The University of Texas at Arlington

Saiful Chowdhury

Saiful  Chowdhury

Assistant Professor

Office: 352 CPB, Email:, Phone: 817 272 5439, FAX: 817 272 3808

Research ProfileCoursesPersonal Page

Protein-protein interactions and protein posttranslational modifications (PTMs) are the major events which regulate signaling cascades in the cells. In disease states, these interaction networks get altered, disrupting normal cellular processes. Understanding the overall network “interactome” or a particular receptor’s interaction network, in diseased and normal states, will provide insight into the physiological and pathological processes of those diseases at a molecular level. Mass spectrometer is a major instrument for identifying and quantifying proteins, but deciphering these large-scale interaction networks in vivo is a major challenge in functional proteomics research. Due to current remarkable advancements in mass spectrometry instrumentations, there is a great opportunity to develop mass spectrometry-based quantitative and chemical proteomics strategies that can give us precise information about signaling complexes in vivo or in vitro. The ‘proteomics and bio-analytical mass spectrometry’ group at UT Arlington focuses on the development of cutting-edge mass spectrometry-supportive novel quantitative and chemical proteomics methods and tools, as well as the application of these methods for proteome-wide identification of protein expressions, protein-protein interactions and PTMs.


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.

Selected Publications:

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 Jan 23. [Epub ahead of print]

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.

B.Sc Honors (First Class) & M.Sc (First Class)

Applied Chemistry and Chemical Technology

University of Dhaka, Dhaka, Bangladesh.


MS in Chemistry, 2001

Florida International University, Miami, FL

Advisor: Dr. Stanislaw F. Wnuk


PhD in Analytical Chemistry, 2006

Washington State University, Pullman, WA

Advisor: Dr. James E. Bruce, Department of Genome Sciences, University of Washington


Postdoctoral Research Associate (Aug. 2006- Dec. 2009)

Pacific Northwest National Laboratory, Richland, WA

Advisor: Dr. Richard D. Smith


Research Fellow (Dec. 2009 - July 2012)

National Institute of Environmental Health Sciences (NIEHS),

NIH Mentor/Co-Mentor: Michael B. Fessler, MD and Dr. Kenneth B. Tomer

Dr. Saiful M. Chowdhury will be joining 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.

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).

Department of Chemistry and Biochemistry

The University of Texas at Arlington · Arlington, Texas 76019-0065 USA

Phone: 817-272-3171 | Fax: 817-272-3808

© 2018 The University of Texas at Arlington

All rights reserved