorgonian Coral Indicates Disruption of Essential Cell Function and Investment in Inflammatory and Other Immune Processes. Integrative and Comparative Biology, 59(4), 830–844. https://doi.org/10.1093/icb/icz107
  • Kamal AHM, Aloor, J. J., Fessler, M. B., & Chowdhury, S. M. (2019). Cross-linking Proteomics Indicates Effects of Simvastatin on the TLR2 Interactome and Reveals ACTR1A as a Novel Regulator of the TLR2 Signal Cascade. Molecular and Cellular Proteomics, 18(9), 1732–1744. https://doi.org/10.1074/mcp.RA119.001377
  • Perry, B. W., Andrew, A. L., Mostafa Kamal, A. H., Card, D. C., Schield, D. R., Pasquesi GIM, Pellegrino, M. W., Mackessy, S. P., Chowdhury, S. M., Secor, S. M., & Castoe, T. A. (2019). Multi-species comparisons of snakes identify coordinated signalling networks underlying post-feeding intestinal regeneration. Proceedings of the Royal Society B, 286(1906), 20190910. https://doi.org/10.1098/rspb.2019.0910
  • Fang, Z., Baghdady, Y. Z., Schug, K. A., & Chowdhury, S. M. (2019). Evaluation of Different Stationary Phases in the Separation of Inter-Cross-Linked Peptides. Journal of Proteome Research, 18(4), 1916–1925. https://doi.org/10.1021/acs.jproteome.9b00114
  • Wanigasekara, M. S., Huang, X., Chakrabarty, J. K., Bugarin, A., & Chowdhury, S. M. (2018). Arginine-selective chemical labeling approach for identification and enrichment of reactive arginine residues in proteins. ACS Omega, 3(10), 14229–14235. https://doi.org/10.1021/acsomega.8b01729
  • Kamal, A. H. M., Fessler, M. B., & Chowdhury, S. M. (2018). Comparative and network-based proteomic analysis of low dose ethanol- and lipopolysaccharide-induced macrophages. PLoS One, 13(2), 1–22. https://doi.org/10.1371/journal.pone.0193104
  • Kamal, A. H. M., Chakrabarty, J. K., Udden, N. S. M., Zaki, M. H., & Chowdhury, S. M. (2018). Inflammatory Proteomic Network Analysis of Statin-treated and Lipopolysaccharide-activated Macrophages. Scientific Reports, 8(164), 1–13. https://doi.org/10.1038/s41598-017-18533-1
  • Mahbub, M. M., Chowdhury, S. M., & Christensen, S. M. (2017). Globular domain structure and function of restriction-like-endonuclease LINEs: similarities to eukaryotic splicing factor Prp8. Mobile DNA, 8(16), 1–15. https://doi.org/10.1186/s13100-017-0097-9
  • Bhawal, R. P., Shahinuzzaman, A. D. A., & Chowdhury, S. M. (2017). Gas-Phase Fragmentation Behavior of Oxidized Prenyl Peptides by CID and ETD Tandem Mass Spectrometry. Journal of the American Society for Mass Spectrometry, 28(4), 704–707. https://doi.org/10.1007/s13361-016-1503-0
  • Chakrabarty, J. K., Naik, A. G., Fessler, M. B., Munske, G. R., & Chowdhury, S. M. (2016). Differential Tandem Mass Spectrometry-Based Cross-Linker: A New Approach for High Confidence in Identifying Protein Cross-Linking. Analytical Chemistry, 88(20), 10215–10222. https://doi.org/10.1021/acs.analchem.6b02886
  • Wanigasekara, M. S. K., & Chowdhury, S. M. (2016). Evaluation of chemical labeling methods for identifying functional arginine residues of proteins by mass spectrometry. Analytica Chimica Acta, 935, 197–206. https://doi.org/10.1016/j.aca.2016.06.051
  • Chowdhury, S. M., Zhu, X., Aloor, J. J., Azzam, K. M., Gabor, K. A., Ge, W., Addo, K. A., Tomer, K. B., Parks, J. S., & Fessler, M. B. (2015). Proteomic Analysis of ABCA1-Null Macrophages Reveals a Role for Stomatin-Like Protein-2 in Raft Composition and Toll-Like Receptor Signaling. Molecular and Cellular Proteomics, 14(7), 1859–1870. https://doi.org/10.1074/mcp.M114.045179
  • Bhawal, R. P., Sadananda, S. C., Bugarin, A., Laposa, B., & Chowdhury, S. M. (2015). Mass Spectrometry Cleavable Strategy for Identification and Differentiation of Prenylated Peptides. Analytical Chemistry, 87(4), 2178–2186. https://doi.org/10.1021/ac503794s
  • Bian, S., & Chowdhury, S. M. (2014). Profiling Protein-Protein Interactions and Protein Structures Using Chemical Cross-linking and Mass Spectrometry. Austin Journal of Biomedical Engineering, 1(4), 1017. http://www.austinpublishinggroup.com/biomedical-engineering/fulltext/ajbe-v1-id1017.pdf
  • Chowdhury, S. M., Munske, G. R., Yang, J., Zhukova, D., Nguyen, H., & Bruce, J. E. (2014). Solid-phase N-terminal peptide enrichment study by optimizing trypsin proteolysis on homoarginine-modified proteins by mass spectrometry. Rapid Communications in Mass Spectrometry, 28(6), 635–644. https://doi.org/10.1002/rcm.6820
  • Du, X., Chowdhury, S. M., Manes, N. P., Wu, S., Mayer, M. U., Adkins, J. N., Anderson, G. A., & Smith, R. D. (2011). Xlink-Identifier: An Automated Data Analysis Platform for Confident Identifications of Chemically Cross-Linked Peptides Using Tandem Mass Spectrometry. Journal of Proteome Research, 10(3), 923–931. https://doi.org/10.1021/pr100848a
  • Chowdhury, S. M., Shi, L., Yoon, H., Ansong, C., Rommereim, L. M., Norbeck, A. D., Auberry, K. J., Moore, R. J., Adkins, J. N., Heffron, F., & Smith, R. D. (2009). A Method for Investigating Protein-Protein Interactions Related to Salmonella Typhimurium Pathogenesis. Journal of Proteome Research, 8(3), 1504–1514. https://doi.org/10.1021/pr800865d
  • Chowdhury, S. M., Du, X., Tolic, N., Wu, S., Moore, R. J., Mayer, M. U., Smith, R. D., & Adkins, J. N. (2009). Identification of Cross-Linked Peptides after Click-Based Enrichment Using Sequential Collision-Induced Dissociation and Electron Transfer Dissociation Tandem Mass Spectrometry. Analytical Chemistry, 81(13), 5524–5532. https://doi.org/10.1021/ac900853k
  • Shi, L., Chowdhury, S. M., Smallwood, H. S., Yoon, H., Mottaz-Brewer, H. M., Norbeck, A. D., McDermott, J. E., Clauss, T. R. W., Heffron, F., Smith, R. D., & Adkins, J. N. (2009). Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Infection with Salmonella enterica. Infection and Immunity, 77(8), 3227–3233. https://doi.org/10.1128/IAI.00063-09
  • Rodland, K. D., Adkins, J. N., Ansong, C., Chowdhury, S. M., Manes, N. P., Shi, L., Yoon, H., Smith, R. D., & Heffron, F. (2008). Use of high-throughput mass spectrometry to elucidate host-pathogen interactions in Salmonella. Future Microbiology, 3(6), 625–634. https://doi.org/10.2217/17460913.3.6.625
  • Chowdhury, S. M., Munske, G. R., Tang, X., & Bruce, J. E. (2006). Collisionally activated dissociation and electron capture dissociation of several mass spectrometry-identifiable chemical cross-linkers. Analytical Chemistry, 78(24), 8183–8193. https://doi.org/10.1021/ac060789h
  • Chowdhury, S. M., Munske, G. R., Ronald, R. C., & Bruce, J. E. (2006). Evaluation of low energy CID and ECD fragmentation behavior of mono-oxidized thio-ether bonds in peptides. Journal of the American Society for Mass Spectrometry, 18(3), 493–501. https://doi.org/10.1016/j.jasms.2006.10.019
  • Chowdhury, S. M., Munske, G. R., Siems, W. F., & Bruce, J. E. (2005). A new maleimide-bound acid-cleavable solid-support reagent for profiling phosphorylation. Rapid Communications in Mass Spectrometry, 19, 899–909. https://doi.org/10.1002/rcm.1869
  • Wnuk, S. F., Chowdhury, S. M., Garcia, P. I., & Robins, M. J. (2002). Stereodefined synthesis of O3′-labeled uracil nucleosides. 3′-[(17)O]-2′-Azido-2′-deoxyuridine 5′-diphosphate as a probe for the mechanism of inactivation of ribonucleotide reductases. Journal of Organic Chemistry, 67(6), 1816–1819. https://doi.org/10.1021/jo010899i
  • Hossain, M. A., Mustafa, A. I., Amin, M. N., & Chowdhury, S. M. (1997). Studies on the quality of three selected varieties of rapeseed and mustard oils and oil cakes. Dhaka University Journal of Science, 45(1), 23–29.