B.Sc. & M.Sc. University of Dhaka, Dhaka, Bangladesh
M.S. Florida International University, 2001 (Stanislaw F. Wnuk)
PhD Washington State University, 2006 (James E. Bruce)
Pacific Northwest National Laboratory, 2006-2009
(Dr. Richard D. Smith)
National Institute of Environmental Health Sciences, 2009 - 2012
(Michael B. Fessler, MD and Dr. Kenneth B. Tomer)
My laboratory focuses on mass spectrometry-based method development in the following specific areas of proteome research in order to study environmental diseases impacted by innate immunity.
1. Global and targeted discovery of protein-protein/protein-ligand interactions by antibody/affinity based enrichment methods in combination with novel mass spectrometry-supportive chemical cross-linking approaches.
2. Identification and quantitative characterization of protein posttranslational modifications (PTMs) by mass spectrometry- supportive chemical probes.
3. Elucidation of protein structures by mass spectrometry.
4. Quantitative proteomics studies for the discovery and validation of cellular protein targets (bio-signatures or bio-markers)
The focused biological application of my research is to understand the role of lipid rafts and Toll-like Receptors (TLRs) in inflammatory signaling pathways. We focus on studying several environmental diseases impacted by innate immunity, such as atherosclerosis, sepsis, asthma, etc. by mass spectrometry-based novel proteomics tools. In addition, the approaches we develop can be generally applied to any biological systems; hence we also welcome researchers to initiate collaborative research efforts with us.
Wanigasekara, M. S. K.; Huang X.; , Chakrabarty, J. K.; Bugarin, A; Chowdhury, S. M. Arginine-Selective Chemical Labeling Approach for Identification and Enrichment of Reactive Arginine Residues in Proteins. ACS Omega, 2018, 3 (10), pp 14229–14235
Kamal, A. H.; Fessler, M. B.; Chowdhury, S. M (2018). Comparative and network- based proteomic analysis of ethanol-treated and LPS-induced Raw 264.7 macrophages- PLoS One. 2018 Feb 26;13(2):e0193104
Kamal, A. H. M.; Chakrabarty, J. K.; Udden, S. M. N.; Zaki, M. H.; Chowdhury, S. M.. Inflammatory Proteomic Network Analysis of Statin-treated and Lipopolysaccharide- activated Macrophages. Scientific reports 2018, 8, 164
Mahbub, M. M.; Chowdhury, S. M.; Christensen, S. M. Globular domain structure and function of restriction-like-endonuclease LINEs: similarities to eukaryotic splicing factor Prp8. Mobile DNA 2017, 8, 16
Bhawal, R. P.; Shahinuzzaman, A. D.; Chowdhury, S. M. Gas-phase fragmentation behavior of oxidized prenyl peptides by CID and ETD tandem mass spectrometry. Journal of the American Society for Mass Spectrometry 2017, 28, 704-707.-Emerging Investigator Focus,
Chakrabarty, J. K.; Naik, A. G.; Fessler, M. B.; Munske, G. R.; Chowdhury, S. M. Differential tandem mass spectrometry-based cross-linker: a new approach for high confidence in identifying protein cross-linking. Analytical Chemistry 2016, 88, 10215- 10222.
Wanigasekara, M. S.; Chowdhury, S. M. Evaluation of chemical labeling methods for identifying functional arginine residues of proteins by mass spectrometry. Analytica Chimica Acta 2016, 935, 197-206.
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. Proteomic analysis of ABCA1-null macrophages reveals a role for stomatin-like protein-2 in raft composition and toll-like receptor signaling. Molecular & Cellular Proteomics: MCP 2015, 14, 1859-1870.
Bhawal R.P.; Sadananda S.C.; Bugarin A., Laposa B.; Chowdhury S.M. "Mass spectrometry cleavable strategy for identification and differentiation of prenylated peptides" Anal Chem. 2015 87, 2178-2186
Chowdhury, S. M*.; Munske, G. R.; Yang, J.; Zhukova, D.; Nguyen, H.; Bruce, J. E.: Solid-phase N-terminal peptide enrichment study by optimizing trypsin proteolysis on homoarginine-modified proteins by mass spectrometry. Rapid Commun Mass Spectrom 2014, 28, 635-44.
Bian, Shenjie and Chowdhury Saiful M*- Profiling protein-protein interactions and protein structures using chemical cross-linking and mass spectrometry- Austin J Biomed Eng, 2014, 1 (4), 3
Du X, Chowdhury, S. M, Manes, M. Wu S, Cumblidge, UM, Adkins, J. N., Anderson, G. A., Smith, R. D. – Xlink-Identifier: An automated data analysis platforms for confident identification of chemically cross-linked peptides using tandem mass spectrometry –J Proteome Res. 2011 Mar 4;10(3):923-31.
Shi L, Chowdhury S. M., Smallwood H.S., Yoon H., Mottaz-Brewer H.M., Norbeck A.D., McDermott J.E., Clauss TR.W., Heffron F, Smith R.D., Adkins J.N. Proteomics investigation of the time course responses of RAW 264.7 macrophages to infection with salmonella enterica –– Infect Immun 2009, 77, (8), 3227-33.
Featured in Biological Science Division research highlights in PNNL. Link: http://www.pnl.gov/science/highlights/highlight.asp?id=656.
Chowdhury, S. M., Du. X, Tolić, N, Wu S, Moore, R. J., Mayer, M. U.,. Smith, R. D., Adkins, J. N. - Identification of cross-linked peptides containing a click-based enrichment group using sequential CID and ETD tandem mass spectrometry – Anal Chem 2009, 81, (13), 5524-32 – high-lighted in online news of Journal of Proteome Research. Link: http://pubs.acs.org/action/showStoryContent?doi=10.1021%2Fon.2009.06.29.395768.
Chowdhury, S. M., Shi, L, Yoon, H, Rommereim, L. M., Norbeck, A. D., Auberry K. J., Moore, R. J., Adkins J. N., Heffron, F. and Smith, R. D. - A method for investigating protein-protein interactions related to Salmonella Typhimurium pathogenesis”– J. Proteome Res., 2009, 8 (3), pp 1504–1514 – Ranked 15 in Top 20 most read articles in JPR for the March of 2009.
Rodland, K. D., Adkins, J. N., Ansong, C, Chowdhury, S, Manes, N. P., Shi, L., Yoon, H., Smith, R. D., Heffron, F. - Use of high-throughput mass spectrometry to elucidate host-pathogen interactions in Salmonella - Future Microbiology, 2008 3(6), 625-634. – Review
Chowdhury, S. M.; Munske, G. R.; Ronald, R. C.; Bruce, J. E., Evaluation of low energy CID and ECD fragmentation behavior of mono-oxidized thio-ether bonds in peptides. Journal of Am. Soc. Mass Spectrom 2007, 18(3):493-501.
Chowdhury SM: Chemical strategies for profiling protein-protein interactions and protein posttranslational modifications (Ph. D. thesis, Washington State University, USA) - 2006
Chowdhury, S. M.; Munske, G. R.; Tang, X; Bruce, J. E., Collisionally activated dissociation and electron capture dissociation of several mass spectrometry-identifiable chemical cross-linkers. Anal. Chem. 2006, 78 (24):8183 -8193.
Chowdhury, S. M.; Munske, G. R.; Siems, W. F.; Bruce, J. E., A new maleimide-bound acid-cleavable solid-support reagent for profiling phosphorylation. Rapid Commun Mass Spectrom 2005, 19(7):899-909
Wnuk, S. F.; Chowdhury, S. M.; Garcia, P. I., Jr.; Robins, M. J., 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. J Org Chem 2002, 67(6):1816-9.
Pacific Northwest National Laboratory (PNNL) postdoctoral fellowship, Aug. 2006 - Dec. 2009.
Laboratory Directed Research and Development (LDRD) grant award, PNNL (Co-principal Investigator, total 250,000 for two years), ranked 2nd out of 22 selected grant proposals.
Fellow Award for Research Excellence (FARE), 2011: National Institute of Health (NIH).