Dr. Jun Qin is among the few people in the world, who can integrate MS instrument design, proteomic method development, bioinformatics, biology and clinical applications into one research program. His research interests evolve around the following questions:
How to measure a real world proteome accurately with high speed and accuracy?
We are developing methods to accurately identify and roughly quantify 8000 proteins in a few hours (from 3 to 8 hours), and quantify accurately 200 proteins of your interests (not just the most abundant proteins) in 30 mins to an hour.
- How to measure endogenous constitutive and induced protein-protein interactions including membrane proteins that are regulated by signal transduction?
How to translate the power of proteomics into healthcare and disease monitoring?
We are developing proteomics assays for noninvasive early diagnosis of diseases and for health monitoring; we are also developing workflows and big data analysis platform for personalized medicine from biopsy samples (for example, needle or endoscope biopsies). We want to offer personalized treatment based on our proteomics and big data analysis.
How to help scientists and doctors to use proteomics for their research and clinical care?
We are producing large datasets of essential and important biological and medical processes and share with the world. We are developing bioinformatics analysis platform and workflows that can provide one-stop services to mass spectrometrist, biologists and medical doctors.
- What are the proteomics landscapes of gastric cancers? What are the deregulated signaling pathways and proteins that have activities (for example, kinase activity or DNA binding activity) lead to the cancer states? How to target them for treatments?
1) Mu JJ, Wang Y, Luo H, Leng M, Zhang J, Yang T, Bessuso D, Jung SY, Qin J. (2007) A proteomic analysis of ATM/ATR substrates identifies the ubiquitin-proteosome system as a regulator for DNA damage checkpoints. J Biol. Chem. 282(24):17330-4.
2) Jung SY, Li Y, Wang Y, Chen Y, Zhao Y, Qin J. (2008) Complications in the assignment of 14 and 28 Da mass shift Detected by mass spectrometry as in vivo methylation from endogenous proteins. Anal. Chem, 80(5):1721-9.
3) Luo H, Li Y, Mu JJ, Zhang J, Tonaka T, Hamamori Y, Jung SY, Wang Y, Qin J. (2008) Regulation of intra-S phase checkpoint by IR-dependent and IR-independent phosphorylation of SMC3. J Biol Chem. 283(28):19176-83. (selected as paper of the week)
4) Liang J, Wan M, Zhang Y, Gu P, Xin H, Jung SY, Qin J, Wong J, Cooney AJ, Liu D, Songyang Z. (2008) Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells. Nat Cell Biol. 10(6):731-9.
5) Chahrour M, Jung SY, Shaw C, Zhou X, Wong ST, Qin J, Zoghbi HY. (2008) MeCP2, a key contributor to neurological disease, activates and represses transcription. Science. 320(5880):1224-9.
6) Zhang J, Shi X, Li Y, Kim BJ, Jia J. Huang Z, Yang T, Fu X, Jung SY, Wang Y. Zhang P, Kim ST, Pan X, and Qin J. (2008) Acetylation of Smc3 by Eco1 is required for S-phase sister chromatid cohesion in both human and yeast. Mol. Cell, 11;31(1):143-51.
7) Kim H, Lee OH, Xin H, Chen LY, Qin J, Chae HK, Lin SY, Safari A, Liu D, Songyang Z. TRF2 functions as a protein hub and regulates telomere maintenance by recognizing specific peptide motifs. Nat Struct Mol Biol. 2009 Apr;16(4):372-9. Epub 2009 Mar 15. PubMed PMID: 19287395.
8) Xu J, Liao L, Qin J, Xu J, Liu D, Songyang Z. Identification of Flightless-I as a substrate of the cytokine-independent survival kinase CISK. J Biol Chem. 2009 May 22;284(21):14377-85. Epub 2009 Mar 17. PubMed PMID: 19293151; PubMed Central PMCID: PMC2682886.
9) McKenna NJ, Cooney AJ, DeMayo FJ, Downes M, Glass CK, Lanz RB, Lazar MA, Mangelsdorf DJ, Moore DD, Qin J, Steffen DL, Tsai MJ, Tsai SY, Yu R, Margolis RN, Evans RM, O'Malley BW. Minireview: Evolution of NURSA, the Nuclear Receptor Signaling Atlas. Mol Endocrinol. 2009 Jun;23(6):740-6. Central PMCID: PMC2691684.
10) Stanisi? V, Malovannaya A, Qin J, Lonard DM, O'Malley BW. OUT Domain-containing ubiquitin aldehyde-binding protein 1 (OTUB1) deubiquitinates estrogen receptor (ER) alpha and affects ERalpha transcriptional activity. J Biol Chem. 2009 Jun 12;284(24):16135-45. Epub 2009 Apr 21. PubMed PMID: 19383985; PubMed Central PMCID: PMC2713518.
11) Wan M, Qin J, Songyang Z, Liu D. OB fold-containing protein 1 (OBFC1), a human homolog of yeast Stn1, associates with TPP1 and is implicated in telomere length regulation. J Biol Chem. 2009 Sep 25;284(39):26725-31. Epub 2009 Aug 1. PubMed PMID: 19648609; PubMed Central PMCID: PMC2785360.
12) Terret ME, Sherwood R, Rahman S, Qin J, Jallepalli PV. Cohesin acetylation speeds the replication fork. Nature. 2009 Nov 12;462(7270):231-4. PubMed PMID:19907496; PubMed Central PMCID: PMC2777716.
13) Feng Q, He B, Jung SY, Song Y, Qin J, Tsai SY, Tsai MJ, O'Malley BW. Biochemical control of CARM1 enzymatic activity by phosphorylation. J Biol Chem. 2009 Dec 25;284(52):36167-74. Epub 2009 Oct 20. PubMed PMID: 19843527; PubMed Central PMCID: PMC2794732.
14) Malovannaya A, Li Y, Bulynko Y, Jung SY, Wang Y, Lanz RB, O'Malley BW, Qin J*, Streamlined analysis schema for high-throughput identification of endogenous protein complexes, Proc Natl Acad Sci U S A; 2010, 107(6):2431-6.
15) Kim BJ, Li Y, Zhang J, Xi Y, Li Y, Yang T, Jung SY, Pan X, Chen R, Li W, Wang Y, Qin J*, Genome-wide reinforcement of cohesin binding at pre-existing cohesin sites in response to ionizing radiation in human cells, J Biol Chem.; 2010, 285(30):22784-92.
16) Malovannaya A, Lanz RB, Jung SY, Bulynko Y, Le NT, Chan DW, Ding C, Shi Y, Yucer N, Krenciute G, Kim BJ, Li C, Chen R, Li W, Wang Y, O'Malley BW, Qin J*, Analysis of the human endogenous coregulator complexome, Cell; 2011, 145(5):787-99.
17) Shi Y1, Xu P, Qin J*, Ubiquitinated proteome: ready for global? Mol Cell Proteomics. 2011 May;10(5):R110.006882.
18) Ding C, Chan DW., Liu W, Liu M, Li D, Song L, Li C, Jin J, Malovannaya A, Jung SY, Zhen B, Wang Y, Qin J*, Proteome-wide profiling of activated transcription factors with a concatenated tandem array of transcription factor response elements, Proc Natl Acad Sci U S A, 2013, 110:17, 6771-6776.
19) Liu Q, Ding C, Liu W, Song L, Liu M, Qi L, Fu T, Malovannaya A, Wang Y, Qin J*, Zhen B*, In-depth Proteomic Characterization of Endogenous Nuclear Receptors in Mouse Liver, Mol Cell Proteomics, 2013, 12:2, 473-484.
20) Ding C, Jiang J, Wei J, Liu W, Zhang W, Liu M, Fu F, Lu T, Song L, Ying W, Chang C, Zhang Y, Ma J, Wei L, Malovannaya A, Jia L, Zhen B, Wang Y, He F, Qian X, Qin J*, A Fast Workflow for Identification and Quantification of Proteomes, Mol Cell Proteomics. 2013, 12(8):2370-80.