Jun Qu, Ph.D

Jun Qu is a Professor in Department of Pharmaceutical Sciences, SUNY-Buffalo, and the Chief Scientist in Bioanalysis, New York Center of Excellence in Bioinformatics and Life Sciences (NYS-COE)

318 Kapoor Hall,
Buffalo, NY 14214-8033
Phone: 716-645-4821

B3-302, 701 Ellicott Street,
Buffalo, NY14203
Phone: 716-881-7513

UB Faculty Page


Dr. Jun Qu's primary appointment is in the Department of Pharmaceutical Sciences at SUNY Buffalo. He recieved his Ph.D in Analytical Chemistry at Tsinghua University, Beijing, China, in 2002. His interests are in Proteomics and Pharmaceutical Analysis, and his research programs in the proteomics field involve: i) High-resolution and large-scale expression profiling of pathological proteomes (e.g. for cardiovascular diseases, colon cancer and infectious diseases, HIV, COPD, etc) for the discovery of disease/therapeutic biomarkers by gel-free LC/MS methods; ii) Sensitive identification, localization and quantification of post-translational modifications in complex proteomes, with the emphases on arginine methylation and phosphorylation. Novel anti-PTM-peptides capture procedure and alternating collision induced dissociation (CID)/electron transferring dissociation (ETD) are employed to obtain abundant PTM information; iii) Targeted quantification of regulatory, marker proteins for clinical study. Dr. Qu's lab possesses many state-of-the-art LC/MS instruments, including a high resolution/accuracy Orbitrap Fusion Lumos, two highly sensitive TSQ triple quadrupole instruments (one Altis, one Quantiva), three ultra-high pressure nano-LC systems, and several HPLC instruments for pre-fraction and ion chromatography. A number of key analytical advances have been developed by his lab that greatly enhanced the proteomic coverage, sensitivity and throughput for proteomic research. As for the Pharmaceutical Analysis of small-molecule drug/markers, Dr. Qu's lab is focusing on the ultra-sensitive quantifications of drug, metabolites and endogenous markers (e.g. corticosteroids, di-hydroxyl-vitamin D metabolites, androgens, etc.) using a novel combination of selective enrichment and micro- or nano-LC/MS.

Selected Publications

For full publication list, click here.

1. An B, Zhang M, Pu J, Shen S, Qu Y, Chen YJ, Huo S, Wang X, Polli JR, Balthasar JP, Herzog D, Ferrari L, Staack RF, Richter WF, Otteneder MB, Benincosa LJ, Zhou S, Vazvaei F, Qu J*. High-throughput, sensitive LC-MS quantification of biotherapeutics and biomarkers using an antibody-free, peptide-level multiple-mechanism enrichment via strategically regulated pH, ionic and solvent strengths. Anal. Chem. 91:3475-3483. (2019)

2. Jones RS, Tu C, Zhang M, Qu J, Morris ME. Characterization and Proteomic-Transcriptomic Investigation of Monocarboxylate Transporter 6 Knockout Mice: Evidence of a Potential Role in Glucose and Lipid Metabolism. Mol. Pharmacol. 96:364-376. (2019)

3. Shen X, Shen S, Li J, Hu Q, Nie L, Tu C, Wang X, Poulsen DJ, Orsburn BC*, Wang J*, Qu J*. IonStar enables high-precision, low-missing-data proteomics quantification in large biological cohorts. Proc Natl Acad Sci USA. In Press. (2018)

4. Qu J*. The future of LC-MS for pharmaceutical analysis: an interview with Jun Qu. Bioanalysis.10(6):375-376. (2018)

5. Wang X, Niu J, Li J, Shen X, Shen S, Straubinger RM, Qu J*. Temporal Effects of Combined Birinapant and Paclitaxel on Pancreatic Cancer Cells Investigated via Large-Scale, Ion-Current-Based Quantitative Proteomics (IonStar). Mol Cell Proteomics. 17(4):655-671. (2018)

6. Zhang M, An B, Qu Y, Shen S, Fu W, Chen YJ, Wang X, Young R, Canty JM Jr., Balthasar JR, Murphy K, Bhattacharyya D, Josephs J, Ferrari L, Zhou S, Bansal S, Vazvaei F*, Qu J*. Sensitive, High-Throughput, and Robust Trapping-Micro-LC-MS Strategy for the Quantification of Biomarkers and Antibody Biotherapeutics. Anal Chem. 90(3):1870-1880. (2018)

7. Fu W, An B, Wang X, Qu J*. Key considerations for LC-MS analysis of protein biotherapeutics in tissues. Bioanalysis. 9(18):1349-1352. (2017)

8. Shen X, Shen S, Li J, Hu Q, Nie L, Tu C, Wang X, Orsburn B, Wang J, Qu J*. An IonStar experimental strategy for MS1 ion current-based quantification using ultra-high-field Orbitrap: reproducible, in-depth and accurate protein measurement in larger cohorts. J Proteome Res. 16(7):2445-2456. (2017)

9. Tu C, Mojica W, Straubinger RM, Li J, Shen S, Qu M, Nie L, Roberts R, An B, Qu J*. Quantitative proteomic profiling of paired cancerous and normal colon epithelial cells isolated freshly from colorectal cancer patients. Proteomics Clin Appl. 11(5-6). (2017)

10. Tu C, Shen S, Sheng Q, Shyr Y, Qu J*. A peptide-retrieval strategy enables significant improvement of quantitative performance without compromising confidence of identification. J Proteomics. 152:276-282. (2016)

11. Tu C, Bu Y, Vujcic M, Shen S, Li J, Qu M, Hangauer D, Clements JL*, Qu J*. Ion Current-based Proteomics Profiling in Understanding the Inhibitory Effect of Tumor Necrosis Factor Alpha on Myogenic Differentiation. J Proteome Res. 15(9):3147-57. (2016)

12. Tu C, Li J, Shen S, Sheng Q, Shyr Y, Qu J*. Performance Investigation of Protoemic Identification by HCD/CID Fragmentations in Combination with High/Low-Resolution Detectors on a Tribrid, High-Field Orbitrap Instrument. PLoS One. 11(7):e0160160. (2016)

13. Qu M, An B, Shen S, Zhang M, Shen X, Duan X, Balthasar JP, Qu J*. Qualitative and quantitative characterization of protein therapeutics with liquid chromatography and mass spectrometry. Mass Spectrom Rev. [Epub ahead of print]. (2016)

14. Shen S, Jiang X, Li J, Straubinger RM, Suarez M, Tu C, Duan X, Thompson AC, Qu J*. Large-Scale, Ion-Current-Based Proteomic Investigation of the Rat Striatal Proteome in a Model of Short- and Long-Term Cocaine Withdrawal. J Proteome Res. 15(5):1702-16. (2016)

15. Shen S, Li J, Hilchey S, Shen X, Tu C, Qiu X, Ng A, Ghaemmaghami S, Wu H, Zand M, Qu J*. An Ion-Current-Based Temporal Proteomic Profiling of Influenza A Virus Infected Mouse Lungs Revealed Underlying Mechanisms of Altered Integrity of the Lung Microvascular Barrier. Proteome Res. In Press. (2016)

16. Shen X, Nair B, Mahajan SD, Jiang X, Li J, Shen S, Tu C, Hsiao CB, Schwartz SA, Qu J*. New insights into the disease progression control mechanisms by comparing Long-term-non-progressors vs. Normal-progressors among HIV-1 positive patients using an ion current-based MS1 proteomics profiling. J Proteome Res. In press (2015)

17. Tu C, Sheng Q, Li J, Ma D, Shen X, Wang X, Shyr Y, Yi Z, Qu J*. Optimization of Search Engines and Postprocessing Approaches to Maximize Peptide and Protein Identification for High-Resolution Mass Data. J Proteome Res. In press (2015)

18. Shen X, Hu Q, Li J, Wang J, Qu J*. Experimental Null Method to Guide the Development of Technical Procedures and to Control False-Positive Discovery in Quantitative Proteomics. J Proteome Res. 14(10):4147-57 (2015)

19. Tu C, Beharry KD, Shen X, Li J, Wang L, Aranda JV, Qu J*. Proteomic profiling of the retinas in a neonatal rat model of oxygen-induced retinopathy with a reproducible ion-current-based MS1 approach. J Proteome Res. 14(5):2109-20 (2015)

20. An B, Zhang M, Johnson RW, Qu J*. Surfactant-Aided Precipitation/On-Pellet-Digestion (SOD) Procedure Provides Robust and Rapid Sample Preparation for Reproducible, Accurate and Sensitive LC-MS Quantification of Therapeutic Protein in Plasma and Tissues. Anal Chem. 87(7):4023-9 (2015)

21. Nouri-Nigjeh E, Sukumaran S, Tu C, Li J, Shen X, Duan X, DuBois DC, Almon RR, Jusko WJ, Qu J*. Highly Multiplexed and Reproducible Ion Current-Based Strategy for Large-Scale Quantitative Proteomics and the Application to Protein Expression Dynamics Induced by Methylprednisolone in 60 Rats. Anal Chem. 86(16):8149-57 (2014)

22. Shen X, Young R, Canty JM, Qu J*. Quantitative proteomics in cardiovascular research: Global and targeted strategies. Proteomics Clin Appl. 8(7-8):488-505 (2014)

23. Qu J*, Young R, Page BJ, Shen X, Tata N, Li J, Duan X, Fallavollita JA, Canty JM Jr. Reproducible Ion-Current-Based Approach for 24-Plex Comparison of the Tissue Proteomes of Hibernating versus Normal Myocardium in Swine Models. J Proteome Res. 13(5):2571-84 (2014)

24. Tu C, Li J, Sheng Q, Zhang M,Qu J*. Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data. J Proteome Res. 13(4):2069-79. (2014).

25. Nouri-Nigjeh E, Zhang M, Ji T, Yu H, An B, Duan X, Balthasar J, Johnson RW, Qu J*. Effects of calibration approaches on the accuracy for LC-MS targeted quantification of therapeutic protein. Anal Chem. 86(7):3575-84. (2014).

26. Tu C, Mammen MJ, Li J, Shen X, Jiang X, Hu Q, Wang J, Sethi S, Qu J*. Large-scale, ion-current-based proteomics investigation of bronchoalveolar lavage fluid in chronic obstructive pulmonary disease patients. J Proteome Res. 13(2):627-39. (2014).

27. Tu C, Li J, Jiang X, Sheflin LG, Pfeffer BA, Behringer M, Fliesler SJ, Qu J*. Ion-current-based proteomic profiling of the retina in a rat model of Smith-Lemli-Opitz syndrome. Mol Cell Proteomics. 12(12):3583-98 (2013).

28. Lott K, Li J, Fisk JC, Wang H, Aletta JM, Qu J*, Read LK. Global proteomic analysis in trypanosomes reveals unique proteins and conserved cellular processes impacted by arginine methylation. J Proteomics. 91:210-25. (2013)

29. Fisk JC, Li J, Wang H, Aletta JM, Qu J*, and Read LK. Proteomic analysis reveals diverse classes of arginine methylproteins in mitochondria of trypanosomes. Mol. Cell. Proteomics. 12(2):302-11 (2013).

30. Tu CJ, Li J, Bu YH, Hangauer D,  Qu J* An ion-current-based, comprehensive and reproducible proteomic strategy for comparative characterization of the cellular responses to novel anti-cancer agents in a prostate cell model. J. Proteomics 77:187-201(2012).

31. Duan X, Dai L, Chen SC, Balthasar JP, Qu J*. Nano-scale lc/srm-ms and on-the-fly orthogonal array optimization for targeted quantification of therapeutic monoclonal antibodies: an application in sensitive and accurate preclinical analysis of a chimeric anti-cea antibody. J. Chromatogr. A, 1251:63-73 (2012).

32. Duan X, Abuqayyas LM, Dai L, Balthasar JP, Qu J*. High-throughput method development for sensitive, accurate and reproducible quantification of therapeutic monoclonal antibodies in tissues using orthogonal array optimization and nano-LC/SRM/MS. Anal Chem. 84:4373-82 (2012).

33. Tu CJ, Li J, Young RF, Page BJ, Engler F, Halfon MS, Canty JM, Qu J*. A Combinatorial Peptide Ligand Libraries Treatment Followed by a Dual-Enzyme, Dual-Activation Approach on a nano-flow LC/Orbitrap/ETD for Comprehensive Analysis of Swine Plasma Proteome. Anal Chem, 83:4802-13 (2011).

34. Duan X, Weinstock-Guttman B, Wang H, Bang E, Li J, Ramanathan M, Qu J* Ultra-sensitive Quantification of Serum Vitamin D Metabolites Using Selective Solid Phase Extraction Coupled to Micro-flow Liquid Chromatography and Isotope-Dilution Mass Spectrometry. Anal. Chem. 82: 2488–2497 (2010).

35. Cao J, Gonzalez-Covarrubias V, Straubinger RM, Wang H, Duan X, Yu H,  Qu J* A rapid, reproducible, on-the-fly orthogonal array optimization method for targeted protein quantification by LC/MS and its application for accurate and sensitive quantification of carbonyl reductases in human liver. Anal. Chem. 82: 2680-2689 (2010)

36. Duan X, Engler FA, Qu J*. Electron transfer dissociation coupled to an Orbitrap analyzer may promise a straightforward and accurate sequencing of disulfide-bridged cyclic peptides: a case study. J Mass Spectr. 45:1477-82 (2010)

37. Wang H; Straubinger RM; Aletta JM; Cao J; Duan X; Yu H; Qu J*. Accurate localization and relative quantification of arginine methylation using nanoflow liquid chromatography coupled to electron transfer dissociation and orbitrap mass spectrometry. J Am Soc Mass Spectrom 20: 507-19 (2009).

38. Duan X; Young R; Straubinger RM; Page, BJ; Cao J; Wang H; Yu H; Canty JM;  Qu J* A Straightforward and Highly Efficient Precipitation/On-pellet Digestion Procedure Coupled to a Long Gradient Nano-LC Separation and Orbitrap Mass Spectrometry for Label-free Expression Profiling of the Swine Heart Mitochondrial Proteome. J. Proteome Res. 6: 2838-2850 (2009).

39. Yu H; Straubinger RM; Cao J; Wang HS; Qu J*. Ultra-sensitive quantification of paclitaxel using selective solid-phase extraction in conjunction with reversed-phase capillary liquid chromatography/tandem mass spectrometry. J. Chromatog. A 1210: 160-7 (2008).

Update date: November, 2019