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Staff information


Sam Payne

Integrative Omics
Scientist, Team Lead
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. Past PI leads include an NSF Microbial Genome Sequencing grant and an internal R&D project on Biological Data Visualization.

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.

Integrative Omics Group website

Research Interests

  • Visual Analytics
  • Bioinformatics
  • Computational Mass Spectrometry

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


  • Bilbao Pena A., B.C. Gibbons, G.W. Slysz, K.L. Crowell, M.E. Monroe, Y.M. Ibrahim, and R.D. Smith, et al. 2018. "An Algorithm to Correct Saturated Mass Spectrometry Ion Abundances for Enhanced Quantitation and Mass Accuracy in Omic Studies." International Journal of Mass Spectrometry 427. PNNL-SA-126312. doi:10.1016/j.ijms.2017.11.003


  • Dasgupta A., J. Lee, R.E. Wilson, R.A. Lafrance, N.O. Cramer, K.A. Cook, and S.H. Payne. 2017. "Familiarity Vs Trust: A Comparative Study of Domain Scientists’ Trust in Visual Analytics and Conventional Analysis Methods." IEEE Transactions on Visualization and Computer Graphics 23, no. 1:271-280. PNNL-SA-117411. doi:10.1109/TVCG.2016.2598544
  • Kyle J.E., K.L. Crowell, C.P. Casey, G.M. Fujimoto, S. Kim, S.E. Dautel, and R.D. Smith, et al. 2017. "LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data." Bioinformatics 33, no. 11:1744-1746. PNNL-SA-118436. doi:10.1093/bioinformatics/btx046
  • Ma J., C.P. Casey, X. Zheng, Y.M. Ibrahim, C.S. Wilkins, R.S. Renslow, and D.G. Thomas, et al. 2017. "PIXiE: An Algorithm for Automated Ion Mobility Arrival Time Extraction and Collision Cross Section Calculation using Global Data Association." Bioinformatics 33, no. 17:2715-2722. PNNL-SA-122828. doi:10.1093/bioinformatics/btx305
  • Nakayasu E.S., M.C. Burnet, H.E. Walukiewicz, C.S. Wilkins, A.K. Shukla, S.M. Brooks, and M.J. Plutz, et al. 2017. "Ancient regulatory role of lysine acetylation in central metabolism." mBio 8, no. 6:Article No. e01894-17. PNNL-SA-124565. doi:10.1128/mBio.01894-17
  • Park J., P.D. Piehowski, C.S. Wilkins, M. Zhou, J.A. Mendoza, G.M. Fujimoto, and B.C. Gibbons, et al. 2017. "Informed-Proteomics: Open Source Software Package for Top-down Proteomics." Nature Methods 14, no. 9:909-914. PNNL-SA-120171. doi:10.1038/nmeth.4388
  • Ting Y.S., J.D. Egertson, J. Bollinger, B. Searle, S.H. Payne, W. Noble, and M.J. Maccoss. 2017. "PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data." Nature Methods 14, no. 9:903-908. PNNL-SA-129704. doi:10.1038/nmeth.4390
  • Yang J., L. Yin, F.H. Lessner, E.S. Nakayasu, S.H. Payne, K. Fixen, and L.A. Gallagher, et al. 2017. "Genes essential for phototrophic growth by a purple alphaproteobacterium." Environmental Microbiology 19, no. 9:3567-3578. PNNL-SA-124648. doi:10.1111/1462-2920.13852
  • Zheng X., N.A. Aly, Y. Zhou, K.T. Dupuis, A. Bilbao Pena, V.L. Paurus, and D.J. Orton, et al. 2017. "A Structural Examination and Collision Cross Section Database for Over 500 Metabolites and Xenobiotics Using Drift Tube Ion Mobility Spectrometry." Chemical Science 8, no. 11:7724-7736. PNNL-SA-126802. doi:10.1039/C7SC03464D


  • Degan M.G., L. Ryadinskiy, G.M. Fujimoto, C.S. Wilkins, C.F. Lichti, and S.H. Payne. 2016. "A Skyline Plugin for Pathway-Centric Data Browsing." Journal of the American Society for Mass Spectrometry 27, no. 11:1752-1757. PNNL-SA-117929. doi:10.1007/s13361-016-1448-3
  • Na S., S.H. Payne, and N. Bandeira. 2016. "Multi-species identification of polymorphic peptide variants via propagation in spectral networks." Molecular & Cellular Proteomics. MCP 15, no. 11:3501-3512. PNNL-SA-110651. doi:10.1074/mcp.O116.060913
  • Ruggles K., Z. Tang, Z. Tang, X. Wang, H. Grover, M. Askenazi, and J. Teubl, et al. 2016. "An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer." Molecular and Cellular Proteomics 15, no. 3:1060-1071. PNNL-SA-105676. doi:10.1074/mcp.M115.056226
  • Sun J., J.D. Todd, J. Thrash, Y. Qian, M.C. Qian, B. Temperton, and J. Guo, et al. 2016. "The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol." Nature Microbiology 1, no. 8:Article No. 16065. PNNL-SA-108154. doi:10.1038/nmicrobiol.2016.65
  • Tabb D.L., X. Wang, S.A. Carr, K. Clauser, P. Mertins, M.C. Chambers, and J.D. Holman, et al. 2016. "Reproducibility of differential proteomic technologies in CPTAC fractionated xenografts." Journal of Proteome Research 15, no. 3:691-706. PNNL-SA-113210. doi:10.1021/acs.jproteome.5b00859
  • Zhang H., T. Liu, Z. Zhang, S.H. Payne, B. Zhang, J.E. McDermott, and J. Zhou, et al. 2016. "Integrated proteogenomic characterization of human high grade serous ovarian cancer." Cell 166, no. 3:755-765. PNNL-SA-107151. doi:10.1016/j.cell.2016.05.069


  • Gibbons B.C., M.C. Chambers, M.E. Monroe, D.L. Tabb, and S.H. Payne. 2015. "Correcting systematic bias and instrument measurement drift with mzRefinery." Bioinformatics 31, no. 23:3838-3840. PNNL-SA-108198. doi:10.1093/bioinformatics/btv437
  • Payne S.H. 2015. "The utility of protein and mRNA correlation." Trends in Biochemical Sciences 40, no. 1:1-3. PNNL-SA-106549. doi:10.1016/j.tibs.2014.10.010
  • Payne S.H., M.E. Monroe, C.C. Overall, G.R. Kiebel, M.G. Degan, B.C. Gibbons, and G.M. Fujimoto, et al. 2015. "The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity." Scientific Data 2. PNNL-SA-108944. doi:10.1038/sdata.2015.41
  • Ting Y.S., J.D. Egertson, S.H. Payne, S. Kim, B. MacLean, L. Kall, and R. Aebersold, et al. 2015. "Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data." Molecular and Cellular Proteomics 14. PNNL-SA-107046. doi:10.1074/mcp.O114.047035
  • Wu C., M.E. Monroe, Z. Xu, G.W. Slysz, S.H. Payne, K.D. Rodland, and T. Liu, et al. 2015. "An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics." Journal of the American Society for Mass Spectrometry 26, no. 12:2002-2008. PNNL-SA-108032. doi:10.1007/s13361-015-1169-z
  • Xu Z., C. Wu, F. Xie, G.W. Slysz, N. Tolic, M.E. Monroe, and V.A. Petyuk, et al. 2015. "Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes." Journal of Proteome Research 14, no. 1:422-433. PNNL-SA-103951. doi:10.1021/pr500840w


  • Amidan B.G., D.J. Orton, B.L. Lamarche, M.E. Monroe, R.J. Moore, A.M. Venzin, and R.D. Smith, et al. 2014. "Signatures for Mass Spectrometry Data Quality." Journal of Proteome Research 13, no. 4:2215-2222. PNNL-SA-97216. doi:10.1021/pr401143e
  • Fujimoto G.M., M.E. Monroe, L.M. Rodriguez, C. Wu, B. MacLean, R.D. Smith, and M. MacCoss, et al. 2014. "Accounting for population variation in targeted proteomics." Journal of Proteome Research 13, no. 1:321-323. PNNL-SA-99100. doi:10.1021/pr4011052
  • Kronewitter S.R., G.W. Slysz, I. Marginean, C.D. Hagler, B.L. Lamarche, R. Zhao, and M.Y. Harris, et al. 2014. "GlyQ-IQ: Glycomics Quintavariate-Informed Quantification with High-Performance Computing and GlycoGrid 4D Visualization." Analytical Chemistry 86, no. 13:6268-6276. PNNL-SA-100272. doi:10.1021/ac501492f
  • Prost S.A., K.L. Crowell, E.S. Baker, Y.M. Ibrahim, B.H. Clowers, M.E. Monroe, and G.A. Anderson, et al. 2014. "Detecting and Removing Data Artifacts in Hadamard Transform Ion Mobility-Mass Spectrometry Measurements." Journal of the American Society for Mass Spectrometry 25, no. 12:2020-2027. PNNL-SA-100086. doi:10.1007/s13361-014-0895-y
  • Ryu S., S.H. Payne, C. Schaab, and W. Xiao. 2014. "Beyond the proteome: Mass Spectrometry Special Interest Group (MS-SIG) at ISMB/ECCB 2013." Bioinformatics 30, no. 14:2089-2090. PNNL-SA-105013. doi:10.1093/bioinformatics/btu116
  • Slysz G.W., L.A. Steinke, D.M. Ward, C.G. Klatt, T.R. Clauss, S.O. Purvine, and S.H. Payne, et al. 2014. "Automated data extraction from in situ protein stable isotope probing studies." Journal of Proteome Research 13, no. 3:1200-1210. PNNL-SA-96672. doi:10.1021/pr400633j
  • Tovchigrechko A., P. Venepally, and S.H. Payne. 2014. "PGP: Parallel Prokaryotic Proteogenomics Pipeline for MPI clusters, high-througput batch clusters and multicore workstations." Bioinformatics 30, no. 10:1469-1470. PNWD-SA-10240. doi:10.1093/bioinformatics/btu051
  • Webb-Robertson B.M., M.M. Matzke, S. Datta, S.H. Payne, J. Kang, L.M. Bramer, and C.D. Nicora, et al. 2014. "Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements." Molecular and Cellular Proteomics 13, no. 12:3639-3646. PNNL-SA-95335. doi:10.1074/mcp.M113.030932
  • Woo S., S. Cha, S. Na, C. Guest, T. Liu, R.D. Smith, and K.D. Rodland, et al. 2014. "Proteogenomic strategies for identification of aberrant cancer peptides using large-scale Next Generation Sequencing data." Proteomics 14, no. 23-24:2719-2730. PNNL-SA-105664. doi:10.1002/pmic.201400206


  • Ansong C., C. Ortega, S.H. Payne, D.H. Haft, L.M. Chauvigne-Hines, M.P. Lewis, and A.R. Ollodart, et al. 2013. "Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis." Chemistry & Biology 20, no. 1:123-133. PNNL-SA-88963. doi:10.1016/j.chembiol.2012.11.008
  • Crowell K.L., E.S. Baker, S.H. Payne, Y.M. Ibrahim, M.E. Monroe, G.W. Slysz, and B.L. Lamarche, et al. 2013. "Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry." International Journal of Mass Spectrometry 354-355. PNNL-SA-95461. doi:10.1016/j.ijms.2013.06.028
  • Crowell K.L., G.W. Slysz, E.S. Baker, B.L. Lamarche, M.E. Monroe, Y.M. Ibrahim, and S.H. Payne, et al. 2013. "LC-IMS-MS Feature Finder: Detecting Multidimensional Liquid Chromatography, Ion Mobility, and Mass Spectrometry Features in Complex Datasets." Bioinformatics 29, no. 21:2804-2805. PNNL-SA-95214. doi:10.1093/bioinformatics/btt465
  • Halim M.F., F. Pfeiffer, J. Zou, A. Frisch, D.H. Haft, S. Wu, and N. Tolic, et al. 2013. "Haloferax volcanii archaeosortase is required for motility, mating, and C-terminal processing of the S-layer glycoprotein." Molecular Microbiology 88, no. 6:1164-1175. PNNL-SA-93808. doi:10.1111/mmi.12248
  • Ivankov D., S.H. Payne, M.Y. Galperin, S. Bonissone, P.A. Pevzner, and D. Frishman. 2013. "How many signal peptides are there in bacteria?." Environmental Microbiology 15, no. 4:983-990. PNWD-SA-9904. doi:10.1111/1462-2920.12105
  • Wu S., R.N. Brown, S.H. Payne, D. Meng, R. Zhao, N. Tolic, and L. Cao, et al. 2013. "Top-down characterization of the post-translationally modified intact periplasmic proteome of the bacterium Novosphingobium aromaticivorans." International Journal of Proteomics 2013. PNNL-SA-91327. doi:10.1155/2013/279590


  • Haft D.H., S.H. Payne, and J.D. Selengut. 2012. "Archaeosortases and Exosortases are Widely Distributed Systems Linking Membrane Transit with Posttranslational Modification." Journal of Bacteriology 194, no. 1:36-48. PNWD-SA-9486. doi:10.1128/JB.06026-11
  • Payne S.H., S. Bonissone, S. Wu, R.N. Brown, D. Ivankov, D. Frishman, and L. Pasa-Tolic, et al. 2012. "Unexpected Diversity of Signal Peptides in Prokaryotes." mBio 3, no. 6:Article No. e00339-12. PNWD-SA-9881. doi:10.1128/mBio.00339-12
  • Peterson E.S., L.A. McCue, A.C. Rutledge, J.L. Jensen, J. Walker, M.A. Kobold, and S.R. Webb, et al. 2012. "VESPA: Software to Facilitate Genomic Annotation of Prokaryotic Organisms Through Integration of Proteomic and Transcriptomic Data." BMC Genomics 13, no. 1:Article No. 131. PNNL-SA-82717. doi:10.1186/1471-2164-13-131
  • Rutledge A.C., M.B. Jones, S. Chauhan, S.O. Purvine, J. Sanford, M.E. Monroe, and H.M. Brewer, et al. 2012. "Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae." PLoS One 7, no. 3:Article No. E33903. PNNL-SA-79961. doi:10.1371/journal.pone.0033903


  • Ansong C., N. Tolic, S.O. Purvine, S. Porwollik, M.B. Jones, H. Yoon, and S.H. Payne, et al. 2011. "Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium." BMC Genomics 12. PNNL-SA-77195. 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.

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