Steven Hall, PhD
Professor
Ob/Gyn, Reproductive Sciences
School of Medicine
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.
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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.
Grants and Projects
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Publications (31)
Top publication keywords:
ProteomicsChromatography, AffinityParotid GlandProteomeMass SpectrometrySjogren's SyndromeDesulfovibrio vulgarisSalivaAcid PhosphataseGlycoproteinsSpectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationPeptidesChromatography, LiquidLectinsSpectrometry, Mass, Electrospray Ionization
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Fluoride-related changes in the fetal cord blood proteome; a pilot study.
Research square 2024 Tuomivaara ST, Goin DE, Fisher SJ, Hall SC, Mattis AN, Den Besten PK -
Multifunctionality of prostatic acid phosphatase in prostate cancer pathogenesis.
Bioscience reports 2021 Alpert E, Akhavan A, Gruzman A, Hansen WJ, Lehrer-Graiwer J, Hall SC, Johansen E, McAllister S, Gulati M, Lin MF, Lingappa VR -
Multifunctionality of Prostatic Acid Phosphatase in Prostate Cancer Pathogenesis.
Bioscience reports 2021 Alpert E, Akhavan A, Gruzman A, Hansen WJ, Lehrer-Graiwer J, Hall SC, Johansen E, McAllister S, Gulati M, Lin MF, Lingappa VR -
Discovery of internalizing antibodies to basal breast cancer cells.
Protein engineering, design & selection : PEDS 2018 Zhou Y, Zou H, Yau C, Zhao L, Hall SC, Drummond DC, Farr-Jones S, Park JW, Benz CC, Marks JD -
Alterations in the Salivary Proteome and N-Glycome of Sjögren's Syndrome Patients.
Journal of proteome research 2017 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
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Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions.
Molecular & cellular proteomics : MCP 2016 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 -
Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported.
Molecular & cellular proteomics : MCP 2016 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, … -
Mass spectrometry-based analyses showing the effects of secretor and blood group status on salivary N-glycosylation.
Clinical proteomics 2015 Albertolle ME, Hassis ME, Ng CJ, Cuison S, Williams K, Prakobphol A, Dykstra AB, Hall SC, Niles RK, Ewa Witkowska H, Fisher SJ -
Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma.
Molecular & cellular proteomics : MCP 2015 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, … -
Urine, peritoneal fluid and omental fat proteomes of reproductive age women: Endometriosis-related changes and associations with endocrine disrupting chemicals.
Journal of proteomics 2014 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 -
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).
Molecular & cellular proteomics : MCP 2013 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, … -
High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris.
Journal of proteome research 2012 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 -
Lectin chromatography/mass spectrometry discovery workflow identifies putative biomarkers of aggressive breast cancers.
Journal of proteome research 2012 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… -
Breaking the bottleneck in the protein biomarker pipeline.
Clinical chemistry 2011 Witkowska HE, Hall SC, Fisher SJ -
Automated iterative MS/MS acquisition: a tool for improving efficiency of protein identification using a LC-MALDI MS workflow.
Analytical chemistry 2011 Liu H, Yang L, Khainovski N, Dong M, Hall SC, Fisher SJ, Biggin MD, Jin J, Witkowska HE -
A lectin affinity workflow targeting glycosite-specific, cancer-related carbohydrate structures in trypsin-digested human plasma.
Analytical biochemistry 2010 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 HPLC method to enrich selectively-glycosylated peptides from complex biological samples.
Journal of visualized experiments : JoVE 2009 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 -
Protein expression is altered during spontaneous sleep in aged Sprague Dawley rats.
Brain research 2009 Vazquez J, Hall SC, Greco MA -
Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma.
Nature biotechnology 2009 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, … -
Acid-catalyzed oxygen-18 labeling of peptides.
Analytical chemistry 2009 Niles R, Witkowska HE, Allen S, Hall SC, Fisher SJ, Hardt M -
Rapid alterations in cortical protein profiles underlie spontaneous sleep and wake bouts.
Journal of cellular biochemistry 2008 Vazquez J, Hall SC, Witkowska HE, Greco MA -
The proteomes of human parotid and submandibular/sublingual gland salivas collected as the ductal secretions.
Journal of proteome research 2008 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, … -
A "tagless" strategy for identification of stable protein complexes genome-wide by multidimensional orthogonal chromatographic separation and iTRAQ reagent tracking.
Journal of proteome research 2008 Dong M, Yang LL, Williams K, Fisher SJ, Hall SC, Biggin MD, Jin J, Witkowska HE -
A mass spectrometry-based strategy for detecting and characterizing endogenous proteinase activities in complex biological samples.
Proteomics 2008 Robinson S, Niles RK, Witkowska HE, Rittenbach KJ, Nichols RJ, Sargent JA, Dixon SE, Prakobphol A, Hall SC, Fisher SJ, Hardt M -
Apolipoprotein E*dipalmitoylphosphatidylcholine particles are ellipsoidal in solution.
Journal of lipid research 2007 Peters-Libeu CA, Newhouse Y, Hall SC, Witkowska HE, Weisgraber KH -
Proteomic and immunoblot analyses of Bartonella quintana total membrane proteins identify antigens recognized by sera from infected patients.
Infection and immunity 2007 Boonjakuakul JK, Gerns HL, Chen YT, Hicks LD, Minnick MF, Dixon SE, Hall SC, Koehler JE -
High-molecular-mass APOBEC3G complexes restrict Alu retrotransposition.
Proceedings of the National Academy of Sciences of the United States of America 2006 Chiu YL, Witkowska HE, Hall SC, Santiago M, Soros VB, Esnault C, Heidmann T, Greene WC -
Assessing the effects of diurnal variation on the composition of human parotid saliva: quantitative analysis of native peptides using iTRAQ reagents.
Analytical chemistry 2005 Hardt M, Witkowska HE, Webb S, Thomas LR, Dixon SE, Hall SC, 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 Hardt M, Thomas LR, Dixon SE, Newport G, Agabian N, Prakobphol A, Hall SC, Witkowska HE, Fisher SJ -
Proteome of Haemophilus ducreyi by 2-D SDS-PAGE and mass spectrometry: strain variation, virulence, and carbohydrate expression.
Journal of proteome research 2003 Scheffler NK, Falick AM, Hall SC, Ray WC, Post DM, Munson RS, Gibson BW -
Desorption/ionization on silicon time-of-flight/time-of-flight mass spectrometry.
Analytical chemistry 2003 Go EP, Prenni JE, Wei J, Jones A, Hall SC, Witkowska HE, Shen Z, Siuzdak G