Steven Hall, PhD

Title(s)Professor, Ob/Gyn, Reproductive Sciences
SchoolSchool of Medicine
Address35 Medical Center Way, #902A
San Francisco CA 94143
Phone415-502-8423
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    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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    Mass Spectrometry Tools in Pursuit of Salivary Biomarkers of Sjogren's Syndrome
    NIH R01DE022031May 1, 2012 - Apr 30, 2018
    Role: Principal Investigator

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    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Multifunctionality of prostatic acid phosphatase in prostate cancer pathogenesis. Biosci Rep. 2021 10 29; 41(10). Alpert E, Akhavan A, Gruzman A, Hansen WJ, Lehrer-Graiwer J, Hall SC, Johansen E, McAllister S, Gulati M, Lin MF, Lingappa VR. PMID: 34677582; PMCID: PMC8536833.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    2. Multifunctionality of Prostatic Acid Phosphatase in Prostate  Cancer Pathogenesis. Biosci Rep. 2021 Oct 04. Alpert E, Akhavan A, Gruzman A, Hansen WJ, Lehrer-Graiwer J, Hall SC, Johansen E, McAllister S, Gulati M, Lin MF, Lingappa VR. PMID: 34605872.
      View in: PubMed   Mentions:    Fields:    
    3. Discovery of internalizing antibodies to basal breast cancer cells. Protein Eng Des Sel. 2018 01 01; 31(1):17-28. Zhou Y, Zou H, Yau C, Zhao L, Hall SC, Drummond DC, Farr-Jones S, Park JW, Benz CC, Marks JD. PMID: 29301020; PMCID: PMC6283401.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    4. Alterations in the Salivary Proteome and N-Glycome of Sjögren's Syndrome Patients. J Proteome Res. 2017 04 07; 16(4):1693-1705. Hall SC, Hassis ME, Williams KE, Albertolle ME, Prakobphol A, Dykstra AB, Laurance M, Ona K, Niles RK, Prasad N, Gormley M, Shiboski C, Criswell LA, Witkowska HE, Fisher SJ. PMID: 28282148; PMCID: PMC9668345.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    5. Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions. Mol Cell Proteomics. 2016 06; 15(6):2186-202. Shatsky M, Dong M, Liu H, Yang LL, Choi M, Singer ME, Geller JT, Fisher SJ, Hall SC, Hazen TC, Brenner SE, Butland G, Jin J, Witkowska HE, Chandonia JM, Biggin MD. PMID: 27099342; PMCID: PMC5083090.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    6. Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported. Mol Cell Proteomics. 2016 05; 15(5):1539-55. Shatsky M, Allen S, Gold BL, Liu NL, Juba TR, Reveco SA, Elias DA, Prathapam R, He J, Yang W, Szakal ED, Liu H, Singer ME, Geller JT, Lam BR, Saini A, Trotter VV, Hall SC, Fisher SJ, Brenner SE, Chhabra SR, Hazen TC, Wall JD, Witkowska HE, Biggin MD, Chandonia JM, Butland G. PMID: 26873250; PMCID: PMC4858938.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    7. Mass spectrometry-based analyses showing the effects of secretor and blood group status on salivary N-glycosylation. Clin Proteomics. 2015; 12:29. Albertolle ME, Hassis ME, Ng CJ, Cuison S, Williams K, Prakobphol A, Dykstra AB, Hall SC, Niles RK, Ewa Witkowska H, Fisher SJ. PMID: 26719750; PMCID: PMC4696288.
      View in: PubMed   Mentions: 4  
    8. Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma. Mol Cell Proteomics. 2015 Sep; 14(9):2357-74. Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA. PMID: 25693799; PMCID: PMC4563721.
      View in: PubMed   Mentions: 68     Fields:    Translation:Humans
    9. Urine, peritoneal fluid and omental fat proteomes of reproductive age women: Endometriosis-related changes and associations with endocrine disrupting chemicals. J Proteomics. 2015 Jan 15; 113:194-205. Williams KE, Miroshnychenko O, Johansen EB, Niles RK, Sundaram R, Kannan K, Albertolle M, Zhou Y, Prasad N, Drake PM, Giudice LC, Hall SC, Witkowska HE, Buck Louis GM, Fisher SJ. PMID: 25284053; PMCID: PMC4467531.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCTClinical Trials
    10. 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. 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. PMID: 23689285; PMCID: PMC3769335.
      View in: PubMed   Mentions: 48     Fields:    Translation:AnimalsCells
    11. High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris. J Proteome Res. 2012 Dec 07; 11(12):5720-35. 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. PMID: 23098413; PMCID: PMC3516867.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    12. Lectin chromatography/mass spectrometry discovery workflow identifies putative biomarkers of aggressive breast cancers. J Proteome Res. 2012 Apr 06; 11(4):2508-20. 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. PMID: 22309216; PMCID: PMC3383053.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    13. Breaking the bottleneck in the protein biomarker pipeline. Clin Chem. 2012 Feb; 58(2):321-3. Witkowska HE, Hall SC, Fisher SJ. PMID: 22140214.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    14. 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. Liu H, Yang L, Khainovski N, Dong M, Hall SC, Fisher SJ, Biggin MD, Jin J, Witkowska HE. PMID: 21761829.
      View in: PubMed   Mentions: 6     Fields:    
    15. A lectin affinity workflow targeting glycosite-specific, cancer-related carbohydrate structures in trypsin-digested human plasma. Anal Biochem. 2011 Jan 01; 408(1):71-85. 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. PMID: 20705048; PMCID: PMC3205961.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    16. A lectin HPLC method to enrich selectively-glycosylated peptides from complex biological samples. J Vis Exp. 2009 Oct 01; (32). 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. PMID: 19798022; PMCID: PMC2762330.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    17. Protein expression is altered during spontaneous sleep in aged Sprague Dawley rats. Brain Res. 2009 Nov 17; 1298:37-45. Vazquez J, Hall SC, Greco MA. PMID: 19729003; PMCID: PMC2778600.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    18. 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. 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. PMID: 19561596; PMCID: PMC2855883.
      View in: PubMed   Mentions: 427     Fields:    Translation:Humans
    19. Acid-catalyzed oxygen-18 labeling of peptides. Anal Chem. 2009 Apr 01; 81(7):2804-9. Niles R, Witkowska HE, Allen S, Hall SC, Fisher SJ, Hardt M. PMID: 19243188; PMCID: PMC2892872.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    20. Rapid alterations in cortical protein profiles underlie spontaneous sleep and wake bouts. J Cell Biochem. 2008 Dec 15; 105(6):1472-84. Vazquez J, Hall SC, Witkowska HE, Greco MA. PMID: 19003977.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    21. The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions. J Proteome Res. 2008 May; 7(5):1994-2006. 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. PMID: 18361515; PMCID: PMC2839126.
      View in: PubMed   Mentions: 153     Fields:    Translation:Humans
    22. 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. Dong M, Yang LL, Williams K, Fisher SJ, Hall SC, Biggin MD, Jin J, Witkowska HE. PMID: 18336004.
      View in: PubMed   Mentions: 23     Fields:    
    23. A mass spectrometry-based strategy for detecting and characterizing endogenous proteinase activities in complex biological samples. Proteomics. 2008 Feb; 8(3):435-45. Robinson S, Niles RK, Witkowska HE, Rittenbach KJ, Nichols RJ, Sargent JA, Dixon SE, Prakobphol A, Hall SC, Fisher SJ, Hardt M. PMID: 18186022.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    24. Apolipoprotein E*dipalmitoylphosphatidylcholine particles are ellipsoidal in solution. J Lipid Res. 2007 May; 48(5):1035-44. Peters-Libeu CA, Newhouse Y, Hall SC, Witkowska HE, Weisgraber KH. PMID: 17308333.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    25. 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. Boonjakuakul JK, Gerns HL, Chen YT, Hicks LD, Minnick MF, Dixon SE, Hall SC, Koehler JE. PMID: 17307937; PMCID: PMC1865797.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCells
    26. High-molecular-mass APOBEC3G complexes restrict Alu retrotransposition. Proc Natl Acad Sci U S A. 2006 Oct 17; 103(42):15588-93. Chiu YL, Witkowska HE, Hall SC, Santiago M, Soros VB, Esnault C, Heidmann T, Greene WC. PMID: 17030807; PMCID: PMC1592537.
      View in: PubMed   Mentions: 152     Fields:    Translation:HumansCells
    27. 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 01; 77(15):4947-54. Hardt M, Witkowska HE, Webb S, Thomas LR, Dixon SE, Hall SC, Fisher SJ. PMID: 16053308.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansCells
    28. 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 01; 44(8):2885-99. Hardt M, Thomas LR, Dixon SE, Newport G, Agabian N, Prakobphol A, Hall SC, Witkowska HE, Fisher SJ. PMID: 15723531.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansCells
    29. 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. Scheffler NK, Falick AM, Hall SC, Ray WC, Post DM, Munson RS, Gibson BW. PMID: 14582649.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    30. Desorption/ionization on silicon time-of-flight/time-of-flight mass spectrometry. Anal Chem. 2003 May 15; 75(10):2504-6. Go EP, Prenni JE, Wei J, Jones A, Hall SC, Witkowska HE, Shen Z, Siuzdak G. PMID: 12918997.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
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