Biological Sciences Staff information
Omic Techn Dev & Prod
Pacific Northwest National Laboratory
PO Box 999
Richland, WA 99352
Dr. Payne's research interests are focused on algorithms for proteomics data analysis and subsequent interpretation and integration. He is a DOE Early Career Investigator for algorithmic research in metaproteomics, or proteomics of environmental communities. The goal of the project is to increase the sensitivity and utility of metaproteomics through better identification algorithms. Additionally, he is PI for an NSF Microbial Genome Sequencing grant, Automated Protoegenomics Annotation for Prokaryotic Genomes. Proteogenomics is the process of using proteomics data to discover novel genes and correct and improve current genome annotation. The project will create a robust pipeline for proteogenomic annotation, and then apply the pipeline to all publicly available prokaryotic proteomics data. Over 80 bacterial and archaeal datasets have been analyzed with the pipeline, and the resulting data is being used as the training set for updating all prokaryotic genomes (a collaboration between NCBI and JGI).
Prior to joining PNNL, Dr. Payne was an Assistant Professor of Informatics at the J. Craig Venter Institute in Rockville, MD. Dr. Payne received a B.S. of computer science at Brigham Young University. He earned his Ph.D. in Bioinformatics from UC, San Diego working with Dr. Vineet Bafna. His research focused on computational proteomics and algorithm design, making a phosphorylation specific scoring method for mass spectrometry data which improved both sensitivity and specificity compared to current methods. He also helped lead the Arabidopsis proteogenomics project.
- Computational Proteomics
Education and Credentials
- B.S. Computer Science, Brigham Young University
- Ph.D Bioinformatics, University of California San Diego
Awards and Recognitions
- 2012 U.S. Department of Energy Office of Science Early Career Research Winner
- Ansong C, C Ortega, SH Payne, DH Haft, LM Chauvigne-Hines, MP Lewis, AR Ollodart, SO Purvine, AK Shukla, S Fortuin, RD Smith, JN Adkins, C Grundner, and AT Wright. 2013. "Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis." Chemistry & Biology 20(1):123-133. doi:10.1016/j.chembiol.2012.11.008
- Crowell KL, ES Baker, SH Payne, YM Ibrahim, ME Monroe, GW Slysz, BL Lamarche, VA Petyuk, PD Piehowski, WF Danielson, III, GA Anderson, and RD Smith. 2013. "Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry." International Journal of Mass Spectrometry 354-355:312-317. doi:10.1016/j.ijms.2013.06.028
- Crowell KL, GW Slysz, ES Baker, BL Lamarche, ME Monroe, YM Ibrahim, SH Payne, GA Anderson, and RD Smith. 2013. "LC-IMS-MS Feature Finder: Detecting Multidimensional Liquid Chromatography, Ion Mobility, and Mass Spectrometry Features in Complex Datasets." Bioinformatics 29(21):2804-2805 . doi:10.1093/bioinformatics/btt465
- Halim MF, F Pfeiffer, J Zou, A Frisch, DH Haft, S Wu, N Tolic, HM Brewer, SH Payne, L Pasa-Tolic, and M Pohlschroder. 2013. "Haloferax volcanii archaeosortase is required for motility, mating, and C-terminal processing of the S-layer glycoprotein." Molecular Microbiology 88(6):1164-1175. doi: 10.1111/mmi.12248
- Ivankov D, SH Payne, MY Galperin, S Bonissone, PA Pevzner, and D Frishman. 2013. "How many signal peptides are there in bacteria?" Environmental Microbiology 15(4):983-990. doi:10.1111/1462-2920.12105
- Wu S, RN Brown, SH Payne, D Meng, R Zhao, N Tolic, L Cao, AK Shukla, ME Monroe, RJ Moore, MS Lipton, and L Pasa-Tolic. 2013. "Top-down characterization of the post-translationally modified intact periplasmic proteome of the bacterium Novosphingobium aromaticivorans ." International Journal of Proteomics 2013:279590. doi:10.1155/2013/279590
- Haft DH, SH Payne, and JD Selengut. 2012. "Archaeosortases and Exosortases are Widely Distributed Systems Linking Membrane Transit with Posttranslational Modification." Journal of Bacteriology 194(1):36-48. doi:10.1128/JB.06026-11
- Payne SH, S Bonissone, S Wu, RN Brown, D Ivankov, D Frishman, L Pasa-Tolic, RD Smith, and PA Pevzner. 2012. "Unexpected Diversity of Signal Peptides in Prokaryotes." mBio 3(6):Article No. e00339-12. doi:10.1128/mBio.00339-12
- Peterson ES, LA McCue, AC Rutledge, JL Jensen, J Walker, MA Kobold, SR Webb, SH Payne, C Ansong, JN Adkins, WR Cannon, and BJM Webb-Robertson. 2012. "VESPA: Software to Facilitate Genomic Annotation of Prokaryotic Organisms Through Integration of Proteomic and Transcriptomic Data." BMC Genomics 13(1):Article No. 131. doi:10.1186/1471-2164-13-131
- Rutledge AC, MB Jones, S Chauhan, SO Purvine, J Sanford, ME Monroe, HM Brewer, SH Payne, C Ansong, BC Frank, RD Smith, S Peterson, VL Motin, and JN Adkins. 2012. "Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae." PLoS One 7(3):Article No. E33903. doi:10.1371/journal.pone.0033903
- Ansong C, N Tolic, SO Purvine, S Porwollik, MB Jones, H Yoon, SH Payne, JL Martin, MC Burnet, ME Monroe, P Venepally, RD Smith, S Peterson, F Heffron, M Mcclelland, and JN Adkins. 2011. "Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium." BMC Genomics 12:Art. No. 433. doi:10.1186/1471-2164-12-433
- Peterson ES, LA McCue, AC Schrimpe-Rutledge, JL Jensen, H Walker, MA Kobold, SR Webb, SH Payne, C Amspmg. JN Adkins, WR Cannon, and BJM Webb-Robertson. 2012. "VESPA: Software to Facilitate Genomic Annotation of Prokaryotic Organisms through Integration of Proteomic and Transcriptomic Data." BMC Genomics 13(1):131. DOI:10.1186/1471-2164-13-131.
- Schrimpe-Rutledge AC, MB Jones, S Chauhan, SO Purvine, JA Sanford, ME Monroe, HM Brewer, SH Payne, C Ansong, BC Frank, RD Smith, SN Peterson, VL Motin, and JN Adkins. 2012. "Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae." PloS One 7(3):e33903. DOI:10.1371/journal.pone.0033903.
- Ansong C, N Tolic, SO Purvine, S Porwollik, M Jones, H Yoon, SH Payne, JL Martin, MC Burnet, ME Monroe, P Venepally, RD Smith, SN Peterson, F Heffron, M McClelland, and JN Adkins. 2011. "Experimental Annotation of Post-Translational Features and Translated Coding Regions in the Pathogen Salmonella Typhimurium." BMC Genomics 12(1):433. DOI:10.1186/1471-2164-12-433.
- Haft DH, SH Payne, and JD Selengut. 2011. "Archaeosortases and Exosortases: Widely Distributed Systems Linking Membrane Transit with Posttranslational Modification." Journal of Bacteriology 194(11):36-48. DOI:10.1128/JB.06026-11.
- Peterson ES, JL Jensen, H Walker, AC Rutledge, LA McCue, SH Payne, JN Adkins, and BJM Webb-Robertson. 2011. VESPA: A Prokaryotic Proteogenomic Data Exploration and Discovery Platform. In RECOMB Satellite Conference on Computational Proteomics, March 11-13, La Jolla, California. University of California, San Diego, La Jolla, California.
- Pieper R, Q Zhang, DJ Clark, ST Huang, MJ Suh, JC Braisted, SH Payne, RD Fleischmann, SN Peterson, and S Tziport. 2011. "Characterizing the Escherichia Coli O157: H7 Proteome Including Protein Associations with Higher Order Assemblies." PloS One 6(11):e26544. DOI:10.1371/journal.pone.0026554.
- Venter E, RD Smith, and SH Payne. 2011. "Proteogenomic Analysis of Bacteria and Archaea: A 46 Organism Case Study." PloS One (611):e27587. DOI:10.1371/journal.pone.0027587.
- Payne SH, ST Huang, and R Pieper. 2010. "A Proteogenomic Update to Yersinia: Enhancing Genome Annotation." BMC Genomics 11(1):460. DOI:10.1186/1471-2164-11-460.
- Albuquerque CP, MB Smolka, SH Payne, V Bafna, J Eng, and H Zhou. 2008. "A Multidimensional Chromatography Technology for In-Depth Phosphoproteome Analysis." Molecular & Cellular Proteomics 7(7):1389-1396. DOI:10.1074/mcp.M700468-MCP200.
- Castellana NE, SH Payne, Z Shen, M Stanke, V Bafna, and SP Briggs. 2008. "Discovery and Revision of Arabidopsis Genes by Proteogenomics." In: Proceedings of the National Academy of Sciences of the United States of America 105(52):21034-21038. DOI:10.1073/pnas.0811066106. DOI:10.1073.pnas.0811066106.
- Payne SH, M Yau, MB Smolka, S Tanner, H Zhou, and V Bafna. 2008. "Phosphorylation-Specific MS/MS Scoring for Rapid and Accurate Phosphoproteome Analysis." Journal of Proteome Research 7(8):3373-3381. DOI:10.1021/pr800129m.
- Rana BK, PA Insel, SH Payne, K Abel, E Beutler, MG Ziegler, NJ Schork, and DT O'Connor. 2007. "Population-Based Sample Reveals Gene-Gender Interactions in Blood Pressure in White Americans." Hypertension 49(1):96-106. DOI:10.1161/01.HYP.0000252029.35106.67.
- Tanner S, SH Payne, S Dasari, Z Shen, PA Wilmarth, LL David, WF Loomis, SP Briggs, and V Bafna. 2007. "Accurate Annotation of Peptide Modifications through Unrestrictive Database Search." Journal of Proteome Research 7(01):170-181. DOI:10.1021/pr070444v.
- Hirose S, SH Payne, and WF Loomis. 2006. "cis-Acting Site Controlling Bidirectional Transcription at the Growth-Differentiation Transition in Dictyostelium Discoideum." Eukaryotic Cell 5(7):1104-1110. DOI:10.1128/EC.00047-06.
- Payne SH and WF Loomis. 2006. "Retention and Loss of Amino Acid Biosynthetic Pathways Based on Analysis of Whole-Genome Sequences." Eukaryotic Cell 5(2):272-276. DOI:10.1128/EC.5.2.272-276.2006.
- Payne SH. 2005. "Metabolic Pathways." Pages 41-57 in: Dictyostelium Genomics. WF Loomis and A Kuspa, Editors, Horizon Press, Far Hills, New Jersey.