> 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, * -Corresponding Author

>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. * -Corresponding Author

> 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. * -Corresponding Author

> Chowdhury, Saiful M; Zhu, Xuewei; Aloor, Jim J; Azzam, Kathleen M; Gabor, Kristin A; Ge, William; Addo, Kezia A; Tomer, Kenneth B; Parks, John S; Fessler, Michael 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. M114. 045179 -2015

> Bhawal, Ruchika P; Sadananda, Sandhya C; Bugarin, Alejandro; Laposa, Brian; Chowdhury, Saiful M; Mass spectrometry cleavable strategy for identification and differentiation of prenylated peptides - Analytical Chemistry - 2015 - *Corresponing author

> Bian, S; Chowdhury, SM*; Profiling Protein-Protein Interactions and Protein Structures Using Chemical Cross-linking and Mass Spectrometry - Austin J Biomed Eng, 1(4) - 1017 - 2014-*Corresponing author

> Chowdhury, Saiful M; Munske, Gerhard R; Yang, Jonathon; Zhukova, Daria; Nguyen, Hamilton; Bruce, James E; 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) P 635-644 - 2014. -*Corresponing author

> 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.

> Du, X; Rorie, J; Chowdhury, S; Adkins, J; Anderson, G; Smith, R; Identification of Protein-Protein Interactions Using Chemical Cross-linking and CID and ETD Tandem Mass Spectrometry - MOLECULAR & CELLULAR PROTEOMICS - S33-S33 - 2009

> Chowdhury, Saiful M; Du, Xiuxia; Tolic, Nikola; Wu, Si; Moore, Ronald J; Mayer, M Uljana; Smith, Richard D; Adkins, Joshua N; 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 - 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.

> Hossain, M. A.; Mustafa, A. I.; Amin, M. N.; Chowdhury, S. M.- Studies on the quality of three selected varieties of rapeseed and mustard oils and oil cakes, Dhaka University Journal of Science (1997), 45(1), 23-29. Publisher: Dhaka University, CODEN: DJOSEM ISSN: 1022-2502.