Samuel Purvine

Computational Scientist

2021

B.B. McGivern, M.M. Tfaily, M.A. Borton, S.M. Kosina, R.A. Daly, C.D. Nicora, S.O. Purvine, A.R. Wong, M.S. Lipton, D.W. Hoyt, T.R. Northen, A.E. Hagerman, K.C. Wrighton. Decrypting bacterial polyphenol metabolism in an anoxic wetland soil, 2021. Nature Communications — *Accepted*

R.M. Wilson, M.M Kolton, C. Petro, P. Hanson, H.M. Heyman, J. E. Kyle, D.W. Hoyt, E.K. Eder, S.O. Purvine, R.K Kolka, S.D. Sebestyen, N.A Griffiths, C.W. Schadt, J. Kostka, J.P. Chanton. Soil metabolome response to whole ecosystem warming at the Spruce and Peatland Responses Under Changing Environments experiment, 2021, PNAS — *Accepted*

C.L. Swift, K.B. Louie, B.P. Bowen, H.M. Olson, S.O. Purvine, A.Salamov, S.J. Mondo, K.V. Solomon, A.T. Wright, T.R. Northen, I.V. Grigoriev, N.P. Keller, M.A. O’Malley. Anaerobic gut fungi are an untapped reservoir of natural products, 2021. PNAS — *Accepted*

C.C. Sánchez, E. Erickson, T. Dong, A.R. Wong, E.K. Eder, D.W. Hoyt, S.O. Purvine, H.D. Mitchell, M.C. Burnet, R.K. Chu, L.M. Markillie, J-F. Cheng, M. Harmon-Smith, R. Evans, K.J. Ramirez, R. Katahira, W. Xiong, M.E. Himmel, V. Subramanian, J.G. Linger, D. Salvachúa. Intracellular pathways for lignin catabolism in white-rot fungi, March 2, 2021. PNAS 118 (9) e2017381118 doi:10.1073/pnas.2017381118

S.D. Gallaher, R.J. Craig, I. Ganesan, S.O. Purvine, S.R. McCorkle, J. Grimwood, D. Strenkert, L. Davidi, M.S. Roth, T.L. Jeffers, M.Lipton, K.K. Niyogi, J.Schmutz, S.M. Theg, C.E. Blaby-Haas, S.S. Merchant. Widespread polycistronic gene expression in green algae, February 16, 2021. PNAS, 118 (7) e2017714118 doi:10.1073/pnas.2017714118

D.L. Suskind, D. Lee, Y-M. Kim, G. Wahbeh, N. Singh, K. Braly, M. Nuding, C.D. Nicora, S.O. Purvine, M.S. Lipton, J.K. Jansson, W.C. Nelson. The Specific Carbohydrate Diet and Diet Modification on Disease Activity and the Intestinal Microbiome in Active Pediatric Crohn’s Disease, 2020. Nutrients 12(12), 3749 doi:10.3390/nu12123749

T. Chroumpi, M. Peng, M. Markillie, H.D. Mitchell, C.D. Nicora, C.M. Hutchinson, V. Paurus, S.O. Purvine, N. Tolic, C.S. Clendinen, G. Orr, S.E. Baker, M.R. Mäkelä, R.P. de Vries. Re-routing of sugar catabolism provides a better insight into fungal flexibility in using plant biomass-derived monomers as substrates, 2020. Frontiers in Plant Science. doi: 10.3389/fbioe.2021.644216

C.A. Zeiner, S. Purvine, E. Zink, S. Wu, L. Paša-Tolic, D.L. Chaput, C.M. Santelli, C.M. Hansel. Mechanisms of Manganese(II) Oxidation by Filamentous Ascomycete Fungi Vary with Species and Time as a Function of Secretome Composition, 10 February 2021. Frontiers in Microbiology, doi: 10.3389/fmicb.2021.610497

2020

Challacombe, J., Hesse, C.N., Bramer, L.M., McCue, LA, M. Lipton, Purvine, S., Nicora, C., Gallegos-Graves, L., Porras-Alfaro, A., Kuske, C.R. “Genomes and Secretomes of Ascomycota Fungi Reveal Diverse Functions in Plant Biomass Decomposition and Pathogenesis”. BMC Genomics (20) https://doi.org/10.1186/s12864-019-6358-x

Lin, V. S., R. F. Volk, A. J. Deleon, L. N. Anderson, S. O. Purvine, A. K. Shukla, H. C. Bernstein, J. N. Smith, and A. T. Wright. 2020. “Structure Dependent Determination of Organophosphate Targets in Mammalian Tissues Using Activity-Based Protein Profiling.” Chemical Research in Toxicology, 33 (2): 414-425. https://doi.org/10.1021/acs.chemrestox.9b00344.

Presley, G. N., J. Zhang, S. O. Purvine, and J. S. Schilling. 2020. “Functional Genomics, Transcriptomics, and Proteomics Reveal Distinct Combat Strategies between Lineages of Wood-Degrading Fungi with Redundant Wood Decay Mechanisms.” Frontiers in Microbiology, 11. https://doi.org/10.3389/fmicb.2020.01646.

Salvachúa, D., A. Z. Werner, I. Pardo, M. Michalska, B. A. Black, B. S. Donohoe, S. J. Haugen, R. Katahira, S. Notonier, K. J. Ramirez, A. Amore, S. O. Purvine, E. M. Zink, P. E. Abraham, R. J. Giannone, S. Poudel, P. D. Laible, R. L. Hettich, and G. T. Beckham. 2020. “Outer Membrane Vesicles Catabolize Lignin-Derived Aromatic Compounds in Pseudomonas putida KT2440.” Proceedings of the National Academy of Sciences of the United States of America 117 (17): 9302-9310. https://doi.org/10.1073/pnas.1921073117.

Wood-Charlson, E. M., Anubhav, D. Auberry, H. Blanco, M. I. Borkum, Y. E. Corilo, K. W. Davenport, S. Deshpande, R. Devarakonda, M. Drake, W. D. Duncan, M. C. Flynn, D. Hays, B. Hu, M. Huntemann, P. E. Li, M. Lipton, C. C. Lo, D. Millard, K. Miller, P. D. Piehowski, S. Purvine, T. B. K. Reddy, M. Shakya, J. C. Sundaramurthi, P. Vangay, Y. Wei, B. E. Wilson, S. Canon, P. S. G. Chain, K. Fagnan, S. Martin, L. A. McCue, C. J. Mungall, N. J. Mouncey, M. E. Maxon, and E. A. Eloe-Fadrosh. 2020. “The National Microbiome Data Collaborative: Enabling Microbiome Science.” Nature Reviews Microbiology 18 (6): 313-314. https://doi.org/10.1038/s41579-020-0377-0.

2019

Booker, A. E., D. W. Hoyt, T. Meulia, E. Eder, C. D. Nicora, S. O. Purvine, R. A. Daly, J. D. Moore, K. Wunch, S. M. Pfiffner, M. S. Lipton, P. J. Mouser, K. C. Wrighton, and M. J. Wilkins. 2019. “Deepsubsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp.” Applied and environmental microbiology 85 (12). https://doi.org/10.1128/AEM.00018-19.

Chacon, S. S., P. N. Reardon, C. J. Burgess, S. Purvine, R. K. Chu, T. R. Clauss, E. Walter, D. D. Myrold, N. Washton, and M. Kleber. 2019. “Mineral Surfaces as Agents of Environmental Proteolysis: Mechanisms and Controls.” Environmental Science and Technology 53 (6): 3018-3026. https://doi.org/10.1021/acs.est.8b05583.

Challacombe, J. F., C. N. Hesse, L. M. Bramer, L. A. McCue, M. Lipton, S. Purvine, C. Nicora, L. V. Gallegos-Graves, A. Porras-Alfaro, and C. R. Kuske. 2019. “Genomes and Secretomes of Ascomycota Fungi Reveal Diverse Functions in Plant Biomass Decomposition and Pathogenesis.” BMC Genomics 20 (1). https://doi.org/10.1186/s12864-019-6358-x.

Evans, M. V., G. Getzinger, J. L. Luek, A. J. Hanson, M. C. McLaughlin, J. Blotevogel, S. A. Welch, C. D. Nicora, S. O. Purvine, C. Xu, D. R. Cole, T. H. Darrah, D. W. Hoyt, T. O. Metz, P. Lee Ferguson, M. S. Lipton, M. J. Wilkins, and P. J. Mouser. 2019. “In Situ Transformation of Ethoxylate and Glycol Surfactants by Shale-Colonizing Microorganisms During Hydraulic Fracturing.” ISME Journal 13 (11): 2690-2700. https://doi.org/10.1038/s41396-019-0466-0.

Martinez, M. A., B. J. Woodcroft, J. C. Ignacio Espinoza, A. A. Zayed, C. M. Singleton, J. A. Boyd, Y. F. Li, S. Purvine, H. Maughan, S. B. Hodgkins, D. Anderson, M. Sederholm, B. Temperton, B. Bolduc, S. R. Saleska, G. W. Tyson, V. I. Rich, and C. IsoGenie Project. 2019. “Discovery and Ecogenomic Context of a Global Caldiserica-Related Phylum Active in Thawing Permafrost, Candidatus Cryosericota Phylum Nov., Ca. Cryosericia Class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the Four Species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. Hinesii sp. nov., Ca. C. Odellii sp. nov., Ca. C. terrychapinii sp. nov.” Systematic and Applied Microbiology 42 (1): 54-66. https://doi.org/10.1016/j.syapm.2018.12.003.

Strenkert, D., S. Schmollinger, S. D. Gallaher, P. A. Salomé, S. O. Purvine, C. D. Nicora, T. Mettler-Altmann, E. Soubeyrand, A. P. M. Weber, M. S. Lipton, G. J. Basset, and S. S. Merchant. 2019. “Multiomics Resolution of Molecular Events During a Day in the Life of Chlamydomonas.” Proceedings of the National Academy of Sciences of the United States of America 116 (6): 2374-2383. https://doi.org/10.1073/pnas.1815238116.

Tfaily, M. M., R. M. Wilson, H. M. Brewer, R. K. Chu, H. M. Heyman, D. W. Hoyt, J. E. Kyle, and S. O. Purvine. 2019. “Single-Throughput Complementary High-Resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures.” Journal of Visualized Experiments 2019 (143). https://doi.org/10.3791/59035.

2018

Borton, M. A., D. W. Hoyt, S. Roux, R. A. Daly, S. A. Welch, C. D. Nicora, S. Purvine, E. K. Eder, A. J. Hanson, J. M. Sheets, D. M. Morgan, R. A. Wolfe, S. Sharma, T. R. Carr, D. R. Cole, P. J. Mouser, M. S. Lipton, M. J. Wilkins, and K. C. Wrighton. 2018. “Coupled Laboratory and Field Investigations Resolve Microbial Interactions That Underpin Persistence in Hydraulically Fractured Shales.” Proceedings of the National Academy of Sciences of the United States of America 115 (28): E6585-E6594. https://doi.org/10.1073/pnas.1800155115.

Callister, S. J., T. L. Fillmore, C. D. Nicora, J. B. Shaw, S. O. Purvine, D. J. Orton, R. A. White III, R. J. Moore, M. C. Burnet, E. S. Nakayasu, S. H. Payne, J. K. Jansson, and L. Paša-Tolić. 2018. “Addressing the Challenge of Soil Metaproteome Complexity by Improving Metaproteome Depth of Coverage through Two-Dimensional Liquid Chromatography.” Soil Biology and Biochemistry 125: 290-299. https://doi.org/10.1016/j.soilbio.2018.07.018.

Daly, P., S. C. López, M. Peng, C. S. Lancefield, S. O. Purvine, Y. M. Kim, E. M. Zink, A. Dohnalkova, V. R. Singan, A. Lipzen, D. Dilworth, M. Wang, V. Ng, E. Robinson, G. Orr, S. E. Baker, P. C. A. Bruijnincx, K. S. Hildén, I. V. Grigoriev, M. R. Mäkelä, and R. P. de Vries. 2018. “Dichomitus squalens Partially Tailors Its Molecular Responses to the Composition of Solid Wood.” Environmental Microbiology 20 (11): 4141-4156. https://doi.org/10.1111/1462-2920.14416.

Gallaher, S. D., S. T. Fitz-Gibbon, D. Strenkert, S. O. Purvine, M. Pellegrini, and S. S. Merchant. 2018. “High-Throughput Sequencing of the Chloroplast and Mitochondrion of Chlamydomonas reinhardtii to Generate Improved de novo Assemblies, Analyze Expression Patterns and Transcript Speciation, and Evaluate Diversity among Laboratory Strains and Wild Isolates.” Plant Journal 93 (3): 545-565. https://doi.org/10.1111/tpj.13788.

Graham, E. B., A. R. Crump, D. W. Kennedy, E. Arntzen, S. Fansler, S. O. Purvine, C. D. Nicora, W. Nelson, M. M. Tfaily, and J. C. Stegen. 2018. “Multi 'Omics Comparison Reveals Metabolome Biochemistry, Not Microbiome Composition or Gene Expression, Corresponds to Elevated Biogeochemical Function in the Hyporheic Zone.” Science of the Total Environment 642: 742-753. https://doi.org/10.1016/j.scitotenv.2018.05.256.

Guo, J., S. Wilken, V. Jimenez, C. J. Choi, C. Ansong, R. Dannebaum, L. Sudek, D. S. Milner, C. Bachy, E. N. Reistetter, V. A. Elrod, D. Klimov, S. O. Purvine, C. L. Wei, G. Kunde-Ramamoorthy, T. A. Richards, U. Goodenough, R. D. Smith, S. J. Callister, and A. Z. Worden. 2018. “Specialized Proteomic Responses and an Ancient Photoprotection Mechanism Sustain Marine Green Algal Growth During Phosphate Limitation.” Nature Microbiology 3 (7): 781-790. https://doi.org/10.1038/s41564-018-0178-7.

Hurley, J. M., M. S. Jankowski, H. De los Santos, A. M. Crowell, S. B. Fordyce, J. D. Zucker, N. Kumar, S. O. Purvine, E. W. Robinson, A. Shukla, E. Zink, W. R. Cannon, S. E. Baker, J. J. Loros, and J. C. Dunlap. 2018. “Circadian Proteomic Analysis Uncovers Mechanisms of Post-Transcriptional Regulation in Metabolic Pathways.” Cell Systems 7 (6): 613-626.e5. https://doi.org/10.1016/j.cels.2018.10.014.

Kushner, I. K., G. Clair, S. O. Purvine, J. Y. Lee, J. N. Adkins, and S. H. Payne. 2018. “Individual Variability of Protein Expression in Human Tissues.” Journal of Proteome Research 17 (11): 3914-3922. https://doi.org/10.1021/acs.jproteome.8b00580.

Menachery, V. D., A. Schäfer, K. E. Burnum-Johnson, H. D. Mitchell, A. J. Eisfeld, K. B. Walters, C. D. Nicora, S. O. Purvine, C. P. Casey, M. E. Monroe, K. K. Weitz, K. G. Stratton, B. J. M. Webb-Robertson, L. E. Gralinski, T. O. Metz, R. D. Smith, K. M. Waters, A. C. Sims, Y. Kawaoka, and R. S. Baric. 2018. “MERS-CoV and H5N1 Influenza Virus Antagonize Antigen Presentation by Altering the Epigenetic Landscape.” Proceedings of the National Academy of Sciences of the United States of America 115 (5): E1012-E1021. https://doi.org/10.1073/pnas.1706928115.

Presley, G. N., E. Panisko, S. O. Purvine, and J. S. Schilling. 2018. “Coupling Secretomics with Enzyme Activities to Compare the Temporal Processes of Wood Metabolism among White and Brown Rot Fungi.” Applied and Environmental Microbiology 84 (16). https://doi.org/10.1128/AEM.000159-18.

Solden, L. M., A. E. Naas, S. Roux, R. A. Daly, W. B. Collins, C. D. Nicora, S. O. Purvine, D. W. Hoyt, J. Schückel, B. Jørgensen, W. Willats, D. E. Spalinger, J. L. Firkins, M. S. Lipton, M. B. Sullivan, P. B. Pope, and K. C. Wrighton. 2018. “Interspecies Cross-Feeding Orchestrates Carbon Degradation in the Rumen Ecosystem.” Nature Microbiology 3 (11): 1274-1284. https://doi.org/10.1038/s41564-018-0225-4.

Woodcroft, B. J., C. M. Singleton, J. A. Boyd, P. N. Evans, J. B. Emerson, A. A. F. Zayed, R. D. Hoelzle, T. O. Lamberton, C. K. McCalley, S. B. Hodgkins, R. M. Wilson, S. O. Purvine, C. D. Nicora, C. Li, S. Frolking, J. P. Chanton, P. M. Crill, S. R. Saleska, V. I. Rich, and G. W. Tyson. 2018. “Genome-Centric View of Carbon Processing in Thawing Permafrost.” Nature 560 (7716): 49-54. https://doi.org/10.1038/s41586-018-0338-1.

2017

Boenisch, M. J., K. L. Broz, S. O. Purvine, W. B. Chrisler, C. D. Nicora, L. R. Connolly, M. Freitag, S. E. Baker, and H. C. Kistler. 2017. “Structural Reorganization of the Fungal Endoplasmic Reticulum Upon Induction of Mycotoxin Biosynthesis.” Scientific Reports 7. https://doi.org/10.1038/srep44296.

Booker, A. E., M. A. Borton, R. A. Daly, S. A. Welch, C. D. Nicora, D. W. Hoyt, T. Wilson, S. O. Purvine, R. A. Wolfe, S. Sharma, P. J. Mouser, D. R. Cole, M. S. Lipton, K. C. Wrighton, and M. J. Wilkins. 2017. “Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales.” mSphere 2 (4). https://doi.org/10.1128/mSphereDirect.00257-17.

Haitjema, C. H., S. P. Gilmore, J. K. Henske, K. V. Solomon, R. De Groot, A. Kuo, S. J. Mondo, A. A. Salamov, K. LaButti, Z. Zhao, J. Chiniquy, K. Barry, H. M. Brewer, S. O. Purvine, A. T. Wright, M. Hainaut, B. Boxma, T. Van Alen, J. H. P. Hackstein, B. Henrissat, S. E. Baker, I. V. Grigoriev, and M. A. O'Malley. 2017. “A Parts List for Fungal Cellulosomes Revealed by Comparative Genomics.” Nature Microbiology 2. https://doi.org/10.1038/nmicrobiol.2017.87.

Kerkhoven, E. J., Y. M. Kim, S. Wei, C. D. Nicora, T. L. Fillmore, S. O. Purvine, B. J. Webb-Robertson, R. D. Smith, S. E. Baker, T. O. Metz, and J. Nielsena. 2017. “Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica.” mBio 8 (3). https://doi.org/10.1128/mBio.00857-17.

Kowalczyk, J. E., C. Khosravi, S. Purvine, A. Dohnalkova, W. B. Chrisler, G. Orr, E. Robinson, E. Zink, A. Wiebenga, M. Peng, E. Battaglia, S. Baker, and R. P. de Vries. 2017. “High Resolution Visualization and Exo-Proteomics Reveal the Physiological Role of XlnR and AraR in Plant Biomass Colonization and Degradation by Aspergillus niger.” Environmental Microbiology 19 (11): 4587-4598. https://doi.org/10.1111/1462-2920.13923.

Ledee, D., M. A. Kang, M. Kajimoto, S. Purvine, H. Brewer, L. Pasa-Tolic, and M. A. Portman. 2017. “Quantitative Cardiac Phosphoproteomics Profiling During Ischemia-Reperfusion in an Immature Swine Model.” American Journal of Physiology - Heart and Circulatory Physiology 313 (1): H125-H137. https://doi.org/10.1152/ajpheart.00842.2016.

Solden, L. M., D. W. Hoyt, W. B. Collins, J. E. Plank, R. A. Daly, E. Hildebrand, T. J. Beavers, R. Wolfe, C. D. Nicora, S. O. Purvine, M. Carstensen, M. S. Lipton, D. E. Spalinger, J. L. Firkins, B. A. Wolfe, and K. C. Wrighton. 2017. “New Roles in Hemicellulosic Sugar Fermentation for the Uncultivated Bacteroidetes Family BS11.” ISME Journal 11 (3): 691-703. https://doi.org/10.1038/ismej.2016.150.

Stoddard, E. G., B. J. Killinger, R. N. Nair, N. C. Sadler, R. F. Volk, S. O. Purvine, A. K. Shukla, J. N. Smith, and A. T. Wright. 2017. “Activity-Based Probes for Isoenzyme- and Site-Specific Functional Characterization of Glutathione S-Transferases.” Journal of the American Chemical Society 139 (45): 16032-16035. https://doi.org/10.1021/jacs.7b07378.

Warshan, D., J. L. Espinoza, R. K. Stuart, R. A. Richter, S. Y. Kim, N. Shapiro, T. Woyke, N. C Kyrpides, K. Barry, V. Singan, E. Lindquist, C. Ansong, S. O. Purvine, H. M. Brewer, P. D. Weyman, C. L. Dupont, and U. Rasmussen. 2017. “Feathermoss and Epiphytic Nostoc Cooperate Differently: Expanding the Spectrum of Plant-Cyanobacteria Symbiosis.” ISME Journal 11 (12): 2821-2833. https://doi.org/10.1038/ismej.2017.134.

Zeiner, C. A., S. O. Purvine, E. M. Zink, L. Paša-Tolić, D. L. Chaput, S. Wu, C. M. Santelli, and C. M. Hansel. 2017. “Quantitative iTRAQ-Based Secretome Analysis Reveals Species-Specific and Temporal Shifts in Carbon Utilization Strategies among Manganese(II)-Oxidizing Ascomycete Fungi.” Fungal Genetics and Biology 106: 61-75. https://doi.org/10.1016/j.fgb.2017.06.004.

2016

Burnum-Johnson, K. E., S. Nie, C. P. Casey, M. E. Monroe, D. J. Orton, Y. M. Ibrahim, M. A. Gritsenko, T. R. W. Clauss, A. K. Shukla, R. J. Moore, S. O. Purvine, T. Shi, W. Qian, T. Liu, E. S. Baker, and R. D. Smith. 2016. “Simultaneous Proteomic Discovery and Targeted Monitoring Using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry.” Molecular and Cellular Proteomics 15 (12): 3694-3705. https://doi.org/10.1074/mcp.M116.061143.

Pomraning, K. R., Y. M. Kim, C. D. Nicora, R. K. Chu, E. L. Bredeweg, S. O. Purvine, D. Hu, T. O. Metz, and S. E. Baker. 2016. “Multi-Omics Analysis Reveals Regulators of the Response to Nitrogen Limitation in Yarrowia lipolytica.” BMC Genomics 17 (1). https://doi.org/10.1186/s12864-016-2471-2.

Salvachúa, D., R. Katahira, N. S. Cleveland, P. Khanna, M. G. Resch, B. A. Black, S. O. Purvine, E. M. Zink, A. Prieto, M. J. Martínez, A. T. Martínez, B. A. Simmons, J. M. Gladden, and G. T. Beckham. 2016. “Lignin Depolymerization by Fungal Secretomes and a Microbial Sink.” Green Chemistry 18 (22): 6046-6062. https://doi.org/10.1039/c6gc01531j.

Solomon, K. V., C. H. Haitjema, J. K. Henske, S. P. Gilmore, D. Borges-Rivera, A. Lipzen, H. M. Brewer, S. O. Purvine, A. T. Wright, M. K. Theodorou, I. V. Grigoriev, A. Regev, D. A. Thompson, and M. A. O'Malley. 2016. “Early-Branching Gut Fungi Possess Large, Comprehensive Array of Biomass-Degrading Enzymes.” Science 351 (6278): 1192-1195. https://doi.org/10.1126/science.aad1431.

Tisoncik-Go, J., D. J. Gasper, J. E. Kyle, A. J. Eisfeld, C. Selinger, M. Hatta, J. Morrison, M. J. Korth, E. M. Zink, Y. M. Kim, A. A. Schepmoes, C. D. Nicora, S. O. Purvine, K. K. Weitz, X. Peng, R. R. Green, S. C. Tilton, B. J. Webb-Robertson, K. M. Waters, T. O. Metz, R. D. Smith, Y. Kawaoka, M. Suresh, L. Josset, and M. G. Katze. 2016. “Integrated Omics Analysis of Pathogenic Host Responses During Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism.” Cell Host and Microbe 19 (2): 254-266. https://doi.org/10.1016/j.chom.2016.01.002.

van Baren, M. J., C. Bachy, E. N. Reistetter, S. O. Purvine, J. Grimwood, S. Sudek, H. Yu, C. Poirier, T. J. Deerinck, A. Kuo, I. V. Grigoriev, C. H. Wong, R. D. Smith, S. J. Callister, C. L. Wei, J. Schmutz, and A. Z. Worden. 2016. “Evidence-Based Green Algal Genomics Reveals Marine Diversity and Ancestral Characteristics of Land Plants.” BMC Genomics 17 (1). https://doi.org/10.1186/s12864-016-2585-6.

Waltman, P. H., J. Guo, E. N. Reistetter, S. Purvine, C. K. Ansong, M. J. Van Baren, C. H. Wong, C. L. Wei, R. D. Smith, S. J. Callister, J. M. Stuart, and A. Z. Worden. 2016. “Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla.” PLoS ONE 11 (7). https://doi.org/10.1371/journal.pone.0155839.

Zeiner, C. A., S. O. Purvine, E. M. Zink, L. Paša-Tolić, D. L. Chaput, S. Haridas, S. Wu, K. LaButti, I. V. Grigoriev, B. Henrissat, C. M. Santelli, and C. M. Hansel. 2016. “Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi.” PLoS ONE 11 (7). https://doi.org/10.1371/journal.pone.0157844.

2015

Aylward, F. O., L. Khadempour, D. M. Tremmel, B. R. McDonald, C. D. Nicora, S. Wu, R. J. Moore, D. J. Orton, M. E. Monroe, P. D. Piehowski, S. O. Purvine, R. D. Smith, M. S. Lipton, K. E. Burnum-Johnson, and C. R. Currie. 2015. “Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants.” PLoS ONE 10 (8). https://doi.org/10.1371/journal.pone.0134752.

Aylward, F. O., L. Khadempour, D. M. Tremmel, B. R. McDonald, C. D. Nicora, S. Wu, R. J. Moore, D. J. Orton, M. E. Monroe, P. D. Piehowski, S. O. Purvine, R. D. Smith, M. S. Lipton, K. E. Burnum-Johnson, and C. R. Currie. 2015. “Erratum: Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants (Plos One (2015) 10:8 (E0134752) (Doi:10.1371/Journal.Pone.0134752)).” PLoS ONE 10 (9). https://doi.org/10.1371/journal.pone.0139151.

Jiang, L., K. Chughtai, S. O. Purvine, Z. M. Bhujwalla, V. Raman, L. Paša-Tolić, R. M. A. Heeren, and K. Glunde. 2015. “MALDI-Mass Spectrometric Imaging Revealing Hypoxia-Driven Lipids and Proteins in a Breast Tumor Model.” Analytical Chemistry 87 (12): 5947-5956. https://doi.org/10.1021/ac504503x.

Kebaabetswe, L. P., A. K. Haick, M. A. Gritsenko, T. L. Fillmore, R. K. Chu, S. O. Purvine, B. J. Webb-Robertson, M. M. Matzke, R. D. Smith, K. M. Waters, T. O. Metz, and T. A. Miura. 2015. “Proteomic Analysis Reveals Down-Regulation of Surfactant Protein B in Murine Type II Pneumocytes Infected with Influenza A Virus.” Virology 483: 96-107. https://doi.org/10.1016/j.virol.2015.03.045.

Payne, S. H., M. E. Monroe, C. C. Overall, G. R. Kiebel, M. Degan, B. C. Gibbons, G. M. Fujimoto, S. O. Purvine, J. N. Adkins, M. S. Lipton, and R. D. Smith. 2015. “The Pacific Northwest National Laboratory Library of Bacterial and Archaeal Proteomic Biodiversity.” Scientific Data 2. https://doi.org/10.1038/sdata.2015.41.

2014

Aevermann, B. D., B. E. Pickett, S. Kumar, E. B. Klem, S. Agnihothram, P. S. Askovich, A. Bankhead, III, M. Bolles, V. Carter, J. Chang, T. R. W. Clauss, P. Dash, A. H. Diercks, A. J. Eisfeld, A. Ellis, S. Fan, M. T. Ferris, L. E. Gralinski, R. R. Green, M. A. Gritsenko, M. Hatta, R. A. Heegel, J. M. Jacobs, S. Jeng, L. Josset, S. M. Kaiser, S. Kelly, G. L. Law, C. Li, J. Li, C. Long, M. L. Luna, M. Matzke, J. McDermott, V. Menachery, T. O. Metz, H. Mitchell, M. E. Monroe, G. Navarro, G. Neumann, R. L. Podyminogin, S. O. Purvine, C. M. Rosenberger, C. J. Sanders, A. A. Schepmoes, A. K. Shukla, A. Sims, P. Sova, V. C. Tam, N. Tchitchek, P. G. Thomas, S. C. Tilton, A. Totura, J. Wang, B. J. Webb-Robertson, J. Wen, J. M. Weiss, F. Yang, B. Yount, Q. Zhang, S. McWeeney, R. D. Smith, K. M. Waters, Y. Kawaoka, R. Baric, A. Aderem, M. G. Katze, and R. H. Scheuermann. 2014. “A Comprehensive Collection of Systems Biology Data Characterizing the Host Response to Viral Infection.” Scientific Data 1. https://doi.org/10.1038/sdata.2014.33.

Mohimani, H., R. D. Kersten, W. T. Liu, M. Wang, S. O. Purvine, S. Wu, H. M. Brewer, L. Pasa-Tolic, N. Bandeira, B. S. Moore, P. A. Pevzner, and P. C. Dorrestein. 2014. “Automated Genome Mining of Ribosomal Peptide Natural Products.” ACS Chemical Biology 9 (7): 1545-1551. https://doi.org/10.1021/cb500199h.

Mudenda, L., S. A. Pierlé, J. E. Turse, G. A. Scoles, S. O. Purvine, C. D. Nicora, T. R. W. Clauss, M. W. Ueti, W. C. Brown, and K. A. Brayton. 2014. “Proteomics Informed by Transcriptomics Identifies Novel Secreted Proteins in Dermacentor andersoni saliva.” International Journal for Parasitology 44 (13): 1029-1037. https://doi.org/10.1016/j.ijpara.2014.07.003.

Slysz, G. W., L. Steinke, D. M. Ward, C. G. Klatt, T. R. W. Clauss, S. O. Purvine, S. H. Payne, G. A. Anderson, R. D. Smith, and M. S. Lipton. 2014. “Automated Data Extraction from in Situ Protein-Stable Isotope Probing Studies.” Journal of Proteome Research 13 (3): 1200-1210. https://doi.org/10.1021/pr400633j.

Su, D., M. J. Gaffrey, J. Guo, K. E. Hatchell, R. K. Chu, T. R. W. Clauss, J. T. Aldrich, S. Wu, S. Purvine, D. G. Camp, R. D. Smith, B. D. Thrall, and W. J. Qian. 2014. “Proteomic Identification and Quantification of S-Glutathionylation in Mouse Macrophages Using Resin-Assisted Enrichment and Isobaric Labeling.” Free Radical Biology and Medicine 67: 460-470. https://doi.org/10.1016/j.freeradbiomed.2013.12.004.

2013

Anderson, L. N., D. E. Culley, B. A. Hofstad, L. M. Chauvigné-Hines, E. M. Zink, S. O. Purvine, R. D. Smith, S. J. Callister, J. M. Magnuson, and A. T. Wright. 2013. “Activity-Based Protein Profiling of Secreted Cellulolytic Enzyme Activity Dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30.” Molecular BioSystems 9 (12): 2992-3000. https://doi.org/10.1039/c3mb70333a.

Ansong, C., C. Ortega, S. H. Payne, D. H. Haft, L. M. Chauvignè-Hines, M. P. Lewis, A. R. Ollodart, S. O. Purvine, A. K. Shukla, S. Fortuin, R. D. Smith, J. N. Adkins, C. Grundner, and A. T. Wright. 2013. “Identification of Widespread Adenosine Nucleotide Binding in Mycobacterium tuberculosis.” Chemistry and Biology 20 (1): 123-133. https://doi.org/10.1016/j.chembiol.2012.11.008.

Aylward, F. O., K. E. Burnum-Johnson, S. G. Tringe, C. Teiling, D. M. Tremmel, J. A. Moeller, J. J. Scott, K. W. Barry, P. D. Piehowski, C. D. Nicor, S. A. Malfatti, M. E. Monroe, S. O. Purvine, L. A. Goodwin, R. D. Smith, G. M. Weinstock, N. M. Gerardo, G. Suen, M. S. Lipton, and C. R. Currie. 2013. “Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens.” Applied and environmental microbiology 79 (12): 3770-3778. https://doi.org/10.1128/AEM.03833-12.

Deatherage Kaiser, B. L., J. Li, J. A. Sanford, Y. M. Kim, S. R. Kronewitter, M. B. Jones, C. T. Peterson, S. N. Peterson, B. C. Frank, S. O. Purvine, J. N. Brown, T. O. Metz, R. D. Smith, F. Heffron, and J. N. Adkins. 2013. “A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection.” PLoS ONE 8 (6). https://doi.org/10.1371/journal.pone.0067155.

Nicora, C. D., B. J. Anderson, S. J. Callister, A. D. Norbeck, S. O. Purvine, J. K. Jansson, O. U. Mason, M. M. David, D. Jurelevicius, R. D. Smith, and M. S. Lipton. 2013. “Amino Acid Treatment Enhances Protein Recovery from Sediment and Soils for Metaproteomic Studies.” Proteomics 13 (18-19): 2776-2785. https://doi.org/10.1002/pmic.201300003.

Wang, D., S. Dasari, M. C. Chambers, J. D. Holman, K. Chen, D. C. Liebler, D. J. Orton, S. O. Purvine, M. E. Monroe, C. Y. Chung, K. L. Rose, and D. L. Tabb. 2013. “Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates.” Genomics, Proteomics and Bioinformatics 11 (2): 86-95. https://doi.org/10.1016/j.gpb.2012.11.004.

2012

Alfaro, J. F., C. X. Gong, M. E. Monroe, J. T. Aldrich, T. R. W. Clauss, S. O. Purvine, Z. Wang, D. G. Camp Ii, J. Shabanowitz, P. Stanley, G. W. Hart, D. F. Hunt, F. Yang, and R. D. Smith. 2012. “Tandem Mass Spectrometry Identifies Many Mouse Brain O-GlcNAcylated Proteins Including EGF Domain-Specific O-GlcNAc Transferase Targets.” Proceedings of the National Academy of Sciences of the United States of America 109 (19): 7280-7285. https://doi.org/10.1073/pnas.1200425109.

Aylward, F. O., K. E. Burnum, J. J. Scott, G. Suen, S. G. Tringe, S. M. Adams, K. W. Barry, C. D. Nicora, P. D. Piehowski, S. O. Purvine, G. J. Starrett, L. A. Goodwin, R. D. Smith, M. S. Lipton, and C. R. Currie. 2012. “Metagenomic and Metaproteomic Insights into Bacterial Communities in Leaf-Cutter Ant Fungus Gardens.” ISME Journal 6 (9): 1688-1701. https://doi.org/10.1038/ismej.2012.10.

Schrimpe-Rutledge, A. C., M. B. Jones, S. Chauhan, S. O. Purvine, J. A. Sanford, M. E. Monroe, H. M. Brewer, S. H. Payne, C. Ansong, B. C. Frank, R. D. Smith, S. N. Peterson, V. L. Motin, and J. N. Adkins. 2012. “Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae.” PLoS ONE 7 (3). https://doi.org/10.1371/journal.pone.0033903.

Shen, Y., N. Tolić, S. O. Purvine, and R. D. Smith. 2012. “Improving Collision Induced Dissociation (CID), High Energy Collision Dissociation (HCD), and Electron Transfer Dissociation (ETD) Fourier Transform MS/MS Degradome-Peptidome Identifications Using High Accuracy Mass Information.” Journal of Proteome Research 11 (2): 668-677. https://doi.org/10.1021/pr200597j.

Zhang, H., F. Yang, W. J. Qian, R. N. Brown, Y. Wang, E. D. Merkley, J. H. Park, M. E. Monroe, S. O. Purvine, R. J. Moore, L. Shi, J. K. Fredrickson, L. Paša-Tolić, R. D. Smith, and M. S. Lipton. 2012. “Erratum: Identification of c -Type Heme-Containing Peptides Using Nonactivated Immobilized Metal Affinity Chromatography Resin Enrichment and Higher-Energy Collisional Dissociation (Analytical Chemistry (2011) 83 (19) (7260-7268) Doi: 10.1021/Ac2000829).” Analytical Chemistry 84 (17): 7591. https://doi.org/10.1021/ac301396b.

2011

Ansong, C., N. Tolić, S. O. Purvine, S. Porwollik, M. Jones, H. Yoon, S. H. Payne, J. L. Martin, M. C. Burnet, M. E. Monroe, P. Venepally, R. D. Smith, S. N. Peterson, F. Heffron, M. McClelland, and J. N. Adkins. 2011. “Experimental Annotation of Post-Translational Features and Translated Coding Regions in the Pathogen Salmonella typhimurium.” BMC Genomics 12. https://doi.org/10.1186/1471-2164-12-433.

Burnum, K. E., S. J. Callister, C. D. Nicora, S. O. Purvine, P. Hugenholtz, F. Warnecke, R. H. Scheffrahn, R. D. Smith, and M. S. Lipton. 2011. “Proteome Insights into the Symbiotic Relationship between a Captive Colony of Nasutitermes corniger and Its Hindgut Microbiome.” ISME Journal 5 (1): 161-164. https://doi.org/10.1038/ismej.2010.97.

Chundawat, S. P. S., M. S. Lipton, S. O. Purvine, N. Uppugundla, D. Gao, V. Balan, and B. E. Dale. 2011. “Proteomics-Based Compositional Analysis of Complex Cellulase-Hemicellulase Mixtures.” Journal of Proteome Research 10 (10): 4365-4372. https://doi.org/10.1021/pr101234z.

Dresang, L. R., J. R. Teuton, H. Feng, J. M. Jacobs, D. G. Camp Ii, S. O. Purvine, M. A. Gritsenko, Z. Li, R. D. Smith, B. Sugden, P. S. Moore, and Y. Chang. 2011. “Coupled Transcriptome and Proteome Analysis of Human Lymphotropic Tumor Viruses: Insights on the Detection and Discovery of Viral Genes.” BMC Genomics 12. https://doi.org/10.1186/1471-2164-12-625.

Polacco, B. J., S. O. Purvine, E. M. Zink, S. P. LaVoie, M. S. Lipton, A. O. Summers, and S. M. Miller. 2011. “Discovering Mercury Protein Modifications in Whole Proteomes Using Natural Isotope Distributions Observed in Liquid Chromatography-Tandem Mass Spectrometry.” Molecular and Cellular Proteomics 10 (8). https://doi.org/10.1074/mcp.M110.004853.

Shen, Y., N. Tolić, F. Xie, R. Zhao, S. O. Purvine, A. A. Schepmoes, R. J. Moore, G. A. Anderson, and R. D. Smith. 2011. “Effectiveness of CID, HCD, and ETD with FT MS/MS for Degradomic-Peptidomic Analysis: Comparison of Peptide Identification Methods.” Journal of Proteome Research 10 (9): 3929-3943. https://doi.org/10.1021/pr200052c.

Stanley, J. R., J. N. Adkins, G. W. Slysz, M. E. Monroe, S. O. Purvine, Y. V. Karpievitch, G. A. Anderson, R. D. Smith, and A. R. Dabney. 2011. “A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics.” Analytical Chemistry 83 (16): 6135-6140. https://doi.org/10.1021/ac2009806.

Wang, Y., F. Yang, Y. Fu, X. Huang, W. Wang, X. Jiang, M. A. Gritsenko, R. Zhao, M. E. Monore, O. C. Pertz, S. O. Purvine, D. J. Orton, J. M. Jacobs, D. G. Camp Ii, R. D. Smith, and R. L. Klemke. 2011. “Spatial Phosphoprotein Profiling Reveals a Compartmentalized Extracellular Signal-Regulated Kinase Switch Governing Neurite Growth and Retraction.” Journal of Biological Chemistry 286 (20): 18190-18201. https://doi.org/10.1074/jbc.M111.236133.

Zhang, H., F. Yang, W. J. Qian, R. N. Brown, Y. Wang, E. D. Merkley, J. H. Park, M. E. Monroe, S. O. Purvine, R. J. Moore, L. Shi, J. K. Fredrickson, L. Paša-Tolić, R. D. Smith, and M. S. Lipton. 2011. “Identification of c-Type Heme-Containing Peptides Using Nonactivated Immobilized Metal Affinity Chromatography Resin Enrichment and Higher-Energy Collisional Dissociation.” Analytical Chemistry 83 (19): 7260-7268. https://doi.org/10.1021/ac2000829.

2010

Ham, B. M., H. Jayachandran, F. Yang, N. Jaitly, A. D. Polpitiya, M. E. Monroe, L. Wang, R. Zhao, S. O. Purvine, E. A. Livesay, D. G. Camp II, S. Rossie, and R. D. Smith. 2010. “Novel Ser/Thr Protein Phosphatase 5 (PP5) Regulated Targets During DNA Damage Identified by Proteomics Analysis.” Journal of Proteome Research 9 (2): 945-953. https://doi.org/10.1021/pr9008207.

Jung, H. J., S. O. Purvine, H. Kim, V. A. Petyuk, S. W. Hyung, M. E. Monroe, D. G. Mun, K. C. Kim, J. M. Park, S. J. Kim, N. Tolic, G. W. Slysz, R. J. Moore, R. Zhao, J. N. Adkins, G. A. Anderson, H. Lee, D. G. Camp, M. H. Yu, R. D. Smith, and S. W. Lee. 2010. “Integrated Post-Experiment Monoisotopic Mass Refinement: An Integrated Approach to Accurately Assign Monoisotopic Precursor Masses to Tandem Mass Spectrometric Data.” Analytical Chemistry 82 (20): 8510-8518. https://doi.org/10.1021/ac101388b.

Lewis, N. E., K. K. Hixson, T. M. Conrad, J. A. Lerman, P. Charusanti, A. D. Polpitiya, J. N. Adkins, G. Schramm, S. O. Purvine, D. Lopez-Ferrer, K. K. Weitz, R. Eils, R. König, R. D. Smith, and B. Ø. Palsson. 2010. “Omic Data from Evolved E. Coli Are Consistent with Computed Optimal Growth from Genome-Scale Models.” Molecular Systems Biology 6. https://doi.org/10.1038/msb.2010.47.

Petyuk, V. A., A. M. Mayampurath, M. E. Monroe, A. D. Polpitiya, S. O. Purvine, G. A. Anderson, D. G. Camp Ii, and R. D. Smith. 2010. “DtaRefinery, a Software Tool for Elimination of Systematic Errors from Parent Ion Mass Measurements in Tandem Mass Spectra Data Sets.” Molecular and Cellular Proteomics 9 (3): 486-496. https://doi.org/10.1074/mcp.M900217-MCP200.

Schutzer, S. E., T. Liu, B. H. Natelson, T. E. Angel, A. A. Schepmoes, S. O. Purvine, K. K. Hixson, M. S. Lipton, D. G. Camp, P. K. Coyle, R. D. Smith, and J. Bergquist. 2010. “Establishing the Proteome of Normal Human Cerebrospinal Fluid.” PLoS ONE 5 (6). https://doi.org/10.1371/journal.pone.0010980.

Shen, Y., T. Liu, N. Tolić, B. O. Petritis, R. Zhao, R. J. Moore, S. O. Purvine, D. G. Camp, and R. D. Smith. 2010. “Strategy for Degradomic-Peptidomic Analysis of Human Blood Plasma.” Journal of Proteome Research 9 (5): 2339-2346. https://doi.org/10.1021/pr901083m.

Shen, Y., N. Tolić, T. Liu, R. Zhao, B. O. Petritis, M. A. Gritsenko, D. G. Camp, R. J. Moore, S. O. Purvine, F. J. Esteva, and R. D. Smith. 2010. “Blood Peptidome-Degradome Profile of Breast Cancer.” PLoS ONE 5 (10). https://doi.org/10.1371/journal.pone.0013133.

Shen, Y., N. Tolić, S. O. Purvine, and R. D. Smith. 2010. “Identification of Disulfide Bonds in Protein Proteolytic Degradation Products Using De Novo -Protein Unique Sequence Tags Approach.” Journal of Proteome Research 9 (8): 4053-4060. https://doi.org/10.1021/pr1002559.

Yang, F., K. M. Waters, J. H. Miller, M. A. Gritsenko, R. Zhao, X. Du, E. A. Livesay, S. O. Purvine, M. E. Monroe, Y. Wang, D. G. Camp, R. D. Smith, and D. L. Stenoien. 2010. “Phosphoproteomics Profiling of Human Skin Fibroblast Cells Reveals Pathways and Proteins Affected by Low Doses of Ionizing Radiation.” PLoS ONE 5 (11). https://doi.org/10.1371/journal.pone.0014152.

Zhang, H., R. N. Brown, W. J. Qian, M. E. Monroe, S. O. Purvine, R. J. Moore, M. A. Gritsenko, L. Shi, M. F. Romine, J. K. Fredrickson, L. Paša-Tolić, R. D. Smith, and M. S. Lipton. 2010. “Quantitative Analysis of Cell Surface Membrane Proteins Using Membrane-Impermeable Chemical Probe Coupled with 18o Labeling.” Journal of Proteome Research 9 (5): 2160-2169. https://doi.org/10.1021/pr9009113.

 2009

Kim, W., M. W. Silby, S. O. Purvine, J. S. Nicoll, K. K. Hixson, M. Monroe, C. D. Nicora, M. S. Lipton, and S. B. Levy. 2009. “Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1.” PLoS ONE 4 (12). https://doi.org/10.1371/journal.pone.0008455.

Sharp, J. L., J. J. Borkowski, D. Schmoyer, D. S. Daly, S. Purvine, W. R. Cannon, and G. B. Hurst. 2009. “Statistically Appraising Process Quality of Affinity Isolation Experiments.” Computational Statistics and Data Analysis 53 (5): 1720-1726. https://doi.org/10.1016/j.csda.2008.05.011.

Springer, D. L., J. H. Miller, S. L. Spinelli, L. Pasa-Tolic, S. O. Purvine, D. S. Daly, R. C. Zangar, S. Jin, N. Blumberg, C. W. Francis, M. B. Taubman, A. E. Casey, S. D. Wittlin, and R. P. Phipps. 2009. “Platelet Proteome Changes Associated with Diabetes and During Platelet Storage for Transfusion.” Journal of Proteome Research 8 (5): 2261-2272. https://doi.org/10.1021/pr800885j.

Yang, F., S. Wu, D. L. Stenoien, R. Zhao, M. E. Monroe, M. A. Gritsenko, S. O. Purvine, A. D. Polpitiya, N. Tolić, Q. Zhang, A. D. Norbeck, D. J. Orton, R. J. Moore, K. Tang, G. A. Anderson, L. Pasa-Tolić, D. G. Camp II, and R. D. Smith. 2009. “Combined Pulsed-Q Dissociation and Electron Transfer Dissociation for Identification and Quantification of iTRAQ -Labeled Phosphopeptides.” Analytical Chemistry 81 (10): 4137-4143. https://doi.org/10.1021/ac802605m.

2008

Ansong, C., S. O. Purvine, J. N. Adkins, M. S. Lipton, and R. D. Smith. 2008. “Proteogenomics: Needs and Roles to Be Filled by Proteomics in Genome Annotation.” Briefings in Functional Genomics and Proteomics 7 (1): 50-62. https://doi.org/10.1093/bfgp/eln010.

Daly, D. S., K. K. Anderson, E. A. Panisko, S. O. Purvine, R. Fang, M. E. Monroe, and S. E. Baker. 2008. “Mixed-Effects Statistical Model for Comparative LC-MS Proteomics Studies.” Journal of Proteome Research 7 (3): 1209-1217. https://doi.org/10.1021/pr070441i.

Ding, S. J., Y. Wang, J. M. Jacobs, W. J. Qian, F. Yang, A. V. Tolmachev, X. Du, W. Wang, R. J. Moore, M. E. Monroe, S. O. Purvine, K. Waters, T. H. Heibeck, J. N. Adkins, D. G. Camp II, R. L. Klemke, and R. D. Smith. 2008. “Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis Applying Dual-Step 18O Labeling Coupled with Immobilized Metal-Ion Affinity Chromatography.” Journal of Proteome Research 7 (10): 4215-4224. https://doi.org/10.1021/pr7007785.

Du, X., F. Yang, N. P. Manes, D. L. Stenoien, M. E. Monroe, J. N. Adkins, D. J. States, S. O. Purvine, D. G. Camp Ii, and R. D. Smith. 2008. “Linear Discriminant Analysis-Based Estimation of the False Discovery Rate for Phosphopeptide Identifications.” Journal of Proteome Research 7 (6): 2195-2203. https://doi.org/10.1021/pr070510t.

Ham, B. M., F. Yang, H. Jayachandran, N. Jaitly, M. E. Monroe, M. A. Gritsenko, E. A. Livesay, R. Zhao, S. O. Purvine, D. Orton, J. N. Adkins, D. G. Camp Ii, S. Rossie, and R. D. Smith. 2008. “The Influence of Sample Preparation and Replicate Analyses on HeLa Cell Phosphoproteome Coverage.” Journal of Proteome Research 7 (6): 2215-2221. https://doi.org/10.1021/pr700575m.

Mathivanan, S., M. Ahmed, N. G. Ahn, H. Alexandre, R. Amanchy, P. C. Andrews, J. S. Bader, B. M. Balgley, M. Bantscheff, K. L. Bennett, E. Björling, B. Blagoev, R. Bose, S. K. Brahmachari, A. S. Burlingame, X. R. Bustelo, G. Cagney, G. T. Cantin, H. L. Cardasis, J. E. Celis, R. Chaerkady, F. Chu, P. A. Cole, C. E. Costello, R. J. Cotter, D. Crockett, J. P. DeLany, A. M. De Marzo, L. V. DeSouza, E. W. Deutsch, E. Dransfield, G. Drewes, A. Droit, M. J. Dunn, K. Elenitoba-Johnson, R. M. Ewing, J. V. Eyk, V. Faca, J. Falkner, X. Fang, C. Fenselau, D. Figeys, P. Gagné, C. Gelfi, K. Gevaert, J. M. Gimble, F. Gnad, R. Goel, P. Gromov, S. M. Hanash, W. S. Hancock, H. C. Harsha, G. Hart, F. Hays, F. He, P. Hebbar, K. Helsens, H. Hermeking, W. Hide, K. Hjernø, D. F. Hochstrasser, O. Hofmann, D. M. Horn, R. H. Hruban, N. Ibarrola, P. James, O. N. Jensen, P. H. Jensen, P. Jung, K. Kandasamy, I. Kheterpal, R. F. Kikuno, U. Korf, R. Körner, B. Kuster, M. S. Kwon, H. J. Lee, Y. J. LeeM. Lefevre, M. Lehvaslaiho, P. Lescuyer, F. Levander, M. S. Lim, C. Löbke, J. A. Loo, M. Mann, L. Martens, J. Martinez-Heredia, M. McComb, J. McRedmond, A. Mehrle, R. Menon, C. A. Miller, H. Mischak, S. S. Mohan, R. Mohmood, H. Molina, M. F. Moran, J. D. Morgan, R. Moritz, M. Morzel, D. C. Muddiman, A. Nalli, J. D. Navarro T. A. Neubert, ,O. Ohara, R. Oliva, G. S. Omenn, M. Oyama, Y. K. Paik, K. Pennington, R. Pepperkok, B. Periaswamy E. F. Petricoin, ,G. G. Poirier, T. S. K. Prasad, S. O. Purvine, B. A. Rahiman, P. Ramachandran, Y. L. Ramachandra, R. H. Rice, J. Rick, R. H. Ronnholm, J. Salonen, J. C. Sanchez, T. Sayd, B. Seshi, K. Shankari, S. J. Sheng, V. Shetty, K. Shivakumar, R. J. Simpson, R. Sirdeshmukh, K. W. Michael Siu, J. C. Smith, R. D. Smith, D. J. States, S. Sugano, M. Sullivan, G. Superti-Furga, M. Takatalo, V. Thongboonkerd, J. C. Trinidad, M. Uhlen, J. Vandekerckhove, J. Vasilescu, T. D. Veenstra, J. M. Vidal-Taboada, M. Vihinen, R. Wait, X. Wang, S. Wiemann, B. Wu, T. Xu, J. R. Yates, J. Zhong, M. Zhou, Y. Zhu, P. Zurbig, and A. Pandey. 2008. “Human Proteinpedia Enables Sharing of Human Protein Data.” Nature Biotechnology 26 (2): 164-167. https://doi.org/10.1038/nbt0208-164.

Mayampurath, A. M., N. Jaitly, S. O. Purvine, M. E. Monroe, K. J. Auberry, J. N. Adkins, and R. D. Smith. 2008. “DeconMSn: A Software Tool for Accurate Parent Ion Monoisotopic Mass Determination for Tandem Mass Spectra.” Bioinformatics 24 (7): 1021-1023. https://doi.org/10.1093/bioinformatics/btn063.

Shen, Y., K. K. Hixson, N. Tolić, D. G. Camp, S. O. Purvine, R. J. Moore, and R. D. Smith. 2008. “Mass Spectrometry Analysis of Proteome-Wide Proteolytic Post-Translational Degradation of Proteins.” Analytical Chemistry 80 (15): 5819-5828. https://doi.org/10.1021/ac800077w.

Shen, Y., N. Tolić, K. K. Hixson, S. O. Purvine, G. A. Anderson, and R. D. Smith. 2008. “De Novo Sequencing of Unique Sequence Tags for Discovery of Post-Translational Modifications of Proteins.” Analytical Chemistry 80 (20): 7742-7754. https://doi.org/10.1021/ac801123p.

hen, Y., N. Tolić, K. K. Hixson, S. O. Purvine, L. Paša-Tolić, W. J. Qian, J. N. Adkins, R. J. Moore, and R. D. Smith. 2008. “Proteome-Wide Identification of Proteins and Their Modifications with Decreased Ambiguities and Improved False Discovery Rates Using Unique Sequence Tags.” Analytical Chemistry 80 (6): 1871-1882. https://doi.org/10.1021/ac702328x.

Tolmachev, A. V., M. E. Monroe, S. O. Purvine, R. J. Moore, N. Jaitly, J. N. Adkins, G. A. Anderson, and R. D. Smith. 2008. “Characterization of Strategies for Obtaining Confident Identifications in Bottom-up Proteomics Measurements Using Hybrid FTMS Instruments.” Analytical Chemistry 80 (22): 8514-8525. https://doi.org/10.1021/ac801376g.

Zhang, Q., A. A. Schepmoes, J. W. C. Brock, S. Wu, R. J. Moore, S. O. Purvine, J. W. Baynes, R. D. Smith, and T. O. Metz. 2008. “Improved Methods for the Enrichment and Analysis of Glycated Peptides.” Analytical Chemistry 80 (24): 9822-9829. https://doi.org/10.1021/ac801704j.

2007

Manes, N. P., J. K. Gustin, J. Rue, H. M. Mottaz, S. O. Purvine, A. D. Norbeck, M. E. Monroe, J. S. D. Zimmer, T. O. Metz, J. N. Adkins, R. D. Smith, and F. Heffron. 2007. “Targeted Protein Degradation by Salmonella under Phagosome-Mimicking Culture Conditions Investigated Using Comparative Peptidomics.” Molecular and Cellular Proteomics 6 (4): 717-727. https://doi.org/10.1074/mcp.M600282-MCP200.

Yang, F., N. Jaitly, H. Jayachandran, Q. Luo, M. E. Monroe, X. Du, M. A. Gritsenko, R. Zhang, D. J. Anderson, S. O. Purvine, J. N. Adkins, R. J. Moore, H. M. Mottaz, S. J. Ding, M. S. Lipton, D. G. Camp II, H. R. Udseth, R. D. Smith, and S. Rossie. 2007. “Applying a Targeted Label-Free Approach Using LC-MS AMT Tags to Evaluate Changes in Protein Phosphorylation Following Phosphatase Inhibition.” Journal of Proteome Research 6 (11): 4489-4497. https://doi.org/10.1021/pr070068e.

Zhang, Q., W. J. Qian, T. V. Knyushko, T. R. W. Clauss, S. O. Purvine, R. J. Moore, C. A. Sacksteder, M. H. Chin, D. J. Smith, D. G. Camp Ii, D. J. Bigelow, and R. D. Smith. 2007. “A Method for Selective Enrichment and Analysis of Nitrotyrosine-Containing Peptides in Complex Proteome Samples.” Journal of Proteome Research 6 (6): 2257-2268. https://doi.org/10.1021/pr0606934.

2006

Adkins, J. N., H. M. Mottaz, A. D. Norbeck, J. K. Gustin, J. Rue, T. R. W. Clauss, S. O. Purvine, K. D. Rodland, F. Heffron, and R. D. Smith. 2006. “Analysis of the Salmonella typhimurium Proteome through Environmental Response toward Infectious Conditions.” Molecular and Cellular Proteomics 5 (8): 1450-1461. https://doi.org/10.1074/mcp.M600139-MCP200.

Liu, T., W. J. Qian, H. M. Mottaz, M. A. Gritsenko, A. D. Norbeck, R. J. Moore, S. O. Purvine, D. G. Camp Ii, and R. D. Smith. 2006. “Evaluation of Multiprotein Immunoaffinity Subtraction for Plasma Proteomics and Candidate Biomaker Discovery Using Mass Spectrometry.” Molecular and Cellular Proteomics 5 (11): 2167-2174. https://doi.org/10.1074/mcp.T600039-MCP200.

Liu, T., W. J. Qiant, M. A. Gritsenko, W. Xiao, L. L. Moldawer, A. Kaushal, M. E. Monroe, S. M. Varnum, R. J. Moore, S. O. Purvine, R. V. Maier, R. W. Davis, R. G. Tompkins, D. G. Camp II, R. D. Smith, H. V. Baker, P. E. Bankey, T. R. Billiar, B. H. Brownstein, S. E. Calvano, C. Campbell-Finnerty, G. Casella, I. H. Chaudry, M. Choudhry, J. P. Cobb, A. De, C. Elson, B. Freeman, R. L. Gamelli, N. S. Gibran, B. G. Harbrecht, D. L. Hayden, D. N. Herndon, J. W. Horton, W. Hubbard, J. L. Hunt, J. L. Johnson, M. B. Klein, J. A. Lederer, T. Logvinenko, S. F. Lowry, J. A. Mannick, P. H. Mason, G. P. McDonald-Smith, B. McKinley, C. L. Miller-Graziano, M. Mindrinos, J. P. Minei, E. E. Moore, F. A. Moore, A. B. Nathens, G. E. O'Keefe, L. G. Rahme, D. G. Remick, D. Schoenfeld, M. B. Shapiro, M. Schwacha, G. M. Silver, J. Storey, M. Toner, H. Shaw Warren, and M. A. West. 2006. “High Dynamic Range Characterization of the Trauma Patient Plasma Proteome.” Molecular and Cellular Proteomics 5 (10): 1899-1913. https://doi.org/10.1074/mcp.M600068-MCP200.

Sacksteder, C. A., J. E. Whittier, Y. Xiong, J. Li, N. A. Galeva, M. E. Jacoby, S. O. Purvine, T. D. Williams, M. C. Rechsteiner, D. J. Bigelow, and T. C. Squier. 2006. “Tertiary Structural Rearrangements Upon Oxidation of Methionine 145 in Calmodulin Promotes Targeted Proteasomal Degradation.” Biophysical Journal 91 (4): 1480-1493. https://doi.org/10.1529/biophysj.106.086033.

Shi, L., J. N. Adkins, J. R. Coleman, A. A. Schepmoes, A. Dohnkova, H. M. Mottaz, A. D. Norbeck, S. O. Purvine, N. P. Manes, H. S. Smallwood, H. Wang, J. Forbes, P. Gros, S. Uzzau, K. D. Rodland, F. Heffron, R. D. Smith, and T. C. Squier. 2006. “Proteomic Analysis of Salmonella enterica Serovar Typhimurium Isolated from Raw 264.7 Macrophages: Identification of a Novel Protein That Contributes to the Replication of Serovar Typhimurium inside Macrophages.” Journal of Biological Chemistry 281 (39): 29131-29140. https://doi.org/10.1074/jbc.M604640200.

2005

Kolker, E., A. F. Picone, M. Y. Galperin, M. F. Romine, R. Higdon, K. S. Makarova, N. Kolker, G. A. Anderson, X. Qiu, K. J. Auberry, G. Babnigg, A. S. Beliaev, P. Edlefsen, D. A. Elias, Y. A. Gorby, T. Holzman, J. A. Klappenbach, K. T. Konstantinidis, M. L. Land, M. S. Lipton, L. A. McCue, M. Monroe, L. Pasa-Tolic, G. Pinchuk, S. Purvine, M. H. Serres, S. Tsapin, B. A. Zakrajsek, W. Zhu, J. Zhou, F. W. Larimer, C. E. Lawrence, M. Riley, F. R. Collart, J. R. Yates Iii, R. D. Smith, C. S. Giometti, K. H. Nealson, J. K. Fredrickson, and J. M. Tiedje. 2005. “Global Profiling of Shewanella oneidensis MR-1: Expression of Hypothetical Genes and Improved Functional Annotations.” Proceedings of the National Academy of Sciences of the United States of America 102 (6): 2099-2104. https://doi.org/10.1073/pnas.0409111102.

2004

Kolker, E., K. S. Makarova, S. Shabalina, A. F. Picone, S. Purvine, T. Holzman, T. Cherny, D. Armbruster, R. S. Munson Jr, G. Kolesov, D. Frishman, and M. Y. Galperin. 2004. “Identification and Functional Analysis of 'Hypothetical' Genes Expressed in Haemophilus influenzae.” Nucleic Acids Research 32 (8): 2353-2361. https://doi.org/10.1093/nar/gkh555.

Purvine, S., N. Kolker, and E. Kolker. 2004. “Spectral Quality Assessment for High-Throughput Tandem Mass Spectrometry Proteomics.” OMICS A Journal of Integrative Biology 8 (3): 255-265. https://doi.org/10.1089/omi.2004.8.255.

Purvine, S., A. F. Picone, and E. Kolker. 2004. “Standard Mixtures for Proteome Studies.” OMICS A Journal of Integrative Biology 8 (1): 79-92. https://doi.org/10.1089/153623104773547507.

Raghunathan, A., N. D. Price, M. Y. Galperin, K. S. Makarova, S. Purvine, A. F. Picone, T. Cherny, T. Xie, T. J. Reilly, R. Munson Jr, R. E. Tyler, B. J. Akerley, A. L. Smith, B. O. Palsson, and E. Kolker. 2004. “In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.” OMICS A Journal of Integrative Biology 8 (1): 25-41. https://doi.org/10.1089/153623104773547471.

2003

Guina, T., S. O. Purvine, E. C. Yi, J. Eng, D. R. Goodlett, R. Aebersold, and S. I. Miller. 2003. “Quantitative Proteomic Analysis Indicates Increased Synthesis of a Quinolone by Pseudomonas aeruginosa Isolates from Cystic Fibrosis Airways.” Proceedings of the National Academy of Sciences of the United States of America 100 (5): 2771-2776. https://doi.org/10.1073/pnas.0435846100.

Guina, T., M. Wu, S. I. Miller, S. O. Purvine, E. C. Yi, J. Eng, D. R. Goodlett, R. Aebersold, R. K. Ernst, and K. A. Lee. 2003. “Proteomic Analysis of Pseudomonas aeruginosa Grown under Magnesium Limitation.” Journal of the American Society for Mass Spectrometry 14 (7): 742-751. https://doi.org/10.1016/S1044-0305(03)00133-8.

Kolker, E., S. Purvine, M. Y. Galperin, S. Stolyar, D. R. Goodlett, A. I. Nesvizhskii, A. Keller, T. Xie, J. K. Eng, E. Yi, L. Hood, A. F. Picone, T. Cherny, B. C. Tjaden, A. F. Siegel, T. J. Reilly, K. S. Makarova, B. O. Palsson, and A. L. Smith. 2003. “Initial Proteome Analysis of Model Microorganism Haemophilus influenzae Strain Rd KW20.” Journal of Bacteriology 185 (15): 4593-4602. https://doi.org/10.1128/JB.185.15.4593-4602.2003.

Purvine, S., J. T. Eppel, E. C. Yi, and D. R. Goodlett. 2003. “Shotgun Collision-Induced Dissociation of Peptides Using a Time of Flight Mass Analyzer.” Proteomics 3 (6): 847-850. https://doi.org/10.1002/pmic.200300362.

Ranish, J. A., E. C. Yi, D. M. Leslie, S. O. Purvine, D. R. Goodlett, J. Eng, and R. Aebersold. 2003. “The Study of Macromolecular Complexes by Quantitative Proteomics.” Nature Genetics 33 (3): 349-355. https://doi.org/10.1038/ng1101.

2002

Keller, A., S. Purvine, A. I. Nesvizhskii, S. Stolyar, D. R. Goodlett, and E. Kolker. 2002. “Experimental Protein Mixture for Validating Tandem Mass Spectral Analysis.” OMICS A Journal of Integrative Biology 6 (2): 207-212. https://doi.org/10.1089/153623102760092805.

Kolker, E., S. Purvine, A. Picone, T. Cherny, B. J. Akerley, R. S. Munson Jr, B. O. Palsson, D. A. Daines, and A. L. Smith. 2002. “H. influenzae Consortium: Integrative Study of H. influenzae-Human Interactions.” OMICS A Journal of Integrative Biology 6 (4): 341-348. https://doi.org/10.1089/153623102321112764.

Yi, E. C., M. Marelli, H. Lee, S. O. Purvine, R. Aebersold, J. D. Aitchison, and D. R. Goodlett. 2002. “Approaching Complete Peroxisome Characterization by Gas-Phase Fractionation.” Electrophoresis 23 (18): 3205-3216. https://doi.org/10.1002/1522-2683(200209)23:18<3205::AID-ELPS3205>3.0.CO;2-Y.

2001

Goodlett, D. R., A. Keller, J. D. Watts, R. Newitt, E. C. Yi, S. Purvine, J. K. Eng, P. V. Haller, R. Aebersold, and E. Kolker. 2001. “Differential Stable Isotope Labeling of Peptides for Quantitation and De Novo Sequence Derivation.” Rapid Communications in Mass Spectrometry 15 (14): 1214-1221. https://doi.org/10.1002/rcm.362.