• Bioassay-Driven, Fractionation-Empowered, Focused Metabolomics for Discovering Bacterial Activators of Aryl Hydrocarbon Receptor.” Huidi Tian, Lei Wang, Rachel Hardy, Lina Kozhaya, Lindsey Placek, Elizabeth Fleming, Julia Oh, Derya Unutmaz, Xudong Yao, Journal of the American Society for Mass Spectrometry, 2024, 10.1021/jasms.3c00386.
  • Tailoring Synthetic Polypeptide Design for Directed Fibril Superstructure Formation and Enhanced Hydrogel Properties.” Yang T, Xue T, Mao J, Chen Y, Tian H, Bartolome A, Xia H, Yao X, Kumar CV, Cheng J, Lin Y. J. Am. Chem. Soc. 2024, 146, 9, 5823–5833. doi: 10.1021/jacs.3c10762
  • Measurement and utilization of the proteomic reactivity by mass spectrometry.” Punzalan, C.; Wang, L.; Bajrami, B.; Yao, X. Mass Spectrometry Reviews, 2024, 43:166–192; DOI:10.1002/mas.21837.


  • Chemical Proteomics of Reactive Molecules.” Lei Wang, Xudong Yao, pp 158-189, “Advances in Chemical Proteomics, 1st Ed” (edited by Xudong Yao) in the Series of “Developments in Organic Chemistry” (Series Editor: Michael B. Smith), Elsevier, 2022


  • α‐Methylene‐β‐lactone scaffold for developing chemical probes at the two ends of the selectivity spectrum.”  Wang, L., L. P. Riel, B. Bajrami, B. Deng, A. R. Howell, X. Yao. ChemBioChem. 2021, 22, 505-515 (Cover Feature).
  • Network Topology of Biological Aging and Geroscience-Guided Approaches to COVID-19.”  Landay A, Bartley JM, Banerjee D, Hargis G, Haynes L, Keshavarzian A, Kuo C-L, Kwon OS, Li S, Li S, Oh J, Ozbolat IT, Ucar D, Xu M, Yao X, Unutmaz D and Kuchel GA. Front. Aging 2021, 2:695218. doi: 10.3389/fragi.2021.695218


  • Treasure Hunt for Peptides with Undefined Chemical Modifications: Proteomics Identification of Differential Albumin Adducts of 2‐Nitroimidazole‐Indocyanine Green in Hypoxic Tumor.” Wang, L.; Dietz, C.; Zhou, F.; Erfanzadeh, M.; Zhu, Q.; Smith, M.B.; Yao, X. J Mass Spectrom 2020, 55, e4376


  • Quantitative Proteomics in Development of Disease Protein Biomarkers.” Lei Wang, Adam J. McShane, Mary Joan Castillo, Xudong Yao, “Proteomic and Metabolomic Approaches to Biomarker Discovery, 2nd Ed” edited by Haleem J. Issaq, Timothy D. Veenstra, 2019.


  • Tuning of human MAIT cell activation by commensal bacteria species and MR1-dependent T-cell presentation.” Cihan Tastan, Ece Karhan, Wei Zhou, Elizabeth Fleming, Anita Y. Voigt, Xudong Yao, Lei Wang, Meghan Horne, Lindsey Placek, Lina Kozhaya, Julia Oh & Derya Unutmaz. Mucosal Immunology, 2018, 11(6), 1591-1605.
  • Directed Evolution of a Picomolar Affinity High Specificity Antibody Targeting Phosphorylated Tau.” D. Li, L. Wang, B.F. Maziuk, X. Yao, B. Wolozin, Y.K.Cho. J Biol Chem. 2018, pii: jbc.RA118.003557. doi: 10.1074/jbc.RA118.003557.
  • Determining Linear Free Energy Relationships in Peptide Fragmentation Using Derivatization and Targeted Mass Spectrometry.” Yuanyuan Shen, Reza Nemati, Lei Wang, and Xudong Yao, Anal. Chem. 2018, 90 (3), pp 1587-1594; DOI: 10.1021/acs.analchem.7b02191.


  • Deposition and Hydrolysis of Serine Dipeptide Lipids of Bacteroidetes Bacteria in Human Arteries: Relationship to Atherosclerosis.” Nemati R, Dietz C, Anstadt EJ, Cervantes J, Liu Y, Dewhirst FE, Clark RB, Finegold S, Gallagher JJ, Smith MB, Yao X, Nichols FC. J Lipid Res. 2017 Aug 16. pii: jlr.M077792. doi: 10.1194/jlr.M077792.
  • “Scaling Proteome-Wide Reactions of Activity-Based Probes.” Song Li, Pamela A. Diego-Limpin, Bekim Bajrami, Santosh Keshipeddy, Ying-Wai Lam, Bin Deng, Vahid Farrokhi, Adam J. McShane, Reza Nemati, Amy R. Howell, and Xudong Yao. Anal. Chem. 2017, 89 (12), pp 6295–6299; DOI: 10.1021/acs.analchem.7b01184.
  • “Simultaneous determination of absolute configuration and quantity of lipopeptides using chiral liquid chromatography-mass spectrometry and diastereomeric internal standards.” Nemati R, Dietz C, Anstadt E, Clark R, Smith MB, Nichols F, Yao X. Anal. Chem. 2017, 89 (6), pp 3583–3589; DOI: 10.1021/acs.analchem.6b04901.


  • “Structural verification via convergent total synthesis of dipeptide–lipids isolated from Porphyromonas gingivalis.” Christopher Dietza, Theresa K. Harta, Reza Nematia, Xudong Yao, Frank C. Nichols, Michael B. Smith, Tetrahedron, 2016, 72(47), 24 7557–7569.


  • Nonisotopic reagents for a cost-effective increase of sample throughput in targeted quantitative proteomics.” Mary Joan Castillo, Adam J. McShane, Min Cai, Yuanyuan Shen, Lei Wang, Xudong Yao. Anal Chem 2015, 87 (18), pp 9209–9216; doi: 10.1021/acs.analchem.5b01727.
  • Development of Structural Marker Peptides for Cystic Fibrosis Transmembrane Conductance Regulator in Cell Plasma Membrane by Reversed-Footprinting Mass Spectrometry.” Vahid Farrokhi, Bekim Bajrami, Reza Nemati, Adam J. McShane, Franz Rueckert, Barrett Wells, Xudong Yao. Anal. Chem. 2015, 87 (17), 8603–8607; doi: 10.1021/acs.analchem.5b01962.
  • Serine dipeptide lipids of Porphyromonas gingivalis inhibit osteoblast differentiation: Relationship to Toll-like receptor 2.” Wang YH, Nemati R, Anstadt E, Liu Y, Son Y, Zhu Q, Yao X, Clark RB, Rowe DW, Nichols FC. Bone. 2015 81, 654-661.
  • An Injectable PEG-BSA-Coumarin-GOx Hydrogel for Fluorescence Turn-on Glucose Detection.” Srinivasan G1, Chen J, Parisi J, Brückner C, Yao X, Lei Y. Appl. Biochem. Biotechnol. 2015,
  • A Stable Human-Cell System Overexpressing Cystic Fibrosis Transmembrane Conductance Regulator Recombinant Protein at the Cell Surface.” Hildebrandt E, Ding H, Mulky A, Dai Q, Aleksandrov AA, Bajrami B, Diego PA, Wu X, Ray M, Naren AP, Riordan JR, Yao X, DeLucas LJ, Urbatsch IL, Kappes JC. Mol. Biotechnol. 2015, 57 (5), 391-405. doi: 10.1007/s12033-014-9830-5.


  • Targeted Proteomic Quantitation of Absolute Expression and Turnover of Cystic Fibrosis Transmembrane Conductance Regulator in Apical Plasma Membrane,” Adam J. McShane; Bekim Bajrami, Alexis Ramos, Pamela Diego-Limpin, Vahid Farrokhi, Bonita Coutermarsh, Bruce Stanton, Timothy Jensen, John R. Riordan, Diana Wetmore, Elizabeth Joseloff, Xudong Yao; Journal of Proteome Research, Special Issue–Proteomics of Human Diseases: Pathogenesis, Diagnosis, Prognosis and Treatment.  2014 Nov 7;13(11):4676-85.
  • Peptide Dimethylation: Fragmentation Control via Distancing the Dimethylamino Group,” Adam J. McShane, Yuanyuan Shen, Mary Joan Castillo, Xudong Yao; Journal of The American Society for Mass Spectrometry, 2014 Oct;25(10):1694-704.
  • “Quantitative Protein Analysis Using Enzymatic [18O]Water Labeling,” Mary Joan Castillo, Kristy J. Reynolds, Alexander Gomes, Catherine Fenselau, and Xudong Yao, Curr Protoc Protein Sci. 2014 Apr 1;76:23.4.1-9.
  • An Overview of Quantitative Proteomic Approaches,” Adam J. McShane, Vahid Farrokhi, Reza Nemati, Song Li, Xudong Yao; “Fundamentals of Advanced Omics Technologies: From Genes to Metabolites,” Comprehensive Analytical Chemistry (Volume 63), edited by Carolina Simó, Alejandro Cifuentes, Virginia García-Cañas, 2014, 111-135.


  • Stable Isotope Dilution Mass Spectrometry for Membrane Transporter Quantitation,” Vahid Farrokhi, Adam J. McShane, Reza Nemati, Xudong Yao; The AAPS Journal, 2013, 15(4), 1222-1231.
  • “Bacterial lipodipeptide, Lipid 654, is a microbiome-associated biomarker for multiple sclerosis,” Vahid Farrokhi, Reza Nemati, Frank C Nichols, Xudong Yao, Emily Anstadt, Mai Fujiwara, James Grady, Daniel Wakefield, Wanda Castro, James Donaldson, Robert B Clark; Clinical & Translational Immunology, 2013, 2, e8; doi:10.1038/cti.2013.11.
  • Serine Lipids of Porphyromonas gingivalis are Human and Mouse Toll-like Receptor 2 Ligands,” Robert B. Clark, Jorge L. Cervantes, Mark W. Maciejewski, Vahid Farrokhi, Reza Nemati, Xudong Yao, Emily Anstadt, Mai Fujiwara, Kyle T. Wright, Caroline Riddle, Carson J. La Vake, Juan C. Salazar, Sydney Finegold, Frank C. Nichols; Infection and Immunity, 2013, 81(9), 3479-3489.
  • Quantitative Proteomics in Development of Disease Protein Biomarkers,” Xudong Yao, Adam J. McShane, Mary Joan Castillo; “Proteomic and Metabolomic Approaches to Biomarker Discovery,” edited by Haleem J. Issaq, Timothy D. Veenstra, 2013, 259-278.


  • Back to Deuterium: Utility of 2H-Labeled Peptides for Targeted Quantitative Proteomics,” Bekim Bajrami, Vahid Farrokhi, Mengtan Zhang, Ardit Shehu, Xudong Yao; International Journal of Mass Spectrometry, 2012, 312, 17-23.
  • Free lipid A Isolated from Porphyromonas Gingivalis Lipopolysaccharide is Contaminated with Phosphorylated Dihydroceramide Lipids: Recovery in Diseased Dental Samples,” Frank C. Nichols, Bekim Bajrami, Robert B. Clark, William Housley, Xudong Yao;  Infection and Immunity, 2012, 80(2), 860-874.


  •  “Derivatization or Not: A Choice in Quantitative Proteomics,” Xudong Yao; Analytical Chemistry, 2011, 83(12), 4427-4439.
  • Phosphorylated Dihydroceramides from Common Human Bacteria are Recovered in Human Tissues,” Nichols FC, Yao X, Bajrami B, Downes J, Finegold SM, Knee E, Gallagher JJ, Housley WJ, Clark RB; PLoS One. 2011, 6(2), e16771.


  • Ultrathroughput Multiple Reaction Monitoring Mass Spectrometry,” Xudong Yao, Bekim Bajrami, Yu Shi; Analytical Chemistry, 2010, 82, 974-979.
  • Site-Preferential Dissociation of Peptides with Active Chemical Modification for Improving Fragment Ion Detection,” Pamela A. C. Diego, Bekim Bajrami, Hui Jiang, Yu Shi, Jose Gascon, Xudong Yao; Analytical Chemistry, 2010, 82, 23-27.
  • Targeted Quantitation of Overexpressed and Endogenous Cystic Fibrosis Transmembrane Conductance Regulator Using Multiple Reaction Monitoring Tandem Mass Spectrometry and Oxygen Stable Isotope Dilution,” Hui Jiang, Alexis A. Ramos, Xudong Yao; Analytical Chemistry, 2010, 82, 336-342.
  • FerriNaphth: a Fluorescence Chemodosimeter for Redox Active Metal Ion,” Randy K. Jackson, Yu Shi, Xudong Yao, Shawn C. Burdette, Dalton Trans., 2010, 39, 4155-4161.
  • Analysis of Monomeric and Dimeric Phosphorylated Forms of Protein Kinase R,” Eric Anderson, Christine Quartararo, Raymond S. Brown, Yu Shi, Xudong Yao, James L. Cole, Biochemistry, 2010, 49, 1217-1225.
  • Design and Synthesis of an Activity-Based Probe Template for Protein Kinase,” Santosh, Keshipeddy, Yu Shi, Xudong Yao, Amy R. Howell; Synlett, 2010, 521-524.


  • Shifting Unoccupied Spectral Space in Mass Spectrum of Peptide Fragment Ions,” Bekim Bajrami, Yu Shi, Pascal Lapierre, Xudong Yao; Journal of American Society for Mass Spectrometry, 2009, 20, 2124-2134.
  • Passive and Active Fragment Ion Mass Defect Labeling: Distinct Proteomics Potential of Iodine-Based Reagents,” Yu Shi, Bekim Bajrami, Xudong Yao; Analytical Chemistry, 2009, 81, 6438-6448.
  •  “18O2-Labeling in Quantitative Proteomic Strategies: a Status Report,” Catherine Fenselau, Xudong Yao; Journal of Proteome Research, 2009, 8, 2140-2143.


  • Averagine-Scaling Analysis of Fragment Ions with Increased Mass Defect in Peptide Mass Spectrometry,” Xudong Yao, Pamela A. C. Diego, Alexis A. Ramos, Yu Shi; Analytical Chemistry, 2008, 80, 7383-7391.
  • Cyclophosphoramidate Ion as Mass Defect Marker for Efficient Detection of Protein Serine Phosphorylation,” Yu Shi, Bekim Bajrami, Martha Morton, Xudong Yao; Analytical Chemistry, 2008, 80, 7614-7623.


  • Oxygen Isotopic Substitution of Peptidyl Phosphates for Modification-Specific Mass Spectrometry,” Yu Shi, Xudong Yao; Analytical Chemistry, 2007, 79, 8454-8462.
  • Proteolytic Labeling with 18O for Comparative Proteomics Studies: Preparation of 18O-Labeled Peptides and 18O/16O Peptide Mixture,” Catherine Fenselau, Xudong Yao; Methods in Molecular Biology, 2007, 359, 135-142 (Edited by Salvatore Sechi).


  • Tandem Parallel Fragmentation of Peptides for Mass Spectrometry,” Alexis Ramos, Hua Yang, Lauren Rosen, Xudong Yao; Analytical Chemistry, 2006, 78, 6391-6397.


(Before joining the University of Connecticut, 2004)


  • Trypsin Catalyzed 16O-to-18O Exchange for Comparative Proteomics: Comparison on Tandem Mass Spectrometry using MALDI-TOF, ESI-QqTOF and ESI-Ion Trap Mass Spectrometers,” M. Heller, H. Mattou, C. Menzel, X. Yao; Journal of American Society for Mass Spectrometry, 2003, 14, 704-718.
  • Dissection of Proteolytic 18O Labeling: Endoprotease-Catalyzed 16O-to-18O Echange of Truncated Peptide Substrates,” X. Yao, C. Afonso, C. Fenselau; Journal of Proteome Research, 2003, 2, 147-152.
  • Fractionation of Cytosolic Proteins on an Immobilized Heparin Column,” K. Shefcheck, X. Yao, C. Fenselau; Analytical Chemistry, 2003, 75, 1691-1698.


  • Proteolytic 18O Labeling for Comparative Proteomics: Evaluation of Endoprotease Glu-C as the Catalytic Agent,” K. J. Reynolds, X. Yao, C. Fenselau; Journal of Proteome Research, 2002, 1, 27-33.


  • Proteolytic 18O Labeling for Comparative Proteomics: Model Studies with Two Serotypes of Adenovirus,” X. Yao, A. Freas, J. Ramirez, P.A. Demirev, C Fenselau; Analytical Chemistry, 2001, 73, 2836-6225.


  • Transition State Imbalance in Proton Transfer from Phenyl Ring Substituted 2-Tetralones to Acetate Ion,” X. Yao, M.A. Gold, R. M. Pollack; Journal of the American Chemical Society, 1999, 121, 6220-6225.
  • Electronic Effects on Enol Acidity and Keto-Enol Equilibrium Constants for Ring-Substituted 2-Tetralones,” X. Yao, R. M. Pollack; Canadian Journal of Chemistry, 1999, 77, 634-638.


  • Transition State Imbalance in the Deprotonation of Substituted 2-Tetralone by Hydroxide Ion,” John Nevy, David Hawkinso, G. Blotny, Xudong Yao, Ralph M. Pollack, Journal of the American Chemical Society, 1997, 119, 12722-12726.
  • Synthesis of α,ω-bis(γ-aminopropyl)polydimethyldiphenylsiloxane,” Anfeng Wang, Caihua Zhou, Lu Wang, Bo Che, Xudong Yao, Sicong Lin; Gaofenzi Xuebao, 1997, (3), 271-276.


  • Study of Powder Adhesive used for Nonwoven Fabrics,” Xudong Yao, Caiyuan Chu, Haojing Yan; Zhongguo Fangzhi Daxue Xuebao, 1995, 21(2), 70-4.


  • Synthetic Studies on Blood-Compatible Biomaterials. III. Synthesis, Characterization and Antithrombogenicity of Dimethyl Diphenyl Polysiloxane/Poly(tetramethylene oxide)-Polyurea Segmented Copolymers,” Sicong Lin, Xudong Yao, Xiangton Tu, Yong Zhu, Charles L. Liotta; Chinese Journal of Polymer Science, 1992, 10(2), 127-36.