Laboratory Fellow, Biochemist, Group Leader
Laboratory Fellow, Biochemist, Group Leader


Joshua Adkins is a biochemist whose research centers primarily on applying cutting-edge mass spectrometry capabilities to nationally important biological research. Josh is an Associate Division Director in the Biological Sciences Division, leading the Integrative Omics group. He has 20 years of experience at PNNL where his research has centered on the comprehensive characterization of proteins through space (associated proteins, structural determinants and localization) and time (before and after treatment, cell cycle, day-night cycle, and evolutionary changes) to better understand biological systems. Josh has used different biological models to highlight the capabilities of PNNL, these models have ranged from host-pathogen interactions to human exercise/physical activity to environmental microbes. Currently, Josh is leading an NIH Common Fund Project within the Molecular Transducers of Physical Activity Consortium (MoTrPAC) and the PI of a National Heart, Lung, and Blood Institute - Lung Map Research Center. He has previously led among other projects a Center for Systems Biology of EnteroPathogens and a Protein Structure Initiative Biology Center. In these roles, he works with leads talented and multidisciplinary teams comprised of scientists from PNNL, universities, and other research organizations.

Disciplines and Skills

  • Integrative omics
  • Proteomics and metabolomics
  • Systems biology
  • Dynamic biological systems
  • Human health (performance and infectious disease)
  • Environmental biology
  • Protein structure and function


  • PhD in Biochemistry and Molecular Biology, Colorado State University
  • BS in Chemistry and Biology, Metropolitan State University of Denver

Affiliations and Professional Service

  • American Chemical Society
  • American Association for the Advancement of Science

Awards and Recognitions

  • External Program Consultant for the NIH Common Fund Program ‘Illuminating the Druggable Genome’, 2021-Present
  • PNNL Executive Secretary for External Review Panel of the PNNL ‘m/q Initiative’, 2020-Present
  • Scientific Working Group Member, PAThosystems Resource Integration Center (PATRIC), NIH-NIAID, 2010-2019
  • NIH-NIAID Steering Committee for Functional Genomics Program, 2014-2018
  • Scientific Working Group Member, Malaria Host-Pathogen Interaction Resource Center, NIH-NIAID, 2013-2018
  • National Academies Keck Futures Initiative (NAKFI) appointee for the Collective Behavior, Beckman Center, CA, 2014
  • Standing Member of Enabling Bioanalytical and Biophysical Technologies, NIH, 2009-2013
  • Scientific Working Group Member, Seattle Structural Genomics Center for Infectious Disease, NIH-NIAID, 2010-2012
  • National Academies Keck Futures Initiative (NAKFI) appointee for the Ecosystem Services, Beckman Center, CA, 2011
  • Scientific Working Group Member, Pathogen Functional Resource Center, NIH-NIAID, 2010
  • Laboratory Director’s Early Career Exceptional Achievement Award, Pacific Northwest National Laboratory, Richland, WA, 2006
  • Inaugural Candidate of the PNNL Scientist and Engineer Development Program, Richland, WA, 2004-2006
  • Preecha Kownin Outstanding Graduate Student Award, College of Natural Sciences, Colorado State University, 2001-2002 Academic Year



  • Clair G., L.M. Bramer, R. Misra, J. Kitzmiller, S. Feng, V.G. Danna, and H.D. Bhotika, et al. 2021. "Proteomic analysis of human lung development." American Journal of Respiratory and Critical Care Medicine. PNNL-SA-155781. 


  • Woo J., S.M. Williams, L. Markillie, S. Feng, C. Tsai, V. Aguilera-Vazquez, and R.L. Sontag, et al. 2021. "High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip." Nature Communications 12. PNNL-SA-159977. doi:10.1038/s41467-021-26514-2
  • Negretti N.M., C.R. Gourley, P.K. Talukdar, G. Clair, C.M. Klappenbach, C.J. Lauritsen, and J.N. Adkins, et al. 2021. "The Campylobacter jejuni CiaD effector co-opts the host cell protein IQGAP1 to promote cell entry." Nature Communications 12, no. 1:1339. PNNL-SA-152634. doi:10.1038/s41467-021-21579-5
  • Campbell C., C. Fingleton, M.S. Zeden, E. Bueno, L. Gallagher, D. Shinde, and J. Ahm, et al. 2021. "Accumulation of Succinyl Coenzyme A Perturbs the Methicillin-Resistant Staphylococcus aureus (MRSA) Succinylome and Is Associated with Increased Susceptibility to Beta-Lactam Antibiotics." mBio, no. 3:DOI: 10.1128/mBio.00530-21. PNNL-SA-166791. doi:10.1128/mBio.00530-21
  • Hutchinson C.M., J.A. Sanford, J.R. Hansen, M.A. Gritsenko, K.D. Rodland, P.D. Piehowski, and W. Qian, et al. 2021. "Assessment of TMT labeling efficiency in large-scale quantitative proteomics: the critical effect of sample pH." ACS Omega 6, no. 19:12660-12666. PNNL-SA-158792. doi:10.1021/acsomega.1c00776
  • Zayed A.A., D. Lücking, M. Mohssen, D. Cronin, B. Bolduc, A.C. Gregory, and K.R. Hargreaves, et al. 2021. "efam: an expanded, metaproteome-supported HMM pro-file database of viral protein families." Bioinformatics btab451, no. btab451:1-7. PNNL-SA-163531. doi:10.1093
  • Velickovic D., R.K. Chu, C. Henkel, A. Koch, N. Tao, J.E. Kyle, and J.N. Adkins, et al. 2021. "Preserved and variable spatial-chemical changes of lipids across tomato leaves in response to central vein wounding reveals potential origin of linolenic acid in signal transduction cascade." Plant-Environment Interactions. PNNL-SA-158820.


  • Nunn K.L., G. Clair, J.N. Adkins, K.M. Engbrecht, T.L. Fillmore, and L.J. Forney. 2020. "Amylases in the human vagina." mSphere 5, no. 6:Article No. e00943-20. PNNL-SA-155005. doi:10.1128/mSphere.00943-20
  • Negretti N.M., Y. Ye, L.M. Malavasi, S.M. Pokharel, S. Huynh, S. Noh, and C. Klima, et al. 2020. "A porcine ligated loop model reveals new insight into the host immune response against Campylobacter jejuni." Gut Microbes 12, no. 1:1-25. PNNL-SA-152772. doi:10.1080/19490976.2020.1814121
  • Chaput G., A. Billings, L. DeDiego, R. Orellana, J.N. Adkins, C.D. Nicora, and Y. Kim, et al. 2020. "Lignin Induced Iron Reduction by Novel sp., Tolumonas lignolytic BRL6-1." PLoS One 15, no. 9:e0233823. PNNL-SA-156112. doi:10.1371/journal.pone.0233823
  • Ogden A.J., W. Boukari, A. Nava, N. Lucinda, G. Sunter, W.R. Curtis, and J.N. Adkins, et al. 2020. "Characterization of Local and Systemic Impact of Whitefly (Bemisia tabaci) Feeding and Whitefly-Transmitted Tomato Mottle Virus Infection on Tomato Leaves by Comprehensive Proteomics." International Journal of Molecular Sciences 21, no. 19:7241. PNNL-SA-153927. doi:10.3390/ijms21197241
  • Sanford JA, CD Nogiec, ME Lindholm, JN Adkins, D Amar, S Dasari, JK Drugan, FM Fernández, S Radom-Aizik, S Schenk, MP Snyder, RP Tracy, P Vanderboom, S Trappe, MJ Walsh. 2020. “Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise.” Cell Reports, 107863
  • Howard-Varona C, M M Lindback, GE Bastien, N Solonenko, AA Zayed, H Jang, B Andreopoulos, HM Brewer, T Glavina del Rio, JN Adkins, S Paul, MB Sullivan, MB Duhaime. 2020. “Phage-specific metabolic reprogramming of virocells.” The ISME journal 14 (4), 881-895
  • Kaiser BLD, JM Jacobs, AA Schepmoes, HM Brewer, B-JM Webb-Robertson, S Valtier, VS Bebarta, JN Adkins. 2020. “Assessment of the Utility of the Oral Fluid and Plasma Proteome for Hydrocodone Usage.” Journal of Medical Toxicology 16 DOI:  10.1007/s13181-019-00731-0
  • Ogden AJ, JJ Bhatt, HM Brewer, J Kintigh, SM Kariuki, S Rudrabhatla, JN Adkins, WR Curtis. 2020. “Phloem Exudate Protein Profiles during Drought and Recovery Reveal Abiotic Stress Responses in Tomato Vasculature.” Int. J. Mol. Sci. 2020, 21(12), 4461;
  • Chaput G, AF Billings, L DeDiego, R Orellana, JN Adkins, R Chu, B Simmons, KM DeAngelis. 2020. “Iron Chelator-Mediated Anoxic Biotransformation of Lignin by Novel sp., Tolumonas lignolytica BRL6-1.” BioRxix doi:


  • Ceja Navarro J., U. Karaoz, M. Bill, Z. Hao, R.A. White, A. Arellano, and L. Ramanculova, et al. 2019. "Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle." Nature Microbiology 4, no. 5:864-875. PNNL-SA-138060. doi:10.1038/s41564-019-0384-y
  • Dou M., G. Clair, C. Tsai, K. Xu, W.B. Chrisler, R.L. Sontag, and R. Zhao, et al. 2019. "High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labelling in a Nanodroplet Sample Preparation Platform." Analytical Chemistry 91, no. 20:13119-13127. PNNL-SA-146297. doi:10.1021/acs.analchem.9b03349
  • Johnston G.P., B. Bradel-Tretheway, P.D. Piehowski, H.M. Brewer, B. Lee, N.T. Usher, and J.L. Zamora, et al. 2019. "Nipah virus-like particle egress is modulated by both cytoskeletal and vesicular trafficking pathways: a validated particle proteomics analysis." mSystems 4, no. 5:Article No. e00194-19. PNNL-SA-142825. doi:10.1128/mSystems.00194-19
  • McClure R.S., J.P. Wendler, J.N. Adkins, J.A. Swanstrom, R. Baric, B. Kaiser, and K.L. Oxford, et al. 2019. "Unified Feature Association Networks through Integration of Transcriptomic and Proteomic Data." PLoS Computational Biology 15, no. 9:e1007241. PNNL-SA-137420. doi:10.1371/journal.pcbi.1007241
  • McDermott J.E., J.R. Cort, E.S. Nakayasu, J.N. Pruneda, C.C. Overall, and J.N. Adkins. 2019. "Prediction of Bacterial E3 Ubiquitin Ligase Effectors using Reduced Amino Acid Peptide Fingerprinting." PeerJ 7:e7055. PNNL-SA-138492. doi:10.7717/peerj.7055
  • Negretti N.M., G. Clair, P.K. Talukdar, C.R. Gourley, S. Huynh, J.N. Adkins, and C.T. Parker, et al. 2019. "Campylobacter jejuni demonstrates conserved proteomic and transcriptomic responses when co-cultured with human INT 407 and Caco-2 epithelial cells." Frontiers in Microbiology 10:Article No. 755. PNNL-SA-144950. doi:10.3389/fmicb.2019.00755
  • Zalis E.A., A.S. Nuxoll, S. Manuse, G. Clair, L.C. Radlinski, B.P. Conlon, and J.N. Adkins, et al. 2019. "Stochastic Variation in Expression of the Tricarboxylic Acid Cycle Produces Persister Cells." mBio 10, no. 5:Article No. e01930-19. PNNL-SA-147078. doi:10.1128/mBio.01930-19
  • Couvillion SP, Y Zhu, G Nagy, JN Adkins, C Ansong, RS Renslow, PD Piehowski, YM Ibrahim, RT Kelly, TO Metz. 2019. “New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells.” Analyst 2019, 144, 794-807DOI: 10.1039/C8AN01574K (Minireview)


  • Akberdin I., D. Collins, R. Hamilton, D.Y. Oshchepkov, A.K. Shukla, C.D. Nicora, and E.S. Nakayasu, et al. 2018. "Rare Earth Elements Alter Redox Balance in Methylomicrobium alcaliphilum 20ZR." Frontiers in Microbiology 27:Article No. 2735. PNNL-SA-139645. doi:10.3389/fmicb.2018.02735
  • Howard-Varona C., K.R. Hargreaves, N.E. Solonenko, L. Markillie, R.A. White, H.M. Brewer, and C.K. Ansong, et al. 2018. "Multiple mechanisms drive phage infection efficiency in nearly-identical hosts." The ISME Journal 12, no. 2018:1605-1618. PNNL-SA-132683. doi:10.1038/s41396-018-0099-8
  • Wu J., A. Sabag-Daigle, M. Borton, L. Kop, B.E. Szkoda, B. Kaiser, and S.R. Lindemann, et al. 2018. "Salmonella-mediated inflammation eliminates competitors for fructose-asparagine in the gut." Infection and Immunity 86, no. 7:e00945-17. PNNL-SA-129012. doi:10.1128/IAI.00945-17


  • Hosseinzadeh P., G. Bhardwaj, V.K. Mulligan, M.D. Shortridge, T.W. Craven, F. Pardo-Avila, and S.A. Rettie, et al. 2017. "Comprehensive computational design of ordered peptide macrocycles." Science 358, no. 6369:1461-1466. PNNL-SA-128820. doi:10.1126/science.aap7577
  • Merkley E.D., L.H. Sego, A. Lin, O.P. Leiser, B. Kaiser, J.N. Adkins, and P.S. Keim, et al. 2017. "Protein Abundances can Distinguish Between Naturally-occurring and Laboratory Strains of Yersinia pestis, the Causative Agent of Plague." PLoS One 12, no. 8:e0183478. PNNL-SA-123853. doi:10.1371/journal.pone.0183478
  • Negretti N.M., C.R. Gourley, G. Clair, J.N. Adkins, and M. Konkel. 2017. "The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species." Scientific Reports 7:Article No. 15455. PNNL-SA-122926. doi:10.1038/s41598-017-15379-5
  • Tan K., B. Kaiser, R. Wu, M. Cuff, Y. Fan, L. Bigelow, and R. Jedrzejczak, et al. 2017. "Insights into PG-binding, conformational change, and dimerization of the OmpAC-terminal domains from Salmonella enterica serovar Typhimurium and Borrelia burgdorferi." Protein Science 26, no. 9:1738-1748. PNNL-SA-126827. doi:10.1002/pro.3209
  • Waters E.M., J.K. Rudkin, S. Coughlan, G. Clair, J.N. Adkins, S. Gore, and G. Xia, et al. 2017. "Redeploying ß-Lactam Antibiotics as a Novel Antivirulence Strategy for the Treatment of Methicillin-Resistant Staphylococcus aureus Infections." The Journal of Infectious Disease 215, no. 1:80-87. PNNL-SA-120576. doi:10.1093/infdis/jiw461


  • Bayles B.R., K.A. Brauman, J.N. Adkins, B.F. Allan, A.M. Ellis, T.L. Goldberg, and C.D. Golden, et al. 2016. "Ecosystem Services Connect Environmental Change to Human Health Outcomes." ECOHEALTH 13, no. 3:443-449. PNNL-SA-119124. doi:10.1007/s10393-016-1137-5
  • Conlon B.P., S.E. Rowe, A.V. Brown-Gandt, A.S. Nuxoll, N.P. Donegan, E.A. Zalis, and G. Clair, et al. 2016. "Persister formation in Staphylococcus aureus is associated with ATP depletion." Nature Microbiology 1:Article No. 16051. PNNL-SA-116412. doi:10.1038/nmicrobiol.2016.51
  • Oxford K.L., J.P. Wendler, J.E. McDermott, R.A. White, J.D. Powell, J.M. Jacobs, and J.N. Adkins, et al. 2016. "The Landscape of Viral Proteomics and Its Potential to Impact Human Health." Expert Review of Proteomics 13, no. 6:579-591. PNNL-SA-116259. doi:10.1080/14789450.2016.1184091
  • Sontag R.L., E.S. Nakayasu, R.N. Brown, G.S. Niemann, M.A. Sydor, O. Sanchez, and C. Ansong, et al. 2016. "Identification of novel host interactors of effectors secreted by Salmonella and Citrobacter: SrfH regulates host kinase ERK2 phosphorylation." mSystems 1, no. 4:e00032-15. PNNL-SA-114706. doi:10.1128/mSystems.00032-15


  • Elfenbein J.R., L.A. Knodler, E.S. Nakayasu, C. Ansong, H.M. Brewer, L. Bogomolnaya, and L.G. Adams, et al. 2015. "Multicopy single-stranded DNA directs intestinal colonization of enteric pathogens." PLoS Genetics 11, no. 9:e1005472. PNNL-SA-112635. doi:10.1371/journal.pgen.1005472
  • Li J., C.C. Overall, E.S. Nakayasu, A.S. Kidwai, M.B. Jones, R. Johnson, and N.T. Nguyen, et al. 2015. "Analysis of the Salmonella regulatory network suggests involvement of SsrB and H-NS in sE-regulated SPI-2 gene expression." Frontiers in Microbiology 6:Article No. 27. PNNL-SA-101010. doi:10.3389/fmicb.2015.00027
  • Li J., C.C. Overall, R. Johnson, M.B. Jones, J.E. McDermott, F. Heffron, and J.N. Adkins, et al. 2015. "ChIP-Seq Analysis of the s E Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response." PLoS One 10, no. 9:Article No. e0138466. PNNL-SA-115504. doi:10.1371/journal.pone.0138466
  • Li J., E.S. Nakayasu, C.C. Overall, R. Johnson, A.S. Kidwai, J.E. McDermott, and C. Ansong, et al. 2015. "Global analysis of Salmonella alternative sigma factor E on protein translation." Journal of Proteome Research 14, no. 4:1716-1726. PNNL-SA-105707. doi:10.1021/pr5010423
  • Nakayasu E.S., M.A. Sydor, R.N. Brown, R.L. Sontag, T. Sobreira, G.W. Slysz, and D.R. Humphrys, et al. 2015. "Identification of Salmonella Typhimurium deubiquitinase SseL substrates by immunoaffinity enrichment and quantitative proteomic analysis." Journal of Proteome Research 14, no. 9:4029-4038. PNNL-SA-101042. doi:10.1021/acs.jproteome.5b00574
  • 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:Article No. 150041. PNNL-SA-108944. doi:10.1038/sdata.2015.41
  • Sontag R.L., C. Mihai, G. Orr, A. Savchenko, T. Skarina, H. Cui, and J.R. Cort, et al. 2015. "Electroporation of Functional Bacterial Effectors into Mammalian Cells." Journal of Visualized Experiments 95:e52296. PNNL-SA-102481. doi:10.3791/52296
  • Suh M., A. Tovchigrechko, V. Thovari, M.A. Rolfe, M. Torralba, J. Wang, and J.N. Adkins, et al. 2015. "Quantitative Differences in the Urinary Proteome of Siblings Discordant for Type 1 Diabetes Include Lysosomal Enzymes." Journal of Proteome Research 14, no. 8:3123-3135. PNWD-SA-10457. doi:10.1021/acs.jproteome.5b00052


  • Brown J.N., H.M. Brewer, C.D. Nicora, K.K. Weitz, M.J. Morris, A.J. Skabelund, and J.N. Adkins, et al. 2014. "Protein and microRNA biomarkers from lavage, urine, and serum in military personnel evaluated for dyspnea." BMC Medical Genomics 7:Article No. 58. PNWD-SA-10347. doi:10.1186/1755-8794-7-58
  • Eletsky A., K. Michalska, S. Houliston, Q. Zhang, M.D. Daily, X. Xu, and H. Cui, et al. 2014. "Structural and Functional Characterization of DUF1471 Domains of Salmonella Proteins SrfN, YdgH/SssB, and YahO." PLoS One 9, no. 7:Article No. e101787. PNNL-SA-101092. doi:10.1371/journal.pone.0101787
  • Kronewitter S.R., I. Marginean, J.T. Cox, R. Zhao, C.D. Hagler, A.K. Shukla, and T.S. Carlson, et al. 2014. "Polysialylated N-Glycans Identified in Human Serum Through Combined Developments in Sample Preparation, Separations and Electrospray ionization-mass spectrometry." Analytical Chemistry 86, no. 17:8700-10. PNNL-SA-102819. doi:10.1021/ac501839b
  • Lu J., R. Wu, J.N. Adkins, A. Joachimiak, and M. Glover. 2014. "Crystal structures of the F and pSLT plasmid TraJ N-terminal regions reveal similar homodimeric PAS folds with functional interchangeability." Biochemistry 53, no. 36:5810-9. PNNL-SA-102622. doi:10.1021/bi500244m
  • Merkley E.D., S. Rysavy, A. Kahraman, R.P. Hafen, V. Daggett, and J.N. Adkins. 2014. "Distance Restraints from Crosslinking Mass Spectrometry: Mining a Molecular Dynamics Simulation Database to Evaluate Lysine-Lysine Distances." Protein Science 23, no. 6:747-759. PNNL-SA-97266. doi:10.1002/pro.2458
  • Nakayasu E.S., S. Wu, M.A. Sydor, A.K. Shukla, K.K. Weitz, R.J. Moore, and K.K. Hixson, et al. 2014. "A Method to determine lysine acetylation stoichiometries." International Journal of Proteomics 2014, Article No. 730725. PNNL-SA-96571. doi:10.1155/2014/730725
  • Shen Y., L. Pasa-Tolic, E.W. Robinson, J.N. Adkins, and R.D. Smith. 2014. "New challenges for proteomics technologies: a mini perspective review." Austin Journal of Proteomics, Bioinformatics & Genomics 1, no. 1:Article No. 3. PNNL-SA-106057.
  • Zaborin A., J. Defazio, M. Kade, B. Kaiser, N. Belogortseva, D.G. Camp, and R.D. Smith, et al. 2014. "Phosphate-Containing Polyethylene Glycol Polymers Prevent Lethal Sepsis by Multidrug-Resistant Pathogens." Antimicrobial Agents and Chemotherapy 58, no. 2:966. PNNL-SA-95501. doi:10.1128/AAC.02183-13


  • 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
  • Ansong C., S. Wu, D. Meng, X. Liu, H.M. Brewer, B. Kaiser, and E.S. Nakayasu, et al. 2013. "Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typimurium in response to infection-like conditions." Proceedings of the National Academy of Sciences of the United States of America 110, no. 25:10153-10158. PNNL-SA-92306. doi:10.1073/pnas.1221210110
  • Conlon B.P., E.S. Nakayasu, L.E. Fleck, M.D. LaFleur, V.M. Isabella, K. Coleman, and S.N. Leonard, et al. 2013. "Activated ClpP kills persisters and eradicates a chronic biofilm infection." Nature 503, no. 7476:365-370. PNNL-SA-98792. doi:10.1038/nature12790
  • 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
  • Kidwai A.S., I.T. Mushamiri, G. Niemann, R.N. Brown, J.N. Adkins, and F. Heffron. 2013. "Diverse Secreted Effectors Are Required for Salmonella Persistence in a Mouse Infection Model." PLoS One 8, no. 8:e70753. PNNL-SA-94347. doi:10.1371/journal.pone.0070753
  • Kim Y., B. Schmidt, A.S. Kidwai, M.B. Jones, B.L. Deatherage, H.M. Brewer, and H.D. Mitchell, et al. 2013. "Salmonella Modulates Metabolism During Growth under Conditions that Induce Expression of Virulence Genes." Molecular Biosystems 9, no. 6:1522-1534. PNNL-SA-89810. doi:10.1039/C3MB25598K
  • Latif H., J.A. Lerman, V.A. Portnoy, Y. Tarasova, H. Nagarajan, A.C. Rutledge, and R.D. Smith, et al. 2013. "The Genome Organization of Thermotoga maritima Reflects Its Lifestyle." PLoS Genetics 9, no. 4:Article No. e1003485. PNNL-SA-94268. doi:10.1371/journal.pgen.1003485
  • Merkley E.D., E.S. Baker, K.L. Crowell, D.J. Orton, T. Taverner, C. Ansong, and Y.M. Ibrahim, et al. 2013. "Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein-Protein Interactions by Chemical Cross-Linking." Journal of the American Society for Mass Spectrometry 24, no. 3:444-449. PNNL-SA-88464. doi:10.1007/s13361-012-0565-x
  • Merkley E.D., J.R. Cort, and J.N. Adkins. 2013. "Cross-Linking and Mass Spectrometry Methodologies to Facilitate Structural Biology: Finding a Path through the Maze." Journal of Structural and Functional Genomics 14, no. 3:77-90. PNNL-SA-94079. doi:10.1007/s10969-013-9160-z
  • Michalska K., R.N. Brown, H. Li, R. Jedrzejczak, G. Niemann, F. Heffron, and J.R. Cort, et al. 2013. "New sub-family of lysozyme-like proteins shows no catalytic activity: crystallographic and biochemical study of STM3605 protein from Salmonella Typhimurium." Journal of Structural and Functional Genomics 14, no. 1:1-10. PNNL-SA-93811. doi:10.1007/s10969-013-9151-0
  • Nakayasu E.S., C. Ansong, J.N. Brown, F. Yang, D. Lopez-Ferrer, W. Qian, and R.D. Smith, et al. 2013. "Evaluation of selected binding domains for the analysis of ubiquitinated proteomes." Journal of the American Society for Mass Spectrometry 24, no. 8:1214-1223. PNNL-SA-83169. doi:10.1007/s13361-013-0619-8
  • Nakayasu E.S., R. Tempel, X.A. Cambronne, V.A. Petyuk, M.B. Jones, M.A. Gritsenko, and M.E. Monroe, et al. 2013. "Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation during Francisella infection." Molecular and Cellular Proteomics 12, no. 11:3297-3309. PNNL-SA-93942. doi:10.1074/mcp.M113.029850
  • Nakayasu E.S., R.N. Brown, C. Ansong, M.A. Sydor, S. Imtiaz, C. Mihai, and R.L. Sontag, et al. 2013. "Multi-omic data integration links Deleted in Breast Cancer 1 (DBC1) Degradation to Chromatin Remodeling in Inflammatory Response." Molecular & Cellular Proteomics. MCP 12, no. 8:2136-2147. PNNL-SA-88392. doi:10.1074/mcp.M112.026138
  • Niemann G., R.N. Brown, I.T. Mushamiri, N.T. Nguyen, R. Taiwo, A. Stufkens, and R.D. Smith, et al. 2013. "RNA Type III Secretion Signals that require Hfq." Journal of Bacteriology 195, no. 10:2119-2125. PNNL-SA-90112. doi:10.1128/JB.00024-13
  • Schmidt B., A. Ebrahim, T.O. Metz, J.N. Adkins, B.O. Palsson, and D.R. Hyduke. 2013. "GIM3E: Condition-specific Models of Cellular Metabolism Developed from Metabolomics and Expression Data." Bioinformatics 29, no. 22:2900-2908. PNNL-SA-96650. doi:10.1093/bioinformatics/btt493
  • Wang J., B.M. Webb-Robertson, M.M. Matzke, S.M. Varnum, J.N. Brown, R.M. Riensche, and J.N. Adkins, et al. 2013. "A Semiautomated Framework for Integrating Expert Knowledge into Disease Marker Identification." Disease Markers 35, no. 5:513-523. PNNL-SA-94068. doi:10.1155/2013/613529


  • Ansong C.K., B.L. Deatherage, D.R. Hyduke, B. Schmidt, J.E. McDermott, M.B. Jones, and S. Chauhan, et al. 2012. "Studying Salmonellae and Yersiniae Host-Pathogen Interactions Using Integrated ‘Omics and Modeling." In Systems Biology. Current Topics in Microbiology and Immunology, edited by M Katze. 21-41. PNNL-SA-135981. doi:10.1007/82_2012_247
  • Bordbar A., M.L. Mo, E.S. Nakayasu, A.C. Rutledge, Y. Kim, T.O. Metz, and M.B. Jones, et al. 2012. "Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation." Molecular Systems Biology 8:558. PNNL-SA-87903. doi:10.1038/msb.2012.21
  • Brown R.N., J.A. Sanford, J.H. Park, B.L. Deatherage, B.L. Champion, R.D. Smith, and F. Heffron, et al. 2012. "A Comprehensive Subcellular Proteomic Survey of Salmonella Grown under Phagosome-Mimicking versus Standard Laboratory Conditions." International Journal of Proteomics 2012, Article No. 123076. PNNL-SA-86438. doi:10.1155/2012/123076
  • Lerman J.A., D.R. Hyduke, H. Latif, V.A. Portnoy, N.E. Lewis, J.D. Orth, and A.C. Rutledge, et al. 2012. "In silico method for modelling metabolism and gene product expression at genome scale." Nature Communications 3:Article No. 929. PNNL-SA-79962. doi:10.1038/ncomms1928
  • Peterson E.S., L.A. McCue, A.C. Rutledge, J.L. Jensen, J. Walker, M.A. Kobold, and S.R. Webb, et al. 2012. "VESPA: Software to Facilitate Genomic Annotation of Prokaryotic Organisms Through Integration of Proteomic and Transcriptomic Data." BMC Genomics 13, no. 1:Article No. 131. PNNL-SA-82717. doi:10.1186/1471-2164-13-131
  • Rutledge A.C., G. Fontes, M.A. Gritsenko, A.D. Norbeck, D.J. Anderson, K.M. Waters, and J.N. Adkins, et al. 2012. "Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics." Journal of Proteome Research 11, no. 7:3520-32. PNNL-SA-77193. doi:10.1021/pr3002996
  • 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


  • Aderem A., J.N. Adkins, C. Ansong, J. Galagan, S. Kaiser, M.J. Korth, and G.L. Law, et al. 2011. "A Systems Biology Approach to Infectious Disease Research: Innovating the Pathogen-Host Research Paradigm." mBio 2, no. 1:Article No. e00325. PNNL-SA-77026. doi:10.1128/mBio.00325-10
  • 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:Article No. 433. PNNL-SA-77195. doi:10.1186/1471-2164-12-433
  • Charusanti P., S. Chauhan, K. Mcateer, J.A. Lerman, D.R. Hyduke, V.L. Motin, and C. Ansong, et al. 2011. "An Experimentally-Supported Genome-Scale Metabolic Network Reconstruction for Yersinia pestis CO92." BMC Systems Biology 5:Article No. 163. PNNL-SA-83355. doi:10.1186/1752-0509-5-163
  • Du X., S.M. Chowdhury, N.P. Manes, S. Wu, M.U. Mayer, J.N. Adkins, and G.A. Anderson, et al. 2011. "Xlink-Identifier: An Automated Data Analysis Platform for Confident Identifications of Chemically Cross-linked Peptides using Tandem Mass Spectrometry." Journal of Proteome Research 10, no. 3:923-931. PNNL-SA-70094. doi:10.1021/pr100848a
  • Heffron F., G. Niemann, H. Yoon, A.S. Kidwai, R.N. Brown, J.E. McDermott, and R.D. Smith, et al. 2011. "Salmonella-secreted Virulence Factors." In Salmonella: From Genome to Function, edited by S Porwollik. 187-223. Norfolk:Caister Academic Press. PNNL-SA-71401.
  • McDermott J.E., A.L. Corrigan, E.S. Peterson, C.S. Oehmen, G. Niemann, E. Cambronne, and D. Sharp, et al. 2011. "Computational prediction of type III and IV secreted effectors in Gram-negative bacteria." Infection and Immunity 79, no. 1:23-32. PNNL-SA-72872. doi:10.1128/IAI.00537-10
  • McDermott J.E., H. Yoon, E.S. Nakayasu, T.O. Metz, D.R. Hyduke, A.S. Kidwai, and B.O. Palsson, et al. 2011. "Technologies and Approaches to Elucidate and Model the Virulence Program of Salmonella." Frontiers in Microbiology 2:Article No. 121. PNNL-SA-78291. doi:10.3389/fmicb.2011.00121
  • McDermott J.E., M.N. Archuleta, B.D. Thrall, J.N. Adkins, and K.M. Waters. 2011. "Controlling the Response: Predictive Modeling of a Highly Central, Pathogen-Targeted Core Response Module in Macrophage Activation." PLoS One 6,no. 2:Article No. e14673. PNWD-SA-9011. doi:10.1371/journal.pone.0014673
  • Niemann G., R.N. Brown, J.K. Gustin, A. Stufkens, A.S. Shaikh-Kidwai, J. Li, and J.E. McDermott, et al. 2011. "Discovery of Novel Secreted Virulence Factors from Salmonella enterica Serovar Typhimurium by Proteomic Analysis of Culture Supernatants." Infection and Immunity 79, no. 1:33-43. PNNL-SA-71385. doi:10.1128/IAI.00771-10
  • Schutzer S.E., T.E. Angel, T. Liu, A.A. Schepmoes, T.R. Clauss, J.N. Adkins, and D.G. Camp, et al. 2011. "Distinct Cerebrospinal Fluid Proteomes Differentiate Post-Treatment Lyme Disease from Chronic Fatigue Syndrome." PLoS One 6, no. 2:Article No. e17287. PNWD-SA-9128. doi:10.1371/journal.pone.0017287
  • 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
  • Thiele I., D.R. Hyduke, B. Steeb, G. Fankam, D.K. Allen, S. Bazzani, and P. Charusanti, et al. 2011. "A community effort towards a knowledge--base and mathematical model of the human pathogen Salmonella Typhimurium LT2." BMC Systems Biology 5:Article No. 8. PNNL-SA-77733. doi:10.1186/1752-0509-5-8
  • Yoon H., C. Ansong, J.E. McDermott, M.A. Gritsenko, R.D. Smith, F. Heffron, and J.N. Adkins. 2011. "Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella." BMC Systems Biology 5:Article No. 100. PNNL-SA-77197. doi:10.1186/1752-0509-5-100
  • Yoon H., C. Ansong, J.N. Adkins, and F. Heffron. 2011. "Discovery of Salmonella Virulence Factors Translocated via Outer Membrane Vesicles to Murine Macrophages." Infection and Immunity 79, no. 6:2182-92. PNNL-SA-70093. doi:10.1128/IAI.01277-10


  • Adkins J.N., H. Mottaz, T.O. Metz, C.K. Ansong, N.P. Manes, R.D. Smith, and F. Heffron. 2010. "Performing Comparative Peptidomics Analyses of Salmonella from Different Growth Conditions." In Peptidomics: Methods and Protocols, Methods in Molecular Biology, edited by Mikhail Soloviev. 13-27. New York, New York:Humana Press, Inc. PNNL-SA-59136.
  • Auberry K.J., G.R. Kiebel, M.E. Monroe, J.N. Adkins, G.A. Anderson, and R.D. Smith. 2010. " A Portal for the Distribution and Sharing of Multi-Disciplinary Pan-Omics Information." Journal of Proteomics and Bioinformatics 3, no. 1:1-4. PNNL-SA-75729. doi:10.4172/jpb.1000114
  • Brown J.N., R. Estep, D. Lopez-Ferrer, H.M. Brewer, T.R. Clauss, N.P. Manes, and M. O'Connor, et al. 2010. "Characterization of Macaque Pulmonary Fluid Proteome During Monkeypox Infection: Dynamics of Host Response." Molecular & Cellular Proteomics. MCP 9, no. 12:2760-2771. PNWD-SA-8911. doi:10.1074/mcp.M110.001875
  • Buchko G.W., G. Niemann, E.S. Baker, M.E. Belov, R.D. Smith, F. Heffron, and J.N. Adkins, et al. 2010. "A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins." Molecular Biosystems 6, no. 12:2448-2458. PNNL-SA-73691. doi:10.1039/c0mb00097c
  • 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 6:390. PNNL-SA-68816. doi:10.1038/msb.2010.47
  • Rana G., G. Rana, T.P. York, J.S. Edmiston, B.K. Zedler, J.G. Pounds, and J.N. Adkins, et al. 2010. "Proteomic biomarkers in plasma that differentiate rapid and slow decline in lung function in adult cigarette smokers with chronic obstructive pulmonary disease (COPD)." Analytical and Bioanalytical Chemistry 397:1809-1819. PNWD-SA-9006. doi:10.1007/s00216-010-3742-4
  • Shah A.R., J.N. Adkins, D.J. Baxter, W.R. Cannon, D. Chavarría-Miranda, S. Choudhury, and I. Gorton, et al. 2010. "Applications in Data-Intensive Computing." In Advances in Computers, edited by M Zelkowitz. 1-70. San Diego, California:Academic Press Inc. PNNL-SA-67358.
  • Shah A.R., N. Jaitly, N. Zuljevic, M.E. Monroe, A.V. Liyu, A.D. Polpitiya, and J.N. Adkins, et al. 2010. "An architecture for real time data acquisition and online signal processing for high throughput tandem mass spectrometry." In 5th IEEE International Conference on e-Science, 88 - 93. Piscataway, New Jersey:IEEE. PNNL-SA-67849. doi:10.1109/e-Science.2009.21
  • Singhal M., A.R. Shah, R.N. Brown, and J.N. Adkins. 2010. "Using support vector machine for improving protein-protein interaction prediction utilizing domain interactions." In ACM-BCB '10: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 537-545. New York:Association for Computing Machinery. PNNL-SA-72152. doi:10.1145/1854776.1854878


  • Ansong C., H. Yoon, S. Porwollik, H. Mottaz-Brewer, B.O. Petritis, N. Jaitly, and J.N. Adkins, et al. 2009. "Global Systems-Level Analysis of Hfq and SmpB Deletion Mutants in Salmonella: Implications for Virulence and Global Protein Translation." PLoS One 4, no. 3:Article No. e4809. PNNL-SA-63141. doi:10.1371/journal.pone.0004809
  • Chowdhury S.M., L. Shi, H. Yoon, C. Ansong, L.M. Rommereim, A.D. Norbeck, and K.J. Auberry, et al. 2009. "A method for investigating protein-protein interactions related to Salmonella typhimurium pathogenesis." Journal of Proteome Research 8, no. 3:1504-1514. PNNL-SA-58873.
  • Chowdhury S.M., X. Du, N. Tolic, S. Wu, R.J. Moore, M.U. Mayer, and R.D. Smith, et al. 2009. "Identification of Cross-Linked Peptides after Click-Based Enrichment Using Sequential Collision-Induced Dissociation and Electron Transfer Dissociation Tandem Mass Spectrometry." Analytical Chemistry 81, no. 13:5524-5532. PNNL-SA-61747. doi:10.1021/ac900853k
  • Jaitly N., A.M. Mayampurath, K.A. Littlefield, J.N. Adkins, G.A. Anderson, and R.D. Smith. 2009. "Decon2LS: An Open-Source Software Package for Automated Processing and Visualization of High Resolution Mass Spectrometry Data." BMC Bioinformatics 10:Article No. 87. PNNL-SA-60537. doi:10.1186/1471-2105-10-87
  • Karpievitch Y., J.R. Stanley, T. Taverner, J. Huang, J.N. Adkins, C. Ansong, and F. Heffron, et al. 2009. "A statistical framework for protein quantitation in bottom-up MS-based proteomics." Bioinformatics 25, no. 16:2028-2034. PNNL-SA-66740. doi:10.1093/bioinformatics/btp362
  • Karpievitch Y., J.R. Stanley, T. Taverner, J. Huang, J.N. Adkins, C. Ansong, and F. Heffron, et al. 2009. "A Statistical Framework for Protein Quantitation in Bottom-Up MS-Based Proteomics." Bioinformatics 25, no. 16:2028-2034. PNNL-SA-70100.
  • Shi L., C. Ansong, H.S. Smallwood, L.M. Rommereim, J.E. McDermott, H.M. Brewer, and A.D. Norbeck, et al. 2009. "Proteome of Salmonella enterica serotype Tyhimurium Grown in Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2, no. 9:388-397. PNNL-SA-68770. doi:10.4172/jpb.1000099
  • Shi L., C. Ansong, H.S. Smallwood, L.M. Rommereim, J.E. McDermott, H.M. Brewer, and A.D. Norbeck, et al. 2009. "Proteome of Salmonella Enterica SerotypeTyphimurium Grown in a Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2, no. 9:388-397. PNNL-SA-60692. doi:10.4172/jpb.1000099
  • Shi L., S.M. Chowdhury, H.S. Smallwood, H. Yoon, H.M. Mottaz-Brewer, A.D. Norbeck, and J.E. McDermott, et al. 2009. "Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Infection with Salmonella enterica." Infection and Immunity 77, no. 8:3227-3233. PNNL-SA-62432. doi:10.1128/IAI.00063-09


  • Ansong C., H. Yoon, A.D. Norbeck, J.K. Gustin, J.E. McDermott, H.M. Mottaz, and J. Rue, et al. 2008. "Proteomics Analysis of the Causative Agent of Typhoid Fever." Journal of Proteome Research 7, no. 2:546-557. PNNL-SA-56065. doi:10.1021/pr070434u
  • 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.
  • Brewer H.M., A.D. Norbeck, J.N. Adkins, N.P. Manes, C. Ansong, L. Shi, and Y. Rikihisa, et al. 2008. "Optimization of proteomic sample preparation procedures for comprehensive protein characterization of pathogenic systems." Journal of Biomolecular Techniques:JBT 19, no. 5:285-295. PNNL-SA-60633.
  • Callister S.J., L.A. McCue, J.E. Turse, M.E. Monroe, K.J. Auberry, R.D. Smith, and J.N. Adkins, et al. 2008. "Comparative Bacterial Proteomics: Analysis of the Core Genome Concept." PLoS One 3, no. 2:Article No. e1542. PNNL-SA-58389. doi:10.1371/journal.pone.0001542
  • 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
  • Du X., S.J. Callister, N.P. Manes, J.N. Adkins, R.A. Alexandridis, X. Zeng, and J. Roh, et al. 2008. "A Computational Strategy to Analyze Label-Free Temporal Bottom-up Proteomics Data." Journal of Proteome Research 7, no. 7:2595-2604. PNNL-SA-55070. doi:10.1021/pr0704837
  • 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.
  • Manes N.P., R.D. Estep, H.M. Mottaz, R.J. Moore, T.R. Clauss, M.E. Monroe, and X. Du, et al. 2008. "Comparative Proteomics of Human Monkeypox and Vaccinia Intracellular Mature and Extracellular Enveloped Virions." Journal of Proteome Research 7, no. 3:960-968. PNNL-SA-54048. doi:10.1021/pr070432+
  • 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
  • Monroe M.E., J.L. Shaw, D.S. Daly, J.N. Adkins, and R.D. Smith. 2008. "MASIC: a software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features." Computational Biology and Chemistry 32, no. 3:215-217. PNNL-SA-52621. doi:10.1016/j.compbiolchem.2008.02.006
  • Petyuk V.A., N. Jaitly, R.J. Moore, J. Ding, T.O. Metz, K. Tang, and M.E. Monroe, et al. 2008. "Elimination of Systematic Mass Measurement Errors in Liquid Chromatography-Mass Spectrometry Based Proteomics using Regression Models and a priori Partial Knowledge of the Sample Content." Analytical Chemistry 80, no. 3:693-706. PNNL-SA-56693. doi:10.1021/ac701863d
  • Polpitiya A.D., W. Qian, N. Jaitly, V.A. Petyuk, J.N. Adkins, D.G. Camp, and G.A. Anderson, et al. 2008. "DAnTE: a statistical tool for quantitative analysis of -omics data." Bioinformatics 24, no. 13:1556-1558. PNNL-SA-58107. doi:10.1093/bioinformatics/btn217
  • Pounds J.G., J.W. Flora, J.N. Adkins, K.M. Lee, G. Rana, G. Rana, and T. Sengupta, et al. 2008. "Characterization of the mouse bronchoalveolar lavage proteome by micro-capillary LC-FTICR mass spectrometry." Journal of Chromatography B 864, no. 1-2:95-101. PNNL-SA-60702.
  • Rodland K.D., J.N. Adkins, C. Ansong, S.M. Chowdhury, N.P. Manes, L. Shi, and H. Yoon, et al. 2008. "Use of high-throughput mass spectrometry to elucidate host pathogen interactions in Salmonella." Future Microbiology 3, no. 6:625-634. PNNL-SA-63699.
  • Rodland K.D., J.N. Adkins, C. Ansong, S.M. Chowdhury, N.P. Manes, L. Shi, and H. Yoon, et al. 2008. "Use of high-throughput mass spectrometry to elucidate host-pathogen interactions in Salmonella." Future Microbiology 3, no. 6:625-634. PNNL-SA-61185. doi:10.2217/17460913.3.6.625
  • 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


  • Gupta N., S. Tanner, N. Jaitly, J.N. Adkins, M.S. Lipton, R. Edwards, and M.F. Romine, et al. 2007. "Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation." Genome Research 17, no. 9:1362-1377. PNNL-SA-52859. doi:0.1101/gr.6427907
  • 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
  • Monroe M.E., N. Tolic, N. Jaitly, J.L. Shaw, J.N. Adkins, and R.D. Smith. 2007. "VIPER: an advanced software package to support high-throughput LC-MS peptide identification." Bioinformatics 23, no. 15:2021-2023. PNNL-SA-52622. doi:10.1093/bioinformatics/btm281
  • Petyuk V.A., W. Qian, M.H. Chin, H.H. Wang, E.A. Livesay, M.E. Monroe, and J.N. Adkins, et al. 2007. "Spatial Mapping of Protein Abundances in the Mouse Brain by Voxelation Integrated with High-Throughput Liquid Chromatography - Mass Spectrometry." Genome Research 17, no. 3:328-336. PNNL-SA-49342. doi:10.1101/gr.5799207
  • Webb-Robertson B.M., E.S. Peterson, M. Singhal, K.R. Klicker, C.S. Oehmen, J.N. Adkins, and S.L. Havre. 2007. "PQuad - A visual analysis platform for proteomic data exploration of microbial organism." Bioinformatics 23, no. 13:1705-1707. PNNL-SA-52772. doi:10.1093/bioinformatics/btm132
  • 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


  • 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
  • Callister S.J., R.C. Barry, J.N. Adkins, E.T. Johnson, W. Qian, B.M. Webb-Robertson, and R.D. Smith, et al. 2006. "Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics." Journal of Proteome Research 5, no. 2:277-286. PNNL-SA-46453. doi:10.1021/pr050300l
  • Ding Y.R., K.K. Hixson, C.S. Giometti, A. Stanley, A. Esteve-Nunez, T. Khare, and S.L. Tollaksen, et al. 2006. "The Proteome of Dissimilatory Metal-reducing Microorganism Geobacter Sulfurreducens under Various Growth Conditions." Biochimica et Biophysica Acta--Proteins and Proteomics 1764, no. 7:1198-1206. PNNL-SA-47069. doi:10.1016/j.bbapap.2006.04.017
  • Fang R., D.A. Elias, M.E. Monroe, Y. Shen, M. McIntosh, P. Wang, and C.D. Goddard, et al. 2006. "Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics. MCP 5, no. 4:714-725. PNNL-SA-47983. doi:10.1074/mcp.M500301-MCP200
  • Hixson K.K., J.N. Adkins, S.E. Baker, R.J. Moore, R.D. Smith, S.L. McCutchen-Maloney, and M.S. Lipton. 2006. "Biomarker Candidate Identification in Yersinia Pestis Using Organism-Wide Semiquantitative Proteomics." Journal of Proteome Research 5, no. 11:3008-3017. PNNL-SA-49565.
  • Jaitly N., M.E. Monroe, V.A. Petyuk, T.R. Clauss, J.N. Adkins, and R.D. Smith. 2006. "Robust Algorithm for Alignment of Liquid Chromatography-Mass Spectrometry Analyses in an Accurate Mass and Time Tag Data Analysis Pipeline." Analytical Chemistry 78, no. 21:7397-7409. PNNL-SA-48693.
  • Petritis K., L.J. Kangas, B. Yan, M.E. Monroe, E.F. Strittmatter, W. Qian, and J.N. Adkins, et al. 2006. "Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information." Analytical Chemistry 78, no. 14:5026-5039. PNNL-SA-50263. doi:10.1021/ac060143p
  • 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: 29131-29140. PNNL-SA-51416. doi:10.1074/jbc.M604640200
  • Tolmachev A.V., M.E. Monroe, N. Jaitly, V.A. Petyuk, J.N. Adkins, and R.D. Smith. 2006. "Mass Measurement Accuracy In Analyses Of Highly Complex Mixtures Based Upon Multidimensional Recalibration." Analytical Chemistry 78, no. 24:8374-8385. PNNL-SA-49340. doi:10.1021/ac0606251
  • Webb-Robertson B.M., W.R. Cannon, J.N. Adkins, and D.K. Gracio. 2006. "The Challenge of Proteomic Data from Molecular Signals to Biological Networks and Disease." In Pacific Symposium On Biocomputing 2006, edited by R.B. Altman, et al, 212-218. Singapore:World Scientific. PNNL-SA-47364. doi:10.1142/9789812701626_0020
  • Yang F., D.L. Stenoien, E.F. Strittmatter, J. Wang, L. Ding, M.S. Lipton, and M.E. Monroe, et al. 2006. "Phosphoproteome Profiling of Human Skin Fibroplast Cells in Response to Low- and High-Dose Irradiation." Journal of Proteome Research 5, no. 5:1252-1260. PNNL-SA-46275. doi:10.1021/pr060028v


  • Adkins J.N., M.E. Monroe, K.J. Auberry, Y. Shen, J.M. Jacobs, D.G. Camp, and F. Vitzthum, et al. 2005. "A Proteomic Study of the HUPO Plasma Proteome Project's Pilot Samples using an Accurate Mass and Time Tag Strategy." Proteomics 5, no. 13:3454-3466. PNWD-SA-6982. doi:10.1002/pmic.200401333
  • Ahram M., E.F. Strittmatter, M.E. Monroe, J.N. Adkins, J.C. Hunter, J.H. Miller, and D.L. Springer. 2005. "Identification of shed proteins from Chinese hamster ovary cells: Application of statistical confidence using human and mouse protein databases." Proteomics 5, no. 7:1815-1826. PNNL-SA-42491.doi:10.1002/pmic.200401072
  • Ahram M., J.N. Adkins, D.L. Auberry, D.S. Wunschel, and D.L. Springer. 2005. "A Proteomic Approach to Characterize Protein Shedding." Proteomics 5, no. 1:123-131. PNNL-SA-39942. doi:10.1002/pmic.200400912
  • Edberg D.D., J.N. Adkins, D.L. Springer, and R.C. Reeves. 2005. "Dynamic and Differential in vivo Modifications of the Isoform HMGA1a and HMGA1b Chromatin Proteins." Journal of Biological Chemistry 280, no. 10:8961-8973. PNNL-SA-43483. doi:10.1074/jbc.M407348200
  • Haab B.B., B.H. Geierstanger, G. Michailidis, F. Vitzthum, S. Forrester, R. Okon, and P. Saviranta, et al. 2005. "Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: Systematic variation between sample types and calibration of mass spectrometry data." Proteomics 5, no. 13:3278-3291. PNWD-SA-7067. doi:10.1002/pmic.200401276
  • Jacobs J.M., J.N. Adkins, W. Qian, T. Liu, Y. Shen, D.G. Camp, and R.D. Smith. 2005. "Utilizing human blood plasma for proteomic biomarker discovery." Journal of Proteome Research 4, no. 4:1073-1085. PNWD-SA-6880. doi:10.1021/pr0500657
  • Kapp E., F. Schutz, L.M. Connolly, J.A. Chakel, J.E. Meza, C.A. Miller, and D. Fenyo, et al. 2005. "An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and Specificity analysis." Proteomics 5, no. 13:3475-3490. PNWD-SA-7064. doi:10.1002/pmic.200500126
  • Markillie L.M., C.T. Lin, J.N. Adkins, D.L. Auberry, E.A. Hill, B.S. Hooker, and P.A. Moore, et al. 2005. "Simple Protein Complex Purification and Identification Method Suitable for High- throughput Mapping of Protein Interaction Networks." Journal of Proteome Research 4, no. 2:268-274. PNNL-SA-42494. doi:10.1021/pr049847a
  • Norbeck A.D., M.E. Monroe, J.N. Adkins, K.K. Anderson, D.S. Daly, and R.D. Smith. 2005. "The utility of accurate mass and LC elution time information in the analysis of complex proteomes." Journal of the American Society for Mass Spectrometry 16, no. 8:1239-1249. PNNL-SA-44395. doi:10.1016/j.jasms.2005.05.009
  • Omenn G., D.J. States, M. Adamski, T.W. Blackwell, R. Menon, H. Hermjakob, and R. Apweiler, et al. 2005. "Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database." Proteomics 5, no. 13:3226-3245. PNWD-SA-7066. doi:10.1002/pmic.200500358
  • Springer D.L., M. Ahram, J.N. Adkins, L.E. Kathmann, and J.H. Miller. 2005. "Characterization of Medium Conditioned by Irradiated Cells Using Proteome-Wide, High-Throughput Mass Spectrometry." Radiation Research 164, no. 5:651-654. PNNL-SA-43789. doi:10.1667/rr3457.1


  • Anderson L.N., M. Polanski, R. Peiper, T. Gatlin, R. Tiramalai, T. Conrads, and T. Veenstra, et al. 2004. "The Human Plasma Proteome: A Nonredundant List Developed by Combination of Four Separate Sources." Molecular & Cellular Proteomics. MCP 3, no. 4:311-326. PNWD-SA-6468. doi:10.1074/mcp.M300127-MCP200


  • Springer D.L., D.L. Auberry, M. Ahram, J.N. Adkins, J.M. Feldhaus, J.H. Wahl, and D.M. Wunsch, et al. 2003. "Characterization of Plasma Membrane Proteins from Ovarian Cancer Cells Using Mass Spectrometry." Disease Markers 19, no. 4-5:219-228. PNNL-SA-40681. doi:10.1155/2004/725617


  • Adkins J.N., S.M. Varnum, K.J. Auberry, R.J. Moore, N. Angell, R.D. Smith, and D.L. Springer, et al. 2002. "Toward a Human Blood Serum Proteome: Analysis by Multidimensional Separation Coupled with Mass Spectrometry." Molecular & Cellular Proteomics. MCP 1, no. 12:947-955. PNWD-SA-5845. doi:10.1074/mcp.m200066-mcp200