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Fundamental and Computational Sciences Directorate

Staff information

Samuel Purvine

Biosystms Dynamics & Simula

PNNL Publications


  • Handakumbura P, KK Hixson, SO Purvine, GC Jansson, and L Pasa Tolic. 2017. "Plant iTRAQ-based proteomics." Current Protocols in Plant Biology 2(2):158-172.  doi:10.1002/cppb.20052
  • Boenisch MJ, KL Broz, SO Purvine, WB Chrisler, CD Nicora, L Connolly, M Freitag, SE Baker, and HC Kistler. 2017. "Structural reorganization of the fungal endoplasmic reticulum upon induction of mycotoxin biosynthesis." Scientific Reports 7:Article No. 44296.  doi:10.1038/srep44296
  • Booker AE, M Borton, R Daly, S Welch, CD Nicora, DW Hoyt, T Wilson, SO Purvine, R Wolfe, S Sharma, PJ Mouser, DR Cole, MS Lipton, KC Wrighton, and MJ Wilkins. 2017. "Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales." mSphere 2:Article No. e00257-17.  doi:10.1128/mSphereDirect.00257-17
  • Haitjema C, SP Gilmore, JK Henske, KV Solomon, RD Groot, A Kuo, SJ Mondo, A Salamov, KM LaButti, ZJ Zhao, J Chiniquy, KW Barry, HM Brewer, SO Purvine, AT Wright, M Hainaut, B Boxma, TA Van Alen, J Hackstein, B Henrissat, SE Baker, IV Grigoriev, and MA O'Malley. 2017. "A Parts List for Fungal Cellulosomes Revealed by Comparative Genomics." Nature Microbiology 2:Article No. 17087.  doi:10.1038/nmicrobiol.2017.87
  • Kerkhoven EJ, YM Kim, S Wei, CD Nicora, TL Fillmore, SO Purvine, BJM Webb-Robertson, RD Smith, SE Baker, TO Metz, and JB Nielsen. 2017. "Leucine biosynthesis is involved in regulating high lipid accumulation in Yarrowia lipolytica." mBio 8(3):Article No. e00857-17.  doi:10.1128/mBio.00857-17
  • Ledee DR, MA Kang, M Kajimoto, SO Purvine, HM Brewer, L Pasa Tolic, and MA 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.  doi:10.1152/ajpheart.00842.2016
  • Solden L, DW Hoyt, WB Collins, JE Plank, R Daly, E Hildebrand, TJ Beavers, R Wolfe, CD Nicora, SO Purvine, M Carstensen, MS Lipton, DE Spalinger, JL Firkins, BA Wolfe, and KC Wrighton. 2017. "New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11." The ISME Journal 11(3):691-703.  doi:10.1038/ismej.2016.150
  • Zeiner CA, SO Purvine, EM Zink, L Pasa Tolic, DL Chaput, S Wu, CM Santelli, and CM 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 : FG & B 106:61-75.  doi:10.1016/j.fgb.2017.06.004


  • Burnum-Johnson KE, S Nie, CP Casey, ME Monroe, DJ Orton, YM Ibrahim, MA Gritsenko, TRW Clauss, AK Shukla, RJ Moore, SO Purvine, T Shi, W Qian, T Liu, ES Baker, and RD 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.  doi:10.1074/mcp.M116.061143
  • Pomraning KR, YM Kim, CD Nicora, RK Chu, EL Bredeweg, SO Purvine, D Hu, TO Metz, and SE Baker. 2016. "Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica." BMC Genomics 17(138):1-18.  doi:10.1186/s12864-016-2471-2
  • Salvachua D, R Katahira, NS Cleveland, P Khanna, MG Resch, BA Black, SO Purvine, EM Zink, A Prieto, MJ Martinez, AT Martinez, BA Simmons, JM Gladden, and GT Beckham. 2016. "Lignin depolymerization by fungal secretomes and a microbial sink." Green Chemistry 18(22):6046-6062.  doi:10.1039/C6GC01531J
  • Solomon KV, C Haitjema, JK Henske, SP Gilmore, D Borges-Rivera, A Lipzen, HM Brewer, SO Purvine, AT Wright, MK Theodorou, IV Grigoriev, A Regev, D Thompson, and MA O'Malley. 2016. "Early-branching Gut Fungi Possess A Large, And Comprehensive Array Of Biomass-Degrading Enzymes." Science 351(6278):1192-1195.  doi:10.1126/science.aad1431
  • Tisoncik-Go J, DJ Gasper, JE Kyle, AJ Eisfeld, C Selinger, M Hatta, J Morrison, MJ Korth, EM Zink, YM Kim, AA Schepmoes, CD Nicora, SO Purvine, KK Weitz, X Peng, R Green, SC Tilton, BJM Webb-Robertson, KM Waters, TO Metz, RD Smith, Y Kawaoka, M Suresh, L Josset, and MG Katze. 2016. "Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism." Cell Host & Microbe 19(2):254-66.  doi:10.1016/j.chom.2016.01.002
  • van Baren MJ, C Bachy, E Reistetter, SO Purvine, J Grimwood, S Sudek, H Yu, C Poirier, TJ Deerinck, A Kuo, IV Grigoriev, CH Wong, RD Smith, SJ Callister, CL Wei, J Schmutz, and AZ Worden. 2016. "Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants." BMC Genomics 17:Article No. 267.  doi:10.1186/s12864-016-2585-6
  • Waltman P, J Guo, E Reistetter, SO Purvine, C Ansong, MJ van Baren, CH Wong, CL Wei, RD Smith, SJ Callister, J Stuart, and AZ Worden. 2016. "Identifying Aspects of the Post-transcriptional Program Governing the Proteome of the Green Algal Micromonas pusilla." PLoS One 11(7):Article No. e0155839.  doi:10.1371/journal.pone.0155839
  • Zeiner CA, SO Purvine, EM Zink, L Pasa Tolic, DL Chaput, S Haridas, S Wu, KM LaButti, IV Grigoriev, B Henrissat, CM Santelli, and CM Hansel. 2016. "Comparative Analysis of Secretome Profiles of Manganese(II)-Oxidizing Ascomycete Fungi." PLoS One 11(7):Article No. e0157844.  doi:10.1371/journal.pone.0157844


  • Aylward FO, L Khadempour, D Tremmel, BR McDonald, CD Nicora, S Wu, RJ Moore, DJ Orton, ME Monroe, PD Piehowski, SO Purvine, RD Smith, MS Lipton, KE Burnum-Johnson, and CR 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):e0134752.  doi:10.1371/journal.pone.0134752
  • Kebaabetswe LP, AK Haick, MA Gritsenko, TL Fillmore, RK Chu, SO Purvine, BJM Webb-Robertson, MM Matzke, RD Smith, KM Waters, TO Metz, and TA Miura. 2015. "Proteomic Analysis Reveals Down-Regulation of Surfactant Protein B in Murine Type II Pneumocytes Infected with Influenza A Virus." Virology 438:96-107.  doi:10.1016/j.virol.2015.03.045
  • Lu J, K Chughtai, SO Purvine, ZM Bhujwalla, V Raman, L Pasa-Tolic, RM 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.  doi:10.1021/ac504503x
  • Payne SH, ME Monroe, CC Overall, GR Kiebel, MG Degan, BC Gibbons, GM Fujimoto, SO Purvine, JN Adkins, MS Lipton, and RD Smith. 2015. "The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity." Scientific Data 2:Art. No. 150041.  doi:10.1038/sdata.2015.41


  • Slysz GW, LA Steinke, DM Ward, CG Klatt, TRW Clauss, SO Purvine, SH Payne, GA Anderson, RD Smith, and MS Lipton. 2014. "Automated data extraction from in situ protein stable isotope probing studies." Journal of Proteome Research 13(3):1200-1210.  doi:10.1021/pr400633j
  • Aevermann B, BE Pickett, S Kumar, EB Klem, S Agnihothram, PS Askovich, A Bankhead, M Bolles, V Carter, JH Chang, TRW Clauss, P Dash, AH Diercks, AJ Eisfeld, AL Ellis, S Fan, MT Ferris, L Gralinski, R Green, MA Gritsenko, M Hatta, RA Heegel, JM Jacobs, S Jeng, L Josset, SM Kaiser, S Kelly, GL Law, C Li, J Li, C Long, ML Luna, MM Matzke, JE McDermott, V Menachery, TO Metz, HD Mitchell, ME Monroe, G Navarro, G Neumann, RL Podyminogin, SO Purvine, C Rosenberger, CJ Sanders, AA Schepmoes, AK Shukla, A Sims, P Sova, VC Tam, N Tchitchek, PG Thomas, SC Tilton, AL Totura, J Wang, BJM Webb-Robertson, J Wen, JM Weiss, F Yang, B Yount, Q Zhang, SK Mcweeney, RD Smith, KM Waters, Y Kawaoka, R Baric, A Aderem, MG Katze, and RH Scheuermann. 2014. "A Comprehensive Collection of Systems Biology Data Characterizing the Host Response to Viral Infection." Scientific Data 1:Article No. 140033.  doi:10.1038/sdata.2014.33
  • Mohimani H, R Kersten, W Liu, M Wang, SO Purvine, S Wu, HM Brewer, L Pasa-Tolic, N Bandeira, BS Moore, PA Pevzner, and PC Dorrestein. 2014. "Automated genome mining of ribosomal peptide natural products." ACS Chemical Biology 9(7):1545-1551.  doi:10.1021/cb500199h
  • Mudenda L, S Aguilar Pierle, JE Turse, GA Scoles, SO Purvine, CD Nicora, TRW Clauss, MW Ueti, WC Brown, and KA Brayton. 2014. "Proteomics informed by transcriptomics identifies novel secreted proteins in Dermacentor andersoni saliva." International Journal for Parasitology 44(13):1029-1037.  doi:10.1016/j.ijpara.2014.07.003
  • Su D, MJ Gaffrey, J Guo, KE Hatchell, RK Chu, TRW Clauss, JT Aldrich, S Wu, SO Purvine, DG Camp, II, RD Smith, BD Thrall, and W Qian. 2014. "Proteomic Identification and Quantification of S-glutathionylation in Mouse Macrophages Using Resin-Assisted Enrichment and Isobaric Labeling." Free Radical Biology & Medicine 67:460-470.  doi:10.1016/j.freeradbiomed.2013.12.004


  • Nicora CD, BJ Anderson, SJ Callister, AD Norbeck, SO Purvine, JK Jansson, OU Mason, M David, DD Jurelevicius, RD Smith, and MS Lipton. 2013. "Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies ." Proteomics 13(18-19):2776-2785.  doi:10.1002/pmic.201300003
  • Anderson LN, DE Culley, BA Hofstad, LM Chauvigne-Hines, EM Zink, SO Purvine, RD Smith, SJ Callister, JM Magnuson, and AT 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.  doi:10.1039/c3mb70333a
  • Ansong C, C Ortega, SH Payne, DH Haft, LM Chauvigne-Hines, MP Lewis, AR Ollodart, SO Purvine, AK Shukla, S Fortuin, RD Smith, JN Adkins, C Grundner, and AT Wright. 2013. "Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis." Chemistry & Biology 20(1):123-133.  doi:10.1016/j.chembiol.2012.11.008
  • Aylward FO, KE Burnum-Johnson, SG Tringe, C Teiling, D Tremmel, J Moeller, JJ Scott, KW Barry, PD Piehowski, CD Nicora, S Malfatti, ME Monroe, SO Purvine, LA Goodwin, RD Smith, G Weinstock, N Gerardo, G Suen, MS Lipton, and CR 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.  doi:10.1128/AEM.03833-12
  • Kaiser BLD, J Li, JA Sanford, YM Kim, SR Kronewitter, MB Jones, C Peterson, SN Peterson, BC Frank, SO Purvine, JN Brown, TO Metz, RD Smith, F Heffron, and JN Adkins. 2013. "A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection." PLoS One 8(6):Article No. e67155.  doi:10.1371/journal.pone.0067155
  • Wang D, S Dasari, MC Chambers, JD Holman, K Chen, D Liebler, DJ Orton, SO Purvine, ME Monroe, CY Chung, KL Rose, and DL Tabb. 2013. "Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates." Genomics, Proteomics & Bioinformatics 11(2):86-95.  doi:10.1016/j.gpb.2012.11.004


  • Alfaro JF, CX Gong, ME Monroe, JT Aldrich, TRW Clauss, SO Purvine, Z Wang, DG Camp, II, J Shabanowitz, P Stanley, GW Hart, DF Hunt, F Yang, and RD 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.  doi:10.1073/pnas.1200425109
  • Aylward FO, KE Burnum, JJ Scott, G Suen, SG Tringe, SM Adams, KW Barry, CD Nicora, PD Piehowski, SO Purvine, GJ Starrett, LA Goodwin, RD Smith, MS Lipton, and CR Currie. 2012. "Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens." The ISME Journal 6(9):1688-1701.  doi:10.1038/ismej.2012.10
  • Rutledge AC, MB Jones, S Chauhan, SO Purvine, J Sanford, ME Monroe, HM Brewer, SH Payne, C Ansong, BC Frank, RD Smith, S Peterson, VL Motin, and JN Adkins. 2012. "Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae." PLoS One 7(3):Article No. E33903.  doi:10.1371/journal.pone.0033903
  • Shen Y, N Tolic, SO Purvine, and RD 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. 


  • Ansong C, N Tolic, SO Purvine, S Porwollik, MB Jones, H Yoon, SH Payne, JL Martin, MC Burnet, ME Monroe, P Venepally, RD Smith, S Peterson, F Heffron, M Mcclelland, and JN Adkins. 2011. "Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium." BMC Genomics 12:Art. No. 433.  doi:10.1186/1471-2164-12-433
  • Burnum KE, SJ Callister, CD Nicora, SO Purvine, P Hugenholtz, F Warnecke, RH Scheffrahn, RD Smith, and MS Lipton. 2011. "Proteome Insights into the Symbiotic Relationship Between a Captive Colony of Nasutitermes corniger and its Hindgut Microbiome." The ISME Journal 5(1):161-164.  doi:10.1038/ismej.2010.97
  • Chundawat SP, MS Lipton, SO Purvine, N Uppugundla, D Gao, V Balan, and BE Dale. 2011. "Proteomics based compositional analysis of complex cellulase-hemicellulase mixtures." Journal of Proteome Research 10(10):4365-4372.  doi:10.1021/pr101234z
  • Dresang LR, JR Teuton, H Feng, JM Jacobs, DG Camp, II, SO Purvine, MA Gritsenko, Z Li, RD Smith, B Sugden, PS 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:Article No. 625.  doi:10.1186/1471-2164-12-625
  • Polacco BJ, SO Purvine, EM Zink, SP LaVoie, MS Lipton, AO Summers, and SM 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(8):Art. No. 10: M110.004853.  doi:10.1074/mcp.M110.004853
  • Shen Y, N Tolic, SO Purvine, and RD Smith. 2011. "Improving CID, HCD, and ETD FT MS/MS degradome-peptidome identifications using high accuracy mass information." Journal of Proteome Research doi:10.1021/pr200597j
  • Shen Y, N Tolic, F Xie, R Zhao, SO Purvine, AA Schepmoes, RJ Moore, GA Anderson, and RD 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.  doi:10.1021/pr200052c
  • Stanley JR, JN Adkins, GW Slysz, ME Monroe, SO Purvine, YV Karpievitch, GA Anderson, RD Smith, and AR Dabney. 2011. "A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics." Analytical Chemistry 83(16):6135-6140.  doi:10.1021/ac2009806
  • Wang Y, F Yang, Y Fu, X Huang, W Wang, X Jiang, MA Gritsenko, R Zhao, ME Monroe, OC Pertz, SO Purvine, DJ Orton, JM Jacobs, DG Camp, II, RD Smith, and RL 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. 
  • Zhang H, F Yang, W Qian, RN Brown, Y Wang, ED Merkley, JH Park, ME Monroe, SO Purvine, RJ Moore, L Shi, JK Fredrickson, L Pasa-Tolic, RD Smith, and MS Lipton. 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(19):7260-7268.  doi:10.1021/ac2000829


  • Ham BM, H Jayachandran, F Yang, N Jaitly, AD Polpitiya, ME Monroe, L Wang, R Zhao, SO Purvine, EA Livesay, DG Camp, II, SS Rossie, and RD 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.  doi:10.1021/pr9008207
  • Jung HJ, SO Purvine, H Kim, VA Petyuk, SW Hyung, ME Monroe, DG Mun, KC Kim, JM Park, SJ Kim, N Tolic, GW Slysz, RJ Moore, R Zhao, JN Adkins, GA Anderson, H Lee, DG Camp, II, MH Yu, RD Smith, and SW 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.  doi:10.1021/ac101388b
  • Lewis NE, KK Hixson, TM Conrad, JA Lerman, P Charusanti, AD Polpitiya, JN Adkins, G Schramm, SO Purvine, D Lopez-Ferrer, KK Weitz, R Eils, R Konig, RD Smith, and BO Palsson. 2010. "Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models." Molecular Systems Biology 6:Article No. 390.  doi:10.1038/msb.2010.47
  • Schutzer SE, T Liu, B Natelson, TE Angel, AA Schepmoes, SO Purvine, KK Hixson, MS Lipton, DG Camp, II, PK Coyle, RD Smith, and J Bergquist. 2010. "Establishing the Proteome of Normal Human Cerebrospinal Fluid ." PLoS One 5(6):e10980-.  doi:10.1371/journal.pone.0010980
  • Shen Y, N Tolic, SO Purvine, and RD 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. 
  • Shen Y, N Tolic, T Liu, R Zhao, BO Petritis, MA Gritsenko, DG Camp, II, RJ Moore, SO Purvine, FJ Esteva, and RD Smith. 2010. " Blood Peptidome-Degradome Profile of Breast Cancer." PLoS One 5(10):Article No.: e13133.  doi:10.1371/journal.pone.0013133
  • Shen Y, T Liu, N Tolic, BO Petritis, R Zhao, RJ Moore, SO Purvine, DG Camp, II, and RD Smith. 2010. "A strategy for degradomic-peptidomic analysis of the human blood plasma ." Journal of Proteome Research 9(5):2339-2346.  doi:10.1021/pr901083m
  • Yang F, KM Waters, JH Miller, MA Gritsenko, R Zhao, X Du, EA Livesay, SO Purvine, ME Monroe, Y Wang, DG Camp, II, RD Smith, and DL Stenoien. 2010. "Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation." PLoS One 5(11):e14152.  doi:10.1371/journal.pone.0014152
  • Zhang H, RN Brown, W Qian, ME Monroe, SO Purvine, RJ Moore, MA Gritsenko, L Shi, MF Romine, JK Fredrickson, L Pasa-Tolic, RD Smith, and MS 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. 


  • Kim W, MW Silby, SO Purvine, JS Nicoll, KK Hixson, ME Monroe, CD Nicora, MS Lipton, and SB Levy. 2009. "Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1." PLoS One 4(12):Article Number: e8455.  doi:10.1371/journal.pone.0008455
  • Petyuk VA, AM Mayampurath, ME Monroe, AD Polpitiya, SO Purvine, GA Anderson, DG Camp, II, and RD Smith. 2009. "DtaRefinery: a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra datasets." Molecular & Cellular Proteomics. MCP 9.3:486-496.  doi:10.1074/mcp.M900217-MCP200
  • Sharp JL, JJ Borkowski, DA Schmoyer, DS Daly, SO Purvine, WR Cannon, and GB Hurst. 2009. "Statistically Appraising Process Quality of Affinity Isolation Experiments ." Computational Statistics & Data Analysis 53(5):1720-1726 (special issue). 
  • Springer DL, JH Miller, SL Spinelli, L Pasa-Tolic, SO Purvine, DS Daly, RC Zangar, S Jin, N Blumberg, CW Francis, MB Taubman, AE Casey, SD Wittlin, and RP Phipps. 2009. "Platelet Proteome Changes Associated with Diabetes and During Platelet Storage for Transfusion." Journal of Proteome Research 8(5):2261-2272. 
  • Yang F, S Wu, DL Stenoien, R Zhao, ME Monroe, MA Gritsenko, SO Purvine, AD Polpitiya, N Tolic, Q Zhang, AD Norbeck, DJ Orton, RJ Moore, K Tang, GA Anderson, L Pasa-Tolic, DG Camp, II, and RD Smith. 2009. "Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ-labeled phosphopeptides." Analytical Chemistry 81(10):4137-4143.  doi:10.1021/ac802605m


  • Ansong C, SO Purvine, JN Adkins, MS Lipton, and RD Smith. 2008. "Proteogenomics: the needs and roles to be filled by proteomics in genome annotation." Briefings in Functional Genomics and Proteomics 7(1):50-62. 
  • Daly DS, KK Anderson, EA Panisko, SO Purvine, R Fang, ME Monroe, and SE Baker. 2008. "A mixed-effects Statistical Model for Comparative LC-MS Proteomics Studies." Journal of Proteome Research 7(3):1209-1217.  doi:10.1021/pr070441i
  • Ding SJ, Y Wang, JM Jacobs, W Qian, F Yang, AV Tolmachev, X Du, W Wang, RJ Moore, ME Monroe, SO Purvine, KM Waters, TH Heibeck, JN Adkins, DG Camp, II, RL Klemke, and RD 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):4215-24.  doi:10.1021/pr7007785
  • Du X, F Yang, NP Manes, DL Stenoien, ME Monroe, JN Adkins, DJ States, SO Purvine, DG Camp, II, and RD Smith. 2008. "Linear Discriminant Analysis - Based Estimation of the False Discovery Rate for Phosphopeptide Identifications ." Journal of Proteome Research 7(6):2195-2203.  doi:10.1021/pr070510t
  • Ham BM, F Yang, H Jayachandran, N Jaitly, ME Monroe, MA Gritsenko, EA Livesay, R Zhao, SO Purvine, DJ Orton, JN Adkins, DG Camp, II, SS Rossie, and RD Smith. 2008. "The Influence of Sample Preparation and Replicate Analyses on HeLa Cell Phosphoproteome Coverage." Journal of Proteome Research 7(6):2215-2221. 
  • Mathivanan S, M Ahmed, NG Ahn, H Alexandre, R Amanchy, PC Andrews, JS Bader, BM Balgley, M Bantscheff, K Bennett, E Bjorling, B Blagoev, R Bose , SK Brahmachari, AS Burlingame, XR Bustelo, G Cagney, GT Cantin, HL Cardasis, JE Celis, R Chaerkady, F Chu, PA Cole, CE Costello, RJ Cotter , D Crockett, JP DeLany , AM De Marzo, LV DeSouza, EW Deutsch, E Dransfield , G Drewes , A Droit , M Dunn, K Elenitoba-Johnson, RM Ewing, J Van Eyk , V Faca , J Falkner , X Fang, C Fenselau , D Figeys , P Gagne , C Gelfi , K Gevaert , J Gimble , F Gnad , R Goel, P Gromov , SM Hanash, WS Hancock, HC Harsha , G Hart , H Faith , F He , P Hebbar , K Helsens , H Hermeking , W Hide , K Hjerno, DF Hochstrasser, O Hofmann, DM Horn , RH Hruban , N Ibarrola , P James , ON Jensen , PH Jensen, P Jung , K Kandasamy, I Kheterpal , R Kikuno , U Korf, R Korner, B Kuster, MS Kwon , HJ Lee , YJ Lee , M Lefevre , M Lehvaslaiho, P Lescuyer, F Levander, MS Lim, C Lobke, J Loo, M Mann, L Martens , J Martinez-Heredia, ME McComb, J McRedmond , A Mehrle, R Menon, CA Miller, H Mischak, SS Mohan, R Mohmood , H Molina , MF Moran , JD Morgan, R Moritz , M Morzel, DC Muddiman, A Nalli , JD Navarro, TA Neubert , O Ohara , R Oliva, G Omenn, M Oyama , YK Paik, K Pennington , R Pepperkok, B Periaswamy, EF Petricoin, GG Poirier, TSK Prasad, SO Purvine, BA Rahiman , P Ramachandran, YL Ramachandra , RH Rice, J Rick , RH Ronnholm , J Salonen , JC Sanchez , T Sayd , B Seshi, K Shankari, SJ Sheng , V Shetty , K Shivakumar, RJ Simpson, R Sirdeshmukh, KWM Siu , JC Smith, RD Smith, DJ States, S Sugano, M Sullivan , G Superti - Furga, M Takatalo , V Thongboonkerd , JC Trinidad , M Uhlen , J Vandekerckhove, J Vasilescu , TD Veenstra, JM Vidal - Taboada, M Vihinen, R Wait , X Wang, S Wiemann, B Wu , T Xu, JR 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. 
  • Mayampurath AM, N Jaitly, SO Purvine, ME Monroe, KJ Auberry, JN Adkins, and RD Smith. 2008. "DeconMSn: A Software Tool for accurate parent ion monoisotopic mass determination for tandem mass spectra." Bioinformatics 24(7):1021-1023.  doi:10.1093/bioinformatics/btn063
  • Shen Y, KK Hixson, N Tolic, DG Camp, II, SO Purvine, RJ Moore, and RD Smith. 2008. "Mass Spectrometry Analysis of Proteome-wide Proteolytic Post-translational Degradation of Proteins." Analytical Chemistry 80(15):5819-5828.  doi:10.1021/ac800077w
  • Shen Y, N Tolic, KK Hixson, SO Purvine, GA Anderson, and RD Smith. 2008. "De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins ." Analytical Chemistry 80(20):7742-7754.  doi:10.1021/ac801123p
  • Shen Y, N Tolic, KK Hixson, SO Purvine, L Pasa-Tolic, W Qian, JN Adkins, RJ Moore, and RD 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):1871-82.  doi:10.1021/ac702328x
  • Tolmachev AV, ME Monroe, SO Purvine, RJ Moore, N Jaitly, JN Adkins, GA Anderson, and RD Smith. 2008. "Characterization of Strategies for Obtaining Confident Identifications in Bottom-Up Proteomics Measurements Using Hybrid FTMS instruments ." Analytical Chemistry 80(22):8514-8525.  doi:10.1021/ac801376g
  • Zhang Q, AA Schepmoes, JW Brock, S Wu, RJ Moore, SO Purvine, J Baynes, RD Smith, and TO Metz. 2008. "Improved Methods for the Enrichment and Analysis of Glycated Peptides ." Analytical Chemistry 80(24):9822-9829.  doi:10.1021/ac801704j


  • Manes NP, JK Gustin, J Rue, HM Mottaz, SO Purvine, AD Norbeck, ME Monroe, JS Zimmer, TO Metz, JN Adkins, RD Smith, and F Heffron. 2007. "Targeted Protein Degradation by Salmonella under Phagosome-Mimicking Culture Conditions Investigated Using Comparative Peptidomics." Molecular & Cellular Proteomics. MCP 6(4):717-727.  doi:10.1074/mcp.M600282-MCP200
  • Yang F, N Jaitly, H Jayachandran, Q Lou, ME Monroe, X Du, MA Gritsenko, R Zhang, DJ Anderson, SO Purvine, JN Adkins, RJ Moore, HM Mottaz, SJ Ding, MS Lipton, DG Camp, II, HR Udseth, RD Smith, and SS 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.  doi:10.1021/pr070068e
  • Zhang Q, W Qian, TV Knyushko, TRW Clauss, SO Purvine, RJ Moore, CA Sacksteder, MH Chin, DJ Smith, DG Camp, II, DJ Bigelow, and RD 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.  doi:10.1021/pr0606934


  • Adkins JN, HM Mottaz, AD Norbeck, JK Gustin, J Rue, TRW Clauss, SO Purvine, KD Rodland, F Heffron, and RD Smith. 2006. "Analysis of the Salmonella typhimurium Proteome through Environmental Response toward Infectious Conditions." Molecular & Cellular Proteomics. MCP 5(8):1450-1461.  doi:10.1074/mcp.M600139-MCP200
  • Liu T, W Qian, HM Mottaz, MA Gritsenko, AD Norbeck, RJ Moore, SO Purvine, DG Camp, II, and RD Smith. 2006. "Evaluation of Multi-Protein Immunoaffinity Subtraction for Plasma Proteomics and Candidate Biomarker Discovery Using Mass Spectrometry ." Molecular & Cellular Proteomics. MCP 5(11):2167-2174. 
  • Liu T, W Qian, MA Gritsenko, W Xiao, LL Moldawer, A Kaushal, ME Monroe, SM Varnum, RJ Moore, SO Purvine, RV Maier, RW Davis, RG Tompkins, DG Camp, II, and RD Smith. 2006. "High Dynamic Range Characterization of the Trauma Patient Plasma Proteome ." Molecular & Cellular Proteomics. MCP 5(10):1899-1913.  doi:10.1074/mcp.M600068-MCP200
  • Sacksteder CA, JE Whittier, Y Xiong, J Li, NA Galeva, ME Jacoby, SO Purvine, TD Williams, MC Rechsteiner, DJ Bigelow, and TC Squier. 2006. "Tertiary Structural Rearrangements upon Oxidation of Methionine145 in Calmodulin Promotes Targeted Proteasomal Degradation." Biophysical Journal 91(4):1480-1493. 
  • Shi L, JN Adkins, JR Coleman, AA Schepmoes, A Dohnalkova, HM Mottaz, AD Norbeck, SO Purvine, NP Manes, HS Smallwood, HH Wang, J Forbes, P Gros, S Uzzau, KD Rodland, F Heffron, RD Smith, and TC 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 281:29131-29140.  doi:10.1074/jbc.M604640200


  • Kolker E, AF Picone, MY Galperin, MF Romine, R Higdon, KS Makarova, N Kolker, GA Anderson, X Qiu, KJ Auberry, G Babnigg, AS Beliaev, P Edlefsen, DA Elias, YA Gorby, T Holzman, J Klappenbach, K Konstantinidis, ML Land, MS Lipton, LA McCue, ME Monroe, L Pasa-Tolic, GE Pinchuk, SO Purvine, M Serres, S Tsapin, BA Zakrajsek, W Zhu, J Zhou, F Larimer, C Lawrence, M Riley, FR Collart, JR Yates, III, RD Smith, CS Giometti, K Nealson, JK Fredrickson, and JM 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. 

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