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Saiful Chowdhury

Saiful Chowdhury

Associate Professor

Office: 352 Chemistry and Physics Building (CPB)
Phone: 817-272-5439
Mentis Profile

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)
Post Doctorate:
Pacific Northwest National Laboratory, 2006-2009
(Dr. Richard D. Smith)
Research Fellow:
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.


Dr. Saiful M. Chowdhury joined the University of Texas at Arlington in August of 2012. He received his B.Sc (honors) and M.Sc degree (first class in both exams) in Applied Chemistry and Chemical Technology (currently, Department of Applied Chemistry and Chemical Engineering) from University of Dhaka, Dhaka, Bangladesh. After graduation, he served as a lecturer of Chemistry and also a lecturer of Chemical Engineering and Polymer Science at two public universities of Bangladesh. He completed another MS in bio-organic chemistry from Florida International University (FIU), Miami, Fl. in 2001. During his MS studies in FIU, he worked with Dr. Stanislaw F. Wnuk and synthesized an isotope-labeled nucleoside analogue which was used to reveal mechanism of inhibition of Ribonucleotide Di Phosphate Reductases (RDPR). In 2006, he earned his PhD in Analytical Chemistry from Washington State University, Pullman WA, under the supervision of Dr. James E. Bruce, who is currently a professor of the Department of Genome Sciences at the University of Washington. During his PhD studies, he developed several mass spectrometry-based bio-analytical methods for studying protein-protein interactions and protein posttranslational modifications (PTMs). After finishing his PhD, he joined as a postdoctoral fellow in the proteomics and mass spectrometry group of Dr. Richard D. Smith in Pacific Northwest National Laboratory, Richland, WA. In his postdoctoral training in Dr. Richard D. Smith’s group at PNNL, he developed several cutting-edge proteomics tools for global and targeted discovery of protein interactions utilizing tandem affinity tags, chemical cross-linking approaches and mass spectrometry. He worked with the systems biology team at PNNL, and applied these methodologies to investigate protein interactions related to Salmonella pathogenesis and also host-pathogen interactions. From Dec. 2009 - July 2012, he was employed as a research fellow in the laboratory of respiratory biology at the National Institute of Environmental Health Sciences (NIEHS) at NIH and conducted research under the mentorship of Michael B. Fessler MD, head of the host-defense group. He was also co-mentored by Dr. Kenneth B. Tomer, head of the mass spectrometry group. At NIEHS, NIH, he studied lipid raft proteome and toll-like receptors (TLRs) signaling using mass spectrometry-based quantitative and chemical proteomics tools.

Recent Publications

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:

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:

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 1504–1514Ranked 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).