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    Steven Hall, PhD

    TitleProfessor
    SchoolUCSF School of Medicine
    DepartmentObGyn, Reproductive Sciences
    Address35 Medical Center way
    San Fancisco CA 94143
    Phone415-502-8423

       Overview 
       Overview
      My research utilizes mass spectrometry as a tool to help solve biological problems at the molecular level. I am involved in many projects that center on identify proteins by generating amino acid sequence information from peptides using tandem mass spectrometry with collision induced dissociation. A large part of my research has focused on developing sample preparation techniques for making biological samples compatible with mass spectrometric analyses. Specifically, I have made significant contributions to developing a protocol that is used worldwide for the mass spectrometric identification of proteins isolated by 1D and 2D gel electrophoresis. In addition, I have made extensive contributions to research projects that utilize HPLC separation of complex biological mixtures. These projects involved interfacing high performance liquid chromatography instruments, on and off-line, to different types of mass spectrometers. Currently, my research continues along these lines but with a more focused emphasis on mass spectrometric applications to proteomics. Recent advances have been made in this field, namely mass spectrometric protocols for identification and relative and absolute quantitation of differentially expressed proteins using isobaric mass tags (iTRAQ) reagents or multiple reaction monitoring, respectively. While these methods have greatly expanded the potential for mining proteomes, their high cost prohibits their use in all but the most generously funded research laboratories. As a provider of mass spectrometry tools to the UCSF proteomics community, my current research centers on implementing and making these types of new technologies available through the Sandler-Moore Mass Spectrometry Core Facility.

      In addition, I play a significant role in the National Cancer Institute's Clinical Proteomic Technology Assessment for Cancer (CPTAC) program. The principle goal of the CPTAC program is technology assessment (primarily mass spectrometry) for early detection of cancer. I currently lead the Experimental Design and Statistics Verification Studies Work Group for the CPTAC program that is composed of approximately thirty bioanalytical scientists and statisticians from UCSF, the Buck Institute for Age Research, the Broad Institute (Harvard/MIT), Purdue University, Vanderbilt University, Memorial Sloan Kettering Cancer Center, University of Washington at Seattle, New York University and the Fred Hutchinson Cancer Research Center. My responsibilities include leading this team towards defining performance characteristics of mass spectrometry-based proteomic measurement systems that includes incorporation of appropriate measurement assessment materials and reference standards, employing statistically designed approaches for the purpose of experimentally determining performance metrics using biologically and clinically relevant samples, and proposing plus evaluating experimental design strategies that employ statistical protocols to effectively analyze the results within and between the participating CPTAC sites.


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       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Abbatiello SE, Mani DR, Schilling B, Maclean B, Zimmerman LJ, Feng X, Cusack MP, Sedransk N, Hall SC, Addona T, Allen S, Dodder NG, Ghosh M, Held JM, Hedrick V, Inerowicz HD, Jackson A, Keshishian H, Kim JW, Lyssand JS, Riley CP, Rudnick P, Sadowski P, Shaddox K, Smith D, Tomazela D, Wahlander A, Waldemarson S, Whitwell CA, You J, Zhang S, Kinsinger CR, Mesri M, Rodriguez H, Borchers CH, Buck C, Fisher SJ, Gibson BW, Liebler D, Maccoss M, Neubert TA, Paulovich A, Regnier F, Skates SJ, Tempst P, Wang M, Carr SA. Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS). Mol Cell Proteomics. 2013 Sep; 12(9):2623-39.
        View in: PubMed
      2. Walian PJ, Allen S, Shatsky M, Zeng L, Szakal ED, Liu H, Hall SC, Fisher SJ, Lam BR, Singer ME, Geller JT, Brenner SE, Chandonia JM, Hazen TC, Witkowska HE, Biggin MD, Jap BK. High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris. J Proteome Res. 2012 Dec 7; 11(12):5720-35.
        View in: PubMed
      3. Drake PM, Schilling B, Niles RK, Prakobphol A, Li B, Jung K, Cho W, Braten M, Inerowicz HD, Williams K, Albertolle M, Held JM, Iacovides D, Sorensen DJ, Griffith OL, Johansen E, Zawadzka AM, Cusack MP, Allen S, Gormley M, Hall SC, Witkowska HE, Gray JW, Regnier F, Gibson BW, Fisher SJ. Lectin chromatography/mass spectrometry discovery workflow identifies putative biomarkers of aggressive breast cancers. J Proteome Res. 2012 Apr 6; 11(4):2508-20.
        View in: PubMed
      4. Witkowska HE, Hall SC, Fisher SJ. Breaking the bottleneck in the protein biomarker pipeline. Clin Chem. 2012 Feb; 58(2):321-3.
        View in: PubMed
      5. Liu H, Yang L, Khainovski N, Dong M, Hall SC, Fisher SJ, Biggin MD, Jin J, Witkowska HE. Automated iterative MS/MS acquisition: a tool for improving efficiency of protein identification using a LC-MALDI MS workflow. Anal Chem. 2011 Aug 15; 83(16):6286-93.
        View in: PubMed
      6. Drake PM, Schilling B, Niles RK, Braten M, Johansen E, Liu H, Lerch M, Sorensen DJ, Li B, Allen S, Hall SC, Witkowska HE, Regnier FE, Gibson BW, Fisher SJ. A lectin affinity workflow targeting glycosite-specific, cancer-related carbohydrate structures in trypsin-digested human plasma. Anal Biochem. 2011 Jan 1; 408(1):71-85.
        View in: PubMed
      7. Johansen E, Schilling B, Lerch M, Niles RK, Liu H, Li B, Allen S, Hall SC, Witkowska HE, Regnier FE, Gibson BW, Fisher SJ, Drake PM. A lectin HPLC method to enrich selectively-glycosylated peptides from complex biological samples. J Vis Exp. 2009; (32).
        View in: PubMed
      8. Vazquez J, Hall SC, Greco MA. Protein expression is altered during spontaneous sleep in aged Sprague Dawley rats. Brain Res. 2009 Nov 17; 1298:37-45.
        View in: PubMed
      9. Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJ, Keshishian H, Hall SC, Allen S, Blackman RK, Borchers CH, Buck C, Cardasis HL, Cusack MP, Dodder NG, Gibson BW, Held JM, Hiltke T, Jackson A, Johansen EB, Kinsinger CR, Li J, Mesri M, Neubert TA, Niles RK, Pulsipher TC, Ransohoff D, Rodriguez H, Rudnick PA, Smith D, Tabb DL, Tegeler TJ, Variyath AM, Vega-Montoto LJ, Wahlander A, Waldemarson S, Wang M, Whiteaker JR, Zhao L, Anderson NL, Fisher SJ, Liebler DC, Paulovich AG, Regnier FE, Tempst P, Carr SA. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol. 2009 Jul; 27(7):633-41.
        View in: PubMed
      10. Niles R, Witkowska HE, Allen S, Hall SC, Fisher SJ, Hardt M. Acid-catalyzed oxygen-18 labeling of peptides. Anal Chem. 2009 Apr 1; 81(7):2804-9.
        View in: PubMed
      11. Vazquez J, Hall SC, Witkowska HE, Greco MA. Rapid alterations in cortical protein profiles underlie spontaneous sleep and wake bouts. J Cell Biochem. 2008 Dec 15; 105(6):1472-84.
        View in: PubMed
      12. Denny P, Hagen FK, Hardt M, Liao L, Yan W, Arellanno M, Bassilian S, Bedi GS, Boontheung P, Cociorva D, Delahunty CM, Denny T, Dunsmore J, Faull KF, Gilligan J, Gonzalez-Begne M, Halgand F, Hall SC, Han X, Henson B, Hewel J, Hu S, Jeffrey S, Jiang J, Loo JA, Ogorzalek Loo RR, Malamud D, Melvin JE, Miroshnychenko O, Navazesh M, Niles R, Park SK, Prakobphol A, Ramachandran P, Richert M, Robinson S, Sondej M, Souda P, Sullivan MA, Takashima J, Than S, Wang J, Whitelegge JP, Witkowska HE, Wolinsky L, Xie Y, Xu T, Yu W, Ytterberg J, Wong DT, Yates JR, Fisher SJ. The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions. J Proteome Res. 2008 May; 7(5):1994-2006.
        View in: PubMed
      13. Dong M, Yang LL, Williams K, Fisher SJ, Hall SC, Biggin MD, Jin J, Witkowska HE. A "tagless" strategy for identification of stable protein complexes genome-wide by multidimensional orthogonal chromatographic separation and iTRAQ reagent tracking. J Proteome Res. 2008 May; 7(5):1836-49.
        View in: PubMed
      14. Robinson S, Niles RK, Witkowska HE, Rittenbach KJ, Nichols RJ, Sargent JA, Dixon SE, Prakobphol A, Hall SC, Fisher SJ, Hardt M. A mass spectrometry-based strategy for detecting and characterizing endogenous proteinase activities in complex biological samples. Proteomics. 2008 Feb; 8(3):435-45.
        View in: PubMed
      15. Peters-Libeu CA, Newhouse Y, Hall SC, Witkowska HE, Weisgraber KH. Apolipoprotein E*dipalmitoylphosphatidylcholine particles are ellipsoidal in solution. J Lipid Res. 2007 May; 48(5):1035-44.
        View in: PubMed
      16. Boonjakuakul JK, Gerns HL, Chen YT, Hicks LD, Minnick MF, Dixon SE, Hall SC, Koehler JE. Proteomic and immunoblot analyses of Bartonella quintana total membrane proteins identify antigens recognized by sera from infected patients. Infect Immun. 2007 May; 75(5):2548-61.
        View in: PubMed
      17. Chiu YL, Witkowska HE, Hall SC, Santiago M, Soros VB, Esnault C, Heidmann T, Greene WC. High-molecular-mass APOBEC3G complexes restrict Alu retrotransposition. Proc Natl Acad Sci U S A. 2006 Oct 17; 103(42):15588-93.
        View in: PubMed
      18. Hardt M, Witkowska HE, Webb S, Thomas LR, Dixon SE, Hall SC, Fisher SJ. Assessing the effects of diurnal variation on the composition of human parotid saliva: quantitative analysis of native peptides using iTRAQ reagents. Anal Chem. 2005 Aug 1; 77(15):4947-54.
        View in: PubMed
      19. Hardt M, Thomas LR, Dixon SE, Newport G, Agabian N, Prakobphol A, Hall SC, Witkowska HE, Fisher SJ. Toward defining the human parotid gland salivary proteome and peptidome: identification and characterization using 2D SDS-PAGE, ultrafiltration, HPLC, and mass spectrometry. Biochemistry. 2005 Mar 1; 44(8):2885-99.
        View in: PubMed
      20. Scheffler NK, Falick AM, Hall SC, Ray WC, Post DM, Munson RS, Gibson BW. Proteome of Haemophilus ducreyi by 2-D SDS-PAGE and mass spectrometry: strain variation, virulence, and carbohydrate expression. J Proteome Res. 2003 Sep-Oct; 2(5):523-33.
        View in: PubMed
      21. Go EP, Prenni JE, Wei J, Jones A, Hall SC, Witkowska HE, Shen Z, Siuzdak G. Desorption/ionization on silicon time-of-flight/time-of-flight mass spectrometry. Anal Chem. 2003 May 15; 75(10):2504-6.
        View in: PubMed
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