Skip to Main Content U.S. Department of Energy

Biological Sciences Staff information

Sam Payne

Sam Payne

Integrative Omics
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
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.

Google Scholar profile.

Research Interests

  • Bioinformatics
  • 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

PNNL Publications


  • Xu Z, C Wu, F Xie, GW Slysz, N Tolic, ME Monroe, VA Petyuk, SH Payne, GM Fujimoto, RJ Moore, TL Fillmore, AA Schepmoes, D Levine, R Townsend, S Davies, S Li, M Ellis, E Boja, H Rodriguez, KD Rodland, T Liu, and RD Smith. 2015. "Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes." Journal of Proteome Research 14(1):422-433.  doi:10.1021/pr500840w
  • Xu Z, C Wu, F Xie, GW Slysz, N Tolic, ME Monroe, VA Petyuk, SH Payne, GM Fujimoto, RJ Moore, TL Fillmore, AA Schepmoes, D Levine, R Townsend, S Davies, S Li, M Ellis, E Boja, R Rivers, H Rodriguez, KD Rodland, T Liu, and RD Smith. 2015. "Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes." Journal of Proteome Research 14(1):422-433.  doi:10.1021/pr500840w


  • Fujimoto GM, ME Monroe, LM Rodriguez, C Wu, B MacLean, RD Smith, M MacCoss, and SH Payne. 2014. "Accounting for population variation in targeted proteomics." Journal of Proteome Research 13(1):321-323.  doi:10.1021/pr4011052
  • Slysz GW, LA Steinke, DM Ward, CG Klatt, TRW Clauss, SO Purvine, SH Payne, GA Anderson, RD Smith, and MS Lipton. 2014. "Automated data extraction from in situ protein stable isotope probing studies." Journal of Proteome Research 13(3):1200-1210.  doi:10.1021/pr400633j
  • Amidan BG, DJ Orton, BL Lamarche, ME Monroe, RJ Moore, AM Venzin, RD Smith, LH Sego, MF Tardiff, and SH Payne. 2014. "Signatures for Mass Spectrometry Data Quality." Journal of Proteome Research 13(4):2215-2222.  doi:10.1021/pr401143e
  • Kronewitter SR, GW Slysz, I Marginean, CD Hagler, BL Lamarche, R Zhao, MY Harris, ME Monroe, CA Polyukh, KL Crowell, TL Fillmore, TS Carlson, DG Camp, II, RJ Moore, SH Payne, GA Anderson, and RD Smith. 2014. "GlyQ-IQ: Glycomics Quintavariate-Informed Quantification with High-Performance Computing and GlycoGrid 4D Visualization." Analytical Chemistry 86(13):6268-6276.  doi:10.1021/ac501492f
  • Prost SA, KL Crowell, ES Baker, YM Ibrahim, BH Clowers, ME Monroe, GA Anderson, RD Smith, and SH Payne. 2014. "Detecting and Removing Data Artifacts in Hadamard Transform Ion Mobility-Mass Spectrometry Measurements." Journal of the American Society for Mass Spectrometry 25(12):2020-2027.  doi:10.1007/s13361-014-0895-y
  • Ryu S, SH Payne, C Schaab, and W Xiao. 2014. "Beyond the proteome: Mass Spectrometry Special Interest Group (MS-SIG) at ISMB/ECCB 2013." Bioinformatics 30(14):2089-2090.  doi:10.1093/bioinformatics/btu116
  • Tovchigrechko A, P Venepally, and SH Payne. 2014. "PGP: Parallel Prokaryotic Proteogenomics Pipeline for MPI clusters, high-througput batch clusters and multicore workstations." Bioinformatics 30(10):1469-1470.  doi:10.1093/bioinformatics/btu051
  • Webb-Robertson BJM, MM Matzke, S Datta, SH Payne, J Kang, LM Bramer, CD Nicora, AK Shukla, TO Metz, KD Rodland, RD Smith, MF Tardiff, JE McDermott, JG Pounds, and KM Waters. 2014. "Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements." Molecular and Cellular Proteomics 13(12):3639-3646.  doi:10.1074/mcp.M113.030932
  • Woo S, SW Cha, S Na, C Guest, T Liu, RD Smith, KD Rodland, SH Payne, and V Bafna. 2014. "Proteogenomic strategies for identification of aberrant cancer peptides using large-scale Next Generation Sequencing data." Proteomics 14(23-24):2719-2730.  doi:10.1002/pmic.201400206


  • 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

Selected Publications








  • Payne SH. 2005. "Metabolic Pathways." Pages 41-57 in: Dictyostelium Genomics. WF Loomis and A Kuspa, Editors, Horizon Press, Far Hills, New Jersey.

Biological Sciences

Seminar Series

Fundamental & Computational Sciences

Research Highlights

View All BSD Highlights