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Fundamental and Computational Sciences Directorate

Staff information

Samuel

Samuel Purvine

Biosystms Dynamics & Simula
Computational Scientist

Biography

Samuel Purvine is a member of the Scientific Resources division at EMSL. He primarily supports the Proteomics Research and Information Storage and Management (PRISM) system as part of the Proteomics Analysis Support Team (PAST). He has been involved with PAST since 2004. This effort has primarily encompassed helping Proteomics Capability users gain access to their data through user education of proteomics, as well as to EMSL’s analysis pipeline, providing users with data packages that often are the end result of a proteomics experiment. Additionally, he has become technical lead or point-of-contact for numerous EMSL user projects that use the Proteomics Capability.

Education and Credentials

  • B.S., Biochemistry, University of Washington, Seattle, Washington, 2000

PNNL Publications

2018

  • 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." The Plant Journal 93, no. 3:545-565. PNNL-SA-135188. doi:10.1111/tpj.13788
  • Menachery V.D., A. Schafer, K.E. Burnum-Johnson, H.D. Mitchell, A.J. Eisfeld-Fenney, K.B. Walters, and C.D. Nicora, et al. 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, no. 5:E1012-E1021. PNNL-SA-126254. doi:10.1073/pnas.1706928115

2017

  • Boenisch M.J., K.L. Broz, S.O. Purvine, W.B. Chrisler, C.D. Nicora, L. Connolly, and M. Freitag, et al. 2017. "Structural reorganization of the fungal endoplasmic reticulum upon induction of mycotoxin biosynthesis." Scientific Reports 7. PNNL-SA-125650. doi:10.1038/srep44296
  • Booker A.E., M. Borton, R. Daly, S. Welch, C.D. Nicora, D.W. Hoyt, and T. Wilson, et al. 2017. "Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales." mSphere 2. PNNL-SA-128950. doi:10.1128/mSphereDirect.00257-17
  • Haitjema C., S.P. Gilmore, J.K. Henske, K.V. Solomon, R.D. Groot, A. Kuo, and S.J. Mondo, et al. 2017. "A Parts List for Fungal Cellulosomes Revealed by Comparative Genomics." Nature Microbiology 2. PNNL-SA-120227. doi:10.1038/nmicrobiol.2017.87
  • Handakumbura P., K.K. Hixson, S.O. Purvine, G.C. Jansson, and L. Pasa Tolic. 2017. "Plant iTRAQ-based proteomics." Current Protocols in Plant Biology 2, no. 2:158-172. PNNL-SA-123355. doi:10.1002/cppb.20052
  • Kerkhoven E.J., Y. Kim, S. Wei, C.D. Nicora, T.L. Fillmore, S.O. Purvine, and B.M. Webb-Robertson, et al. 2017. "Leucine biosynthesis is involved in regulating high lipid accumulation in Yarrowia lipolytica." mBio 8, no. 3:Article No. e00857-17. PNNL-SA-122829. doi:10.1128/mBio.00857-17
  • Kowalczyk J.E., C. Khosravi, S.O. Purvine, A. Dohnalkova, W.B. Chrisler, G. Orr, and E.W. Robinson, et al. 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, no. 11:4587-4598. PNNL-SA-134692. doi:10.1111/1462-2920.13923
  • Ledee D.R., M.A. Kang, M. Kajimoto, S.O. Purvine, H.M. 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, no. 1:H125-H137. PNNL-SA-128530. doi:10.1152/ajpheart.00842.2016
  • Solden L., D.W. Hoyt, W.B. Collins, J.E. Plank, R. Daly, E. Hildebrand, and T.J. Beavers, et al. 2017. "New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11." The ISME Journal 11, no. 3:691-703. PNNL-SA-115562. doi:10.1038/ismej.2016.150
  • Stoddard E.G., B.J. Killinger, R.N. Nair, N.C. Sadler, R.F. Volk, S.O. Purvine, and A.K. Shukla, et al. 2017. "Activity-Based Probes for Isoenzyme- and Site-Specific Functional Characterization of Glutathione S- Transferases." Journal of the American Chemical Society 139, no. 45:16032-16035. PNNL-SA-127421. doi:10.1021/jacs.7b07378
  • Warshan D., J.L. Espinoza, R. Stuart, A.R. Richter, S. Kim, N. Shapiro, and T. Woyke, et al. 2017. "Feathermoss and epiphytic Nostoc cooperate differently: expanding the spectrum of plant-cyanobacteria symbiosis." The ISME Journal 11. PNNL-SA-127738. doi:10.1038/ismej.2017.134
  • Zeiner C.A., S.O. Purvine, E.M. Zink, L. Pasa Tolic, D.L. Chaput, S. Wu, and C.M. Santelli, et al. 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 : FG & B 106. PNNL-SA-122328. doi: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, and M.A. Gritsenko, et al. 2016. "Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Molecular and Cellular Proteomics 15, no. 12:3694-3705. PNNL-SA-118308. doi:10.1074/mcp.M116.061143
  • Pomraning K.R., Y. Kim, C.D. Nicora, R.K. Chu, E.L. Bredeweg, S.O. Purvine, and D. Hu, et al. 2016. "Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica." BMC Genomics 17, no. 138:1-18. PNNL-SA-112784. doi:10.1186/s12864-016-2471-2
  • Salvachua D., R. Katahira, N.S. Cleveland, P. Khanna, M.G. Resch, B.A. Black, and S.O. Purvine, et al. 2016. "Lignin depolymerization by fungal secretomes and a microbial sink." Green Chemistry 18, no. 22:6046-6062. PNNL-SA-120640. doi:10.1039/C6GC01531J
  • Solomon K.V., C. Haitjema, J.K. Henske, S.P. Gilmore, D. Borges-Rivera, A. Lipzen, and H.M. Brewer, et al. 2016. "Early-branching Gut Fungi Possess A Large, And Comprehensive Array Of Biomass-Degrading Enzymes." Science 351, no. 6278:1192-1195. PNNL-SA-115073. doi:10.1126/science.aad1431
  • Tisoncik-Go J., D.J. Gasper, J.E. Kyle, A.J. Eisfeld, C. Selinger, M. Hatta, and J. Morrison, et al. 2016. "Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism." Cell Host & Microbe 19, no. 2:254-66. PNWD-SA-10483. doi:10.1016/j.chom.2016.01.002
  • van Baren M.J., C. Bachy, E. Reistetter, S.O. Purvine, J. Grimwood, S. Sudek, and H. Yu, et al. 2016. "Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants." BMC Genomics 17. PNNL-SA-114561. doi:10.1186/s12864-016-2585-6
  • Waltman P., J. Guo, E. Reistetter, S.O. Purvine, C. Ansong, M.J. van Baren, and C. Wong, et al. 2016. "Identifying Aspects of the Post-transcriptional Program Governing the Proteome of the Green Algal Micromonas pusilla." PLoS One 11, no. 7:Article No. e0155839. PNNL-SA-115265. doi:10.1371/journal.pone.0155839
  • Zeiner C.A., S.O. Purvine, E.M. Zink, L. Pasa Tolic, D.L. Chaput, S. Haridas, and S. Wu, et al. 2016. "Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi." PLoS One 11, no. 7:Article No. e0157844. PNNL-SA-121069. doi:10.1371/journal.pone.0157844

2015

  • Aylward F.O., L. Khadempour, D. Tremmel, B.R. McDonald, C.D. Nicora, S. Wu, and R.J. Moore, et al. 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, no. 8:e0134752. PNNL-SA-108498. doi:10.1371/journal.pone.0134752
  • Kebaabetswe L.P., A.K. Haick, M.A. Gritsenko, T.L. Fillmore, R.K. Chu, S.O. Purvine, and B.M. Webb-Robertson, et al. 2015. "Proteomic Analysis Reveals Down-Regulation of Surfactant Protein B in Murine Type II Pneumocytes Infected with Influenza A Virus." Virology 438. PNWD-SA-10439. doi:10.1016/j.virol.2015.03.045
  • Lu J., K. Chughtai, S.O. Purvine, Z.M. Bhujwalla, V. Raman, L. Pasa-Tolic, and R.M. Heeren, et al. 2015. "MALDI-mass spectrometric imaging revealing hypoxia-driven lipids and proteins in a breast tumor model." Analytical Chemistry 87, no. 12:5947-5956. PNNL-SA-110776. doi:10.1021/ac504503x
  • 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

2014

  • Aevermann B., B.E. Pickett, S. Kumar, E.B. Klem, S. Agnihothram, P.S. Askovich, and A. Bankhead, et al. 2014. "A Comprehensive Collection of Systems Biology Data Characterizing the Host Response to Viral Infection." Scientific Data 1. PNNL-SA-101269. doi:10.1038/sdata.2014.33
  • Mohimani H., R. Kersten, W. Liu, M. Wang, S.O. Purvine, S. Wu, and H.M. Brewer, et al. 2014. "Automated genome mining of ribosomal peptide natural products." ACS Chemical Biology 9, no. 7:1545-1551. PNNL-SA-99212. doi:10.1021/cb500199h
  • Mudenda L., S. Aguilar Pierle, J.E. Turse, G.A. Scoles, S.O. Purvine, C.D. Nicora, and T.R. Clauss, et al. 2014. "Proteomics informed by transcriptomics identifies novel secreted proteins in Dermacentor andersoni saliva." International Journal for Parasitology 44, no. 13:1029-1037. PNNL-SA-105510. doi:10.1016/j.ijpara.2014.07.003
  • 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
  • Su D., M.J. Gaffrey, J. Guo, K.E. Hatchell, R.K. Chu, T.R. Clauss, and J.T. Aldrich, et al. 2014. "Proteomic Identification and Quantification of S-glutathionylation in Mouse Macrophages Using Resin-Assisted Enrichment and Isobaric Labeling." Free Radical Biology & Medicine 67. PNNL-SA-96702. doi:10.1016/j.freeradbiomed.2013.12.004

2013

  • Anderson L.N., D.E. Culley, B.A. Hofstad, L.M. Chauvigne-Hines, E.M. Zink, S.O. Purvine, and R.D. Smith, et al. 2013. "Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30." Molecular Biosystems 9, no. 12:2992-3000. PNNL-SA-97265. doi:10.1039/c3mb70333a
  • 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
  • Aylward F.O., K.E. Burnum-Johnson, S.G. Tringe, C. Teiling, D. Tremmel, J. Moeller, and J.J. Scott, et al. 2013. "Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens." Applied and Environmental Microbiology 79, no. 12:3770-3778. PNNL-SA-92750. doi:10.1128/AEM.03833-12
  • Kaiser B., J. Li, J.A. Sanford, Y. Kim, S.R. Kronewitter, M.B. Jones, and C. Peterson, et al. 2013. "A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection." PLoS One 8, no. 6:Article No. e67155. PNNL-SA-85342. doi:10.1371/journal.pone.0067155
  • Nicora C.D., B.J. Anderson, S.J. Callister, A.D. Norbeck, S.O. Purvine, J.K. Jansson, and O.U. Mason, et al. 2013. "Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies." Proteomics 13, no. 18-19:2776-2785. PNNL-SA-92783. doi:10.1002/pmic.201300003
  • Wang D., S. Dasari, M.C. Chambers, J.D. Holman, K. Chen, D. Liebler, and D.J. Orton, et al. 2013. "Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates." Genomics, Proteomics & Bioinformatics 11, no. 2:86-95. PNNL-SA-98549. doi:10.1016/j.gpb.2012.11.004

2012

  • Alfaro J.F., C. Gong, M.E. Monroe, J.T. Aldrich, T.R. Clauss, S.O. Purvine, and Z. Wang, et al. 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, no. 19:7280-7285. PNNL-SA-84997. doi:10.1073/pnas.1200425109
  • Aylward F.O., K.E. Burnum, J.J. Scott, G. Suen, S.G. Tringe, S.M. Adams, and K.W. Barry, et al. 2012. "Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens." The ISME Journal 6, no. 9:1688-1701. PNNL-SA-82393. doi:10.1038/ismej.2012.10
  • 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
  • Shen Y., N. Tolic, 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, no. 2:668-677. PNNL-SA-79420.

2011

  • 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
  • Burnum K.E., S.J. Callister, C.D. Nicora, S.O. Purvine, P. Hugenholtz, F. Warnecke, and R.H. Scheffrahn, et al. 2011. "Proteome Insights into the Symbiotic Relationship Between a Captive Colony of Nasutitermes corniger and its Hindgut Microbiome." The ISME Journal 5, no. 1:161-164. PNNL-SA-68831. doi:10.1038/ismej.2010.97
  • Chundawat S.P., 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, no. 10:4365-4372. PNNL-SA-78193. doi:10.1021/pr101234z
  • Dresang L.R., J.R. Teuton, H. Feng, J.M. Jacobs, D.G. Camp, S.O. Purvine, and M.A. Gritsenko, et al. 2011. "Coupled Transcriptome and Proteome Analysis of Human Lymphotropic Tumor Viruses: Insights on the Detection and Discovery of Viral Genes." BMC Genomics 12. PNNL-SA-84775. doi: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 & Cellular Proteomics. MCP 10, no. 8:Art. No. 10: M110.004853. PNNL-SA-80519. doi:10.1074/mcp.M110.004853
  • Shen Y., N. Tolic, F. Xie, R. Zhao, S.O. Purvine, A.A. Schepmoes, and R.J. Moore, et al. 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, no. 9:3929-3943. PNNL-SA-75441. doi:10.1021/pr200052c
  • Shen Y., N. Tolic, S.O. Purvine, and R.D. Smith. 2011. "Improving CID, HCD, and ETD FT MS/MS degradome-peptidome identifications using high accuracy mass information." Journal of Proteome Research. PNNL-SA-81060. doi:10.1021/pr200597j
  • Stanley J.R., J.N. Adkins, G.W. Slysz, M.E. Monroe, S.O. Purvine, Y.V. Karpievitch, and G.A. Anderson, et al. 2011. "A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics." Analytical Chemistry 83, no. 16:6135-6140. PNNL-SA-72379. doi:10.1021/ac2009806
  • Wang Y., F. Yang, Y. Fu, X. Huang, W. Wang, X. Jiang, and M.A. Gritsenko, et al. 2011. "Spatial Phosphoprotein Profiling Reveals a Compartmentalized Extracellular Signal-regulated Kinase Switch Governing Neurite Growth and Retraction." Journal of Biological Chemistry 286, no. 20:18190-18201. PNNL-SA-79165.
  • Zhang H., F. Yang, W. Qian, R.N. Brown, Y. Wang, E.D. Merkley, and J.H. Park, et al. 2011. "Identification of c-Type Heme-Containing Peptides Using Non-Activated Immobilized Metal Affinity Cchromatography Resin Enrichment and Higher-Energy Collisional Dissociation." Analytical Chemistry 83, no. 19:7260-7268. PNNL-SA-77198. doi:10.1021/ac2000829

2010

  • Ham B.M., H. Jayachandran, F. Yang, N. Jaitly, A.D. Polpitiya, M.E. Monroe, and L. Wang, et al. 2010. "Novel Ser/Thr Protein Phosphatase 5 (PP5) Regulated Targets during DNA Damage Identified by Proteomics Analysis." Journal of Proteome Research 9, no. 2:945-953. PNNL-SA-69020. doi:10.1021/pr9008207
  • Jung H., S.O. Purvine, H. Kim, V.A. Petyuk, S. Hyung, M.E. Monroe, and D. Mun, et al. 2010. "Integrated Post-Experiment Monoisotopic Mass Refinement: An Integrated Approach to Accurately Assign Monoisotopic Precursor Masses to Tandem Mass Spectrometric Data." Analytical Chemistry 82, no. 20:8510-8518. PNNL-SA-74157. doi:10.1021/ac101388b
  • Lewis N.E., K.K. Hixson, T.M. Conrad, J.A. Lerman, P. Charusanti, P. Charusanti, and A.D. Polpitiya, et al. 2010. "Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models." Molecular Systems Biology 6. PNNL-SA-68816. doi:10.1038/msb.2010.47
  • Schutzer S.E., T. Liu, B. Natelson, T.E. Angel, A.A. Schepmoes, S.O. Purvine, and K.K. Hixson, et al. 2010. "Establishing the Proteome of Normal Human Cerebrospinal Fluid." PLoS One 5, no. 6:e10980-. PNWD-SA-8931. doi:10.1371/journal.pone.0010980
  • Shen Y., N. Tolic, 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, no. 8:4053-4060. PNNL-SA-73098.
  • Shen Y., N. Tolic, T. Liu, R. Zhao, B.O. Petritis, M.A. Gritsenko, and D.G. Camp, et al. 2010. "Blood Peptidome-Degradome Profile of Breast Cancer." PLoS One 5, no. 10:Article No.: e13133. PNNL-SA-70095. doi:10.1371/journal.pone.0013133
  • Shen Y., T. Liu, N. Tolic, B.O. Petritis, R. Zhao, R.J. Moore, and S.O. Purvine, et al. 2010. "A strategy for degradomic-peptidomic analysis of the human blood plasma." Journal of Proteome Research 9, no. 5:2339-2346. PNNL-SA-71375. doi:10.1021/pr901083m
  • Yang F., K.M. Waters, J.H. Miller, M.A. Gritsenko, R. Zhao, X. Du, and E.A. Livesay, et al. 2010. "Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation." PLoS One 5, no. 11:e14152. PNNL-SA-73768. doi:10.1371/journal.pone.0014152
  • Zhang H., R.N. Brown, W. Qian, M.E. Monroe, S.O. Purvine, R.J. Moore, and M.A. Gritsenko, et al. 2010. "Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling." Journal of Proteome Research 9, no. 5:2160-2169. PNNL-SA-67314.

2009

  • Kim W., M.W. Silby, S.O. Purvine, J.S. Nicoll, K.K. Hixson, M.E. Monroe, and C.D. Nicora, et al. 2009. "Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1." PLoS One 4, no. 12:Article Number: e8455. PNNL-SA-68830. doi:10.1371/journal.pone.0008455
  • Petyuk V.A., A.M. Mayampurath, M.E. Monroe, A.D. Polpitiya, S.O. Purvine, G.A. Anderson, and D.G. Camp, et al. 2009. "DtaRefinery: a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra datasets." Molecular & Cellular Proteomics. MCP 9.3. PNNL-SA-62317. doi:10.1074/mcp.M900217-MCP200
  • Sharp J.L., J.J. Borkowski, D.A. Schmoyer, D.S. Daly, S.O. Purvine, W.R. Cannon, and G.B. Hurst. 2009. "Statistically Appraising Process Quality of Affinity Isolation Experiments." Computational Statistics & Data Analysis 53, no. 5:1720-1726 (special issue). PNNL-SA-59018.
  • Springer D.L., J.H. Miller, S.L. Spinelli, L. Pasa-Tolic, S.O. Purvine, D.S. Daly, and R.C. Zangar, et al. 2009. "Platelet Proteome Changes Associated with Diabetes and During Platelet Storage for Transfusion." Journal of Proteome Research 8, no. 5:2261-2272. PNWD-SA-8399.
  • Yang F., S. Wu, D.L. Stenoien, R. Zhao, M.E. Monroe, M.A. Gritsenko, and S.O. Purvine, et al. 2009. "Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ-labeled phosphopeptides." Analytical Chemistry 81, no. 10:4137-4143. PNNL-SA-63701. doi:10.1021/ac802605m

2008

  • Ansong C., S.O. Purvine, J.N. Adkins, M.S. Lipton, and R.D. Smith. 2008. "Proteogenomics: the needs and roles to be filled by proteomics in genome annotation." Briefings in Functional Genomics and Proteomics 7, no. 1:50-62. PNNL-SA-57607.
  • Daly D.S., K.K. Anderson, E.A. Panisko, S.O. Purvine, R. Fang, M.E. Monroe, and S.E. Baker. 2008. "A mixed-effects Statistical Model for Comparative LC-MS Proteomics Studies." Journal of Proteome Research 7, no. 3:1209-1217. PNNL-SA-57824. doi:10.1021/pr070441i
  • Ding S., Y. Wang, J.M. Jacobs, W. Qian, F. Yang, A.V. Tolmachev, and X. Du, et al. 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, no. 10:4215-24. PNNL-SA-52241. doi:10.1021/pr7007785
  • Du X., F. Yang, N.P. Manes, D.L. Stenoien, M.E. Monroe, J.N. Adkins, and D.J. States, et al. 2008. "Linear Discriminant Analysis - Based Estimation of the False Discovery Rate for Phosphopeptide Identifications." Journal of Proteome Research 7, no. 6:2195-2203. PNNL-SA-56421. doi:10.1021/pr070510t
  • Ham B.M., F. Yang, H. Jayachandran, N. Jaitly, M.E. Monroe, M.A. Gritsenko, and E.A. Livesay, et al. 2008. "The Influence of Sample Preparation and Replicate Analyses on HeLa Cell Phosphoproteome Coverage." Journal of Proteome Research 7, no. 6:2215-2221. PNWD-SA-7904.
  • Mathivanan S., M. Ahmed, M. Ahmed, N.G. Ahn, H. Alexandre, H. Alexandre, and R. Amanchy, et al. 2008. "Human Proteinpedia enables sharing of human protein data." Nature Biotechnology 26, no. 2:164-167. PNNL-SA-61184.
  • 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, no. 7:1021-1023. PNNL-SA-56275. doi:10.1093/bioinformatics/btn063
  • Shen Y., K.K. Hixson, N. Tolic, 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, no. 15:5819-5828. PNNL-SA-58041. doi:10.1021/ac800077w
  • Shen Y., N. Tolic, 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, no. 20:7742-7754. PNNL-SA-60782. doi:10.1021/ac801123p
  • Shen Y., N. Tolic, K.K. Hixson, S.O. Purvine, L. Pasa-Tolic, W. Qian, and J.N. Adkins, et al. 2008. "Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags." Analytical Chemistry 80, no. 6:1871-82. PNNL-SA-56012. doi:10.1021/ac702328x
  • Tolmachev A.V., M.E. Monroe, S.O. Purvine, R.J. Moore, N. Jaitly, J.N. Adkins, and G.A. Anderson, et al. 2008. "Characterization of Strategies for Obtaining Confident Identifications in Bottom-Up Proteomics Measurements Using Hybrid FTMS instruments." Analytical Chemistry 80, no. 22:8514-8525. PNNL-SA-61186. doi:10.1021/ac801376g
  • Zhang Q., A.A. Schepmoes, J.W. Brock, S. Wu, R.J. Moore, S.O. Purvine, and J. Baynes, et al. 2008. "Improved Methods for the Enrichment and Analysis of Glycated Peptides." Analytical Chemistry 80, no. 24:9822-9829. PNNL-SA-61746. doi:10.1021/ac801704j

2007

  • Manes N.P., J.K. Gustin, J. Rue, H.M. Mottaz, S.O. Purvine, A.D. Norbeck, and M.E. Monroe, et al. 2007. "Targeted Protein Degradation by Salmonella under Phagosome-Mimicking Culture Conditions Investigated Using Comparative Peptidomics." Molecular & Cellular Proteomics. MCP 6, no. 4:717-727. PNNL-SA-50929. doi:10.1074/mcp.M600282-MCP200
  • Yang F., N. Jaitly, H. Jayachandran, Q. Lou, M.E. Monroe, X. Du, and M.A. Gritsenko, et al. 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, no. 11:4489-4497. PNNL-SA-52332. doi:10.1021/pr070068e
  • Zhang Q., W. Qian, T.V. Knyushko, T.R. Clauss, S.O. Purvine, R.J. Moore, and C.A. Sacksteder, et al. 2007. "A Method for Selective Enrichment and Analysis of Nitrotyrosine-Containing Peptides in Complex Proteome Samples." Journal of Proteome Research 6, no. 6:2257-2268. PNNL-SA-53248. doi:10.1021/pr0606934

2006

  • Adkins J.N., H.M. Mottaz, A.D. Norbeck, J.K. Gustin, J. Rue, T.R. Clauss, and S.O. Purvine, et al. 2006. "Analysis of the Salmonella typhimurium Proteome through Environmental Response toward Infectious Conditions." Molecular & Cellular Proteomics. MCP 5, no. 8:1450-1461. PNNL-SA-46556. doi:10.1074/mcp.M600139-MCP200
  • Liu T., W. Qian, H.M. Mottaz, M.A. Gritsenko, A.D. Norbeck, R.J. Moore, and S.O. Purvine, et al. 2006. "Evaluation of Multi-Protein Immunoaffinity Subtraction for Plasma Proteomics and Candidate Biomarker Discovery Using Mass Spectrometry." Molecular & Cellular Proteomics. MCP 5, no. 11:2167-2174. PNWD-SA-7363.
  • Liu T., W. Qian, M.A. Gritsenko, W. Xiao, L.L. Moldawer, A. Kaushal, and M.E. Monroe, et al. 2006. "High Dynamic Range Characterization of the Trauma Patient Plasma Proteome." Molecular & Cellular Proteomics. MCP 5, no. 10:1899-1913. PNWD-SA-7271. doi:10.1074/mcp.M600068-MCP200
  • Sacksteder C.A., J.E. Whittier, Y. Xiong, J. Li, N.A. Galeva, M.E. Jacoby, and S.O. Purvine, et al. 2006. "Tertiary Structural Rearrangements upon Oxidation of Methionine145 in Calmodulin Promotes Targeted Proteasomal Degradation." Biophysical Journal 91, no. 4:1480-1493. PNWD-SA-6773.
  • Shi L., J.N. Adkins, J.R. Coleman, A.A. Schepmoes, A. Dohnalkova, H.M. Mottaz, and A.D. Norbeck, et al. 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. PNNL-SA-51416. doi:10.1074/jbc.M604640200

2005

  • Kolker E., A.F. Picone, M.Y. Galperin, M.F. Romine, R. Higdon, K.S. Makarova, and N. Kolker, et al. 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, no. 6:2099-2104. PNNL-SA-43139.

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