Biomedical Scientist
Biomedical Scientist


Dr. Jacobs is a biomedical scientist who leads the Cell Signaling and Communications team in the Environmental Molecular Sciences Division and the Environmental Molecular Sciences Laboratory (EMSL) user program. He has extensive experience in the development and application of advanced proteomic analysis techniques and has authored >80 publications and review articles detailing the proteomics analysis pipeline utilized at PNNL. He currently serves as the Associate Director of the National Institute of General Medical Sciences Biomedical Technology Research Resource for Proteomic Integrative Biology, in addition to serving as principal investigator and project manager of multiple proteomics cores and projects within the National Institute of Environmental Health Sciences, National Institute on Drug Abuse, National Institute of Allergy and Infectious Diseases, National Institute on Alcohol Abuse and Alcoholism, and the National Cancer Institute. His diverse expertise lies in the study of complex mammalian and microbial systems, including clinically relevant cohorts and studies, with a focus on understanding the molecular nature of chronic liver disease. He is extensively experienced, knowledgeable, and practiced with proteomic data analysis, its interpretation, and its application to complex biological systems and has an extensive history of productive collaborations with leading researchers in their fields. He leads diverse research project teams at PNNL for the execution of such applications, but with personal knowledge of the extensive technical analysis, data interpretation, and utilization of the advanced proteomics technologies and related instrumentation.

Disciplines and Skills

  • Biochemistry and proteomics


  • PhD in Biochemistry, Montana State University
  • BS in Biochemistry, Brigham Young University


  • Jacobs, J.M., Burnum-Johnson, K.E., Baker, E.M., Smith, R.D., Gritsenko, M.A., Orton, D. 2017. Biomarkers for liver fibrosis. U.S. Patent 9,651,563
  • Jacobs, J.M., Burnum-Johnson, K.E., Baker, E.M., Smith, R.D., Gritsenko, M.A., Orton, D. 2015. Biomarkers for liver fibrosis. U.S. Patent 9,134,326.
  • Metz, T.O., Qian, W., Jacobs, J.M., Polpitiya, A.D., Camp, II D.G., Smith, R.D. 2014. Serum markers for type II diabetes mellitus. U.S. Patent 8,673,644 B2
  • Metz, T.O., Qian, W., Jacobs, J.M., Camp, II D.G., Smith, R.D. 2011. Method for identifying type I diabetes mellitus in humans.  U.S. Patent 7,923,253 B2
  • Lin, S., Lemus, A., Williams, H.R., Jacobs, P.T., Addy, T.O., Jacobs, J.M. 2007. Method for sterilizing devices in a container. U.S. Patent 7,179,419
  • Lin, S., Lemus, A., Williams, H.R., Jacobs, P.T., Addy, T.O., Jacobs, J.M. 2002. Method for sterilizing devices in a container. U.S. Patent 6,495,100.
  • Addy, T.O., Jacobs, P.T., Lin, S., Jacobs, J.M. 2001. Sterilized device in diffusion-restricted container. U.S. Patent 6,319,480.
  • Addy, T.O., Jacobs, P.T., Lin, S., Jacobs, J.M. 2001. Sterilized article within diffusion-restricted containers. U.S. Patent 6,174,502 B1.
  • Addy, T.O., Jacobs, P.T., Lin, S., Jacobs, J.M. 2000. Method for sterilizing an interior of an article. U.S. Patent 6,132,680.
  • Addy, T.O., Jacobs, P.T., Lin, S., Jacobs, J.M. 2000. Method for sterilizing an interior of an article. U.S. Patent 6,068,817.
  • Addy, T.O., Jacobs, P.T., Lin, S., Jacobs, J.M. 2000. Method of sterilization using pretreatment with hydrogen peroxide. U.S. Patent 6,030,579.
  • Addy, T.O., Jacobs, P.T., Lin, S., Jacobs, J.M. 1999. Method of sterilization using pretreatment with hydrogen peroxide. U.S. Patent 5,980,825.
  • Addy, T.O., Jacobs, P.T., Lin, S., Jacobs, J.M. 1999. Method of sterilization in diffusion restricted environments. U.S. Patent 5,961,921.



  • Kaiser B, JM Jacobs, AA Schepmoes, HM Brewer, BM Webb-Robertson, S Valtier, and VS Bebarta, et al. 2020. "Assessment of the Utility of the Oral Fluid and Plasma Proteome for Hydrocodone Usage." Journal of Medical Toxicology 16, no. 1:49-60. PNNL-SA-121218. doi:10.1007/s13181-019-00731-0
  • Tsai, CF, Smith, JS, Eiger, DS, Martin, K, Liu, T, Smith, RD, Shi, T, Rajagopal, S, Jacobs, JM. 2020. Mass spectrometry-based proteomics for analysis of hydrophilic phosphopeptides. Book Chapter, Methods in Molecular Biology. 
  • Orwoll, ES, Wiedrick, J, Nielson, CM, Jacobs, J, Baker, E.S., Piehowski, P, Petyuk, V, Gao, Y, Shi, T, Smith, RD, Bauer, DC, Cummings, SR, Lapidus, J. 2020. Proteomic assessment of serum biomarkers of longevity in older men. Aging Cell epub.


  • Moghieb A.M., L. Tesfay, S. Nie, M.A. Gritsenko, T.L. Fillmore, J.M. Jacobs, and R.D. Smith, et al. 2019. "A Targeted Mass Spectrometric Assay for Reliable Sensitive Hepcidin Quantification." Scientific Reports 9, no. 1:Article No. 7264. PNNL-SA-138022. doi:10.1038/s41598-019-43756-9
  • Nagarajan A., M. Zhou, A.Y. Nguyen, M.L. Liberton, K. Kedia, T. Shi, and P.D. Piehowski, et al. 2019. "Proteomic insights into phycobilisome degradation, a selective and tightly controlled process in the fast growing cyanobacterium Synechococcus elongatus UTEX 2973." Biomolecules 9, no. 8:Article Number 374. PNNL-SA-146394. doi:10.3390/biom9080374
  • Nielson C., J.M. Jacobs, and E.S. Orwoll. 2019. "Proteomic studies of bone and skeletal health outcomes." Bone 126. PNNL-SA-147327. doi:10.1016/j.bone.2019.03.032
  • Stevens S., T. Liu, F.R. Bahjat, V.A. Petyuk, A.A. Schepmoes, R.L. Sontag, and M.A. Gritsenko, et al. 2019. "Preconditioning in the Rhesus Macaque Induces a Proteomic Signature Following Cerebral Ischemia that Is Associated with Neuroprotection." Translational Stroke Research 10, no. 4:440-448. PNWD-SA-10567. doi:10.1007/s12975-018-0670-7
  • Tsai C., J.S. Smith, K. Krajewski, R. Zhao, A.M. Moghieb, C.D. Nicora, and X. Xiong, et al. 2019. "Tandem Mass Tag Labeling Facilitates Reversed-Phase Liquid Chromatography-Mass Spectrometry Analysis of Hydrophilic Phosphopeptides." Analytical Chemistry 91, no. 18:11606-11613. PNNL-SA-142808. doi:10.1021/acs.analchem.9b01814
  • Zhang P., M.J. Gaffrey, Y. Zhu, W.B. Chrisler, T.L. Fillmore, L. Yi, and C.D. Nicora, et al. 2019. "Carrier-assisted single-tube processing approach for targeted proteomics analysis of low numbers of mammalian cells." Analytical Chemistry 91, no. 2:1441-1451. PNNL-SA-138130. doi:10.1021/acs.analchem.8b04258


  • Kedia K., J.P. Wendler, E.M. Baker, K.E. Burnum-Johnson, L.G. Jarsberg, K.G. Stratton, and A.T. Wright, et al. 2018. "Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis." Tuberculosis 112. PNNL-SA-137966. doi:10.1016/
  • Orwoll E.S., J. Wiedrick, J.M. Jacobs, E.M. Baker, P.D. Piehowski, V.A. Petyuk, and Y. Gao, et al. 2018. "High-throughput serum proteomics for the identification of protein biomarkers of mortality in older men." Aging Cell 17, no. 2:Article No. e12717. PNNL-SA-131443. doi:10.1111/acel.12717


  • Eisfeld A.J., P. Halfmann, J.P. Wendler, J.E. Kyle, K.E. Burnum-Johnson, Z. Peralta, and T. Maemura, et al. 2017. "Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis." Cell Host & Microbe 22, no. 6:817-829. PNNL-SA-120881. doi:10.1016/j.chom.2017.10.011
  • Liberton M.L., W.B. Chrisler, C.D. Nicora, R.J. Moore, R.D. Smith, D.W. Koppenaal, and H.B. Pakrasi, et al. 2017. "Phycobilisome Truncation Causes Widespread Proteome Changes in Synechocystis sp. PCC 6803." PLoS One 12, no. 3:e0173251. PNNL-SA-112677. doi:10.1371/journal.pone.0173251
  • Nielson C., J. Wiedrick, J. Shen, J.M. Jacobs, E.M. Baker, A. Baraff, and P.D. Piehowski, et al. 2017. "Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics." Journal of Bone and Mineral Research 32, no. 7:1559-1567. PNNL-SA-111322. doi:10.1002/jbmr.3125
  • Sigal G.B., M. Segal, A. Mathew, L.G. Jarlsberg, M. Wang, S. Barbero, and N. Small, et al. 2017. "Biomarkers of Tuberculosis Severity and Treatment Effect: A Directed Screen of 70 Host Markers in a Randomized Clinical Trial." Ebiomedicine 25. PNNL-SA-129994. doi:10.1016/j.ebiom.2017.10.018


  • Hiras J., Y. Wu, K. Deng, C.D. Nicora, J.T. Aldrich, D. Frey, and S. Kolinko, et al. 2016. "Comparative community proteomics demonstrates the unexpected importance of an actinobacterial glycoside hydrolase family 12 protein for crystalline cellulose hydrolysis." mBio7, no. 4:Article No. e01106-16. PNNL-SA-120275. doi:10.1128/mBio.01106-16
  • Liberton M.L., R. Saha, J.M. Jacobs, A.Y. Nguyen, M.A. Gritsenko, R.D. Smith, and D.W. Koppenaal, et al. 2016. "Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium." Molecular and Cellular Proteomics 15, no. 6:2021-2032. PNNL-SA-121062. doi:10.1074/mcp.M115.057240
  • Liberton M.L., R. Saha, J.M. Jacobs, A.Y. Nguyen, M.A. Gritsenko, R.D. Smith, and D.W. Koppenaal, et al. 2016. "Proteomics analysis of isolated plasma membrane and thylakoid membrane from Synechocystis sp. PCC 6803." Molecular and Cellular Proteomics 15, no. 6:2021-2032. PNNL-SA-112674. doi:10.1074/mcp.M115.057240
  • Nakayasu E.S., C.D. Nicora, A.C. Sims, K.E. Burnum-Johnson, Y. Kim, J.E. Kyle, and M.M. Matzke, et al. 2016. "MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses." mSystems 1, no. 3:e00043-16. PNNL-SA-114737. doi:10.1128/mSystems.00043-16
  • Nielson C., K. Jones, R.F. Chun, J.M. Jacobs, Y. Wang, M. Hewison, and J.S. Adams, et al. 2016. "Free 25-Hydroxyvitamin D: Impact of Vitamin D Binding Protein Assays on Racial-Genotypic Associations." Journal of Clinical Endocrinology and Metabolism 101, no. 5:2226-2234. PNNL-SA-120076. doi:10.1210/jc.2016-1104
  • Nielson C., K. Jones, R.F. Chun, J.M. Jacobs, Y. Wang, M. Hewison, and J.S. Adams, et al. 2016. "Role of Assay Type in Determining Free 25-Hydroxyvitamin D Levels in Diverse Populations." The New England Journal of Medicine 374, no. 17:1695-1696. PNNL-SA-108708. doi:10.1056/NEJMc1513502
  • 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
  • Velasquez C., E. Cheng, M. Shuda, P.J. Lee-Oesterreich, L. Pogge von Strandmann, M.A. Gritsenko, and J.M. Jacobs, et al. 2016. "Mitotic protein kinase CDK1 phosphorylation of mRNA translation regulator 4E-BP1 Ser83 may contribute to cell transformation." Proceedings of the National Academy of Sciences of the United States of America vol. 113, no. 30:8466-8471. PNNL-SA-116951. doi:10.1073/pnas.1607768113


  • Yu J., M.L. Liberton, P. Cliften, R. Head, J.M. Jacobs, R.D. Smith, and D.W. Koppenaal, et al. 2015. "Synechococcus elongatus UTEX 2973, a fast growing cyanobacterial chassis for biosynthesis using light and CO2." Scientific Reports 5. PNNL-SA-105375. doi:10.1038/srep08132


  • 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
  • Baker E.S., K.E. Burnum-Johnson, J.M. Jacobs, D.L. Diamond, R.N. Brown, Y.M. Ibrahim, and D.J. Orton, et al. 2014. "Advancing the High Throughput Identification of Liver Fibrosis Protein Signatures Using Multiplexed Ion Mobility Spectrometry." Molecular and Cellular Proteomics 13, no. 4:1119-1127. PNNL-SA-90826. doi:10.1074/mcp.M113.034595
  • Dominy S., J.N. Brown, M.I. Ryder, M.A. Gritsenko, J.M. Jacobs, and R.D. Smith. 2014. "Proteomic Analysis of Saliva in HIV-positive Heroin Addicts Reveals Proteins Correlated with Cognition." PLoS One 9, no. 4:e89366. PNNL-SA-95909. doi:10.1371/journal.pone.0089366
  • Govey P.M., J.M. Jacobs, S.C. Tilton, A.E. Loiselle, Y. Zhang, W.M. Freeman, and K.M. Waters, et al. 2014. "Integrative Transcriptomic and Proteomic Analysis of Osteocytic Cells Exposed to Fluid Flow Reveals Novel Mechano-Sensitive Signaling Pathways." Journal of Biomechanics 47, no. 8:1838-1845. PNWD-SA-10062. doi:10.1016/j.jbiomech.2014.03.022
  • Guo J., A.Y. Nguyen, Z. Dai, D. Su, M.J. Gaffrey, R.J. Moore, and J.M. Jacobs, et al. 2014. "Proteome-wide Light/Dark Modulation of Thiol Oxidation in Cyanobacteria Revealed by Quantitative Site-Specific Redox Proteomics." Molecular & Cellular Proteomics. MCP 13, no. 12:3270-3285. PNNL-SA-100244. doi:10.1074/mcp.M114.041160
  • Welkie D.G., X. Zhang, L.M. Markillie, R.C. Taylor, G. Orr, J.M. Jacobs, and K. Bhide, et al. 2014. "Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light-dark cycle." BMC Genomics15. PNNL-SA-104956. 


  • Price R.W., J. Peterson, D. Fuchs, T.E. Angel, H. Zetterberg, L. Hagberg, and S.S. Spudich, et al. 2013. "Approach to Cerebrospinal Fluid (CSF) Biomarker Discovery and Evaluation in HIV Infection." Journal of Neuroimmune Pharmacology 8, no. 5:1147-1158. PNNL-SA-98546. doi:10.1007/s11481-013-9491-3
  • 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


  • Angel T.E., J.M. Jacobs, R.P. Smith, M.S. Pasternack, S. Elias, M.A. Gritsenko, and A.K. Shukla, et al. 2012. "Cerebrospinal Fluid Proteome of Patients with Acute Lyme Disease." Journal of Proteome Research 11, no. 10:4814-4822. PNNL-SA-79143. doi:10.1021/pr300577p
  • Angel T.E., J.M. Jacobs, S.S. Spudich, M.A. Gritsenko, D. Fuchs, T. Liegler, and H. Zetterberg, et al. 2012. "The cerebrospinal fluid proteome in HIV infection: change associated with disease severity." Clinical Proteomics 9. PNNL-SA-81597. doi:10.1186/1559-0275-9-3
  • Aryal U.K., J. Stockel, E.A. Welsh, M.A. Gritsenko, C.D. Nicora, D.W. Koppenaal, and R.D. Smith, et al. 2012. "Dynamic proteome analysis of Cyanothece sp. ATCC 51142 under constant light." Journal of Proteome Research 11, no. 2:609-619. PNNL-SA-80375. doi:10.1021/pr200959x
  • Brown J.N., G.M. Ortiz, T.E. Angel, J.M. Jacobs, M.A. Gritsenko, E.Y. Chan, and D.E. Purdy, et al. 2012. "Morphine Produces Immunosuppressive Effects in Non-human Primates at the Proteomic and Cellular Levels." Molecular & Cellular Proteomics. MCP 11, no. 9:605-618. PNNL-SA-83778. doi:10.1074/mcp.M111.016121
  • Diamond D.L., A. Krasnoselski, K.E. Burnum, M.E. Monroe, B.M. Webb-Robertson, J.E. McDermott, and M.M. Yeh, et al. 2012. "Proteome and Computational Analyses Reveal New Insights into the Mechanisms of Hepatitis C Virus Mediated Liver Disease Posttransplantation." Hepatology 56, no. 1:28-38. PNWD-SA-9552. doi:10.1002/hep.25649


  • Aryal U.K., J. Stockel, R.K. Krovvidi, M.A. Gritsenko, M.E. Monroe, R.J. Moore, and D.W. Koppenaal, et al. 2011. "Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles." BMC Systems Biology 5. PNNL-SA-81418. doi:10.1186/1752-0509-5-194
  • 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
  • Matzke M.M., K.M. Waters, T.O. Metz, J.M. Jacobs, A. Sims, R. Baric, and J.G. Pounds, et al. 2011. "Improved Quality Control Processing of Peptide-centric LC-MS Proteomics Data." Bioinformatics 27, no. 20:2866-2872. PNNL-SA-76540. 
  • Stockel J., J.M. Jacobs, T.R. Elvitigala, M.L. Liberton, E.A. Welsh, A.D. Polpitiya, and M.A. Gritsenko, et al. 2011. "Diurnal Rhythms Result in Significant Changes in the Cellular Protein Complement in the Cyanobacterium Cyanothece 51142." PLoS One 6, no. 2:Article No.: e16680. PNNL-SA-78209. doi:10.1371/journal.pone.0016680
  • Teeguarden J.G., B.M. Webb-Robertson, K.M. Waters, A. Murray, E. Kisin, S.M. Varnum, and J.M. Jacobs, et al. 2011. "Comparative Proteomics and Pulmonary Toxicity of Instilled Single Walled Carbon Nanotubes, Crocidolite Asbestos and Ultrafine Carbon Black in Mice." Toxicological Sciences 120, no. 1:123-135. PNNL-SA-74369. doi:10.1093/toxsci/kfq363
  • 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 Chemistry286, no. 20:18190-18201. PNNL-SA-79165. 
  • Waters K.M., J.M. Jacobs, M.A. Gritsenko, and N.J. Karin. 2011. "Regulation of gene expression and subcellular protein distribution in MLO-Y4 osteocytic cells by lysophosphatidic acid: Relevance to dendrite outgrowth." Bone 48, no. 6:1328-35. PNNL-SA-74808. doi:10.1016/j.bone.2011.02.020
  • Webb-Robertson B.M., M.M. Matzke, J.M. Jacobs, J.G. Pounds, and K.M. Waters. 2011. "A Statistical Selection Strategy for Normalization Procedures in LC-MS Proteomics Experiments through Dataset Dependent Ranking of Normalization Scaling Factors." Proteomics 11, no. 24:4736-4741. PNNL-SA-78392. doi:10.1002/pmic.201100078


  • Angel T.E., B.J. Luft, X. Yang, C.D. Nicora, D.G. Camp, J.M. Jacobs, and R.D. Smith. 2010. "Proteome Analysis of Borrelia burgdorferi Response to Environmental Change." PLoS One 5, no. 11:Article No.: e13800. PNNL-SA-74148. doi:10.1371/journal.pone.0013800
  • Brown J.N., R. Palermo, C.R. Baskin, M.A. Gritsenko, P.J. Sabourin, P.J. Sabourin, and J.P. Long, et al. 2010. "Macaque Proteome Response to Highly Pathogenic Avian Influenza and 1918 Reassortant Influenza Virus Infections." Journal of Virology 84, no. 22:12058-12068. PNWD-SA-9238. 
  • Diamond D.L., A.J. Syder, J.M. Jacobs, C.M. Sorensen, K. Walters, S. Proll, and J.E. McDermott, et al. 2010. "Temporal Proteome and Lipidome Profiles Reveal HCV-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics." PLoS Pathogens 6, no. 1:Art. No. e1000719. PNWD-SA-8678. doi:10.1371/journal.ppat.1000719
  • Webb-Robertson B.M., L.A. McCue, K.M. Waters, M.M. Matzke, J.M. Jacobs, T.O. Metz, and S.M. Varnum, et al. 2010. "Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-based Proteomics Data." Journal of Proteome Research 9, no. 11:5748-5756. PNNL-SA-72886. 
  • Wegener K.M., A.K. Singh, J.M. Jacobs, T.R. Elvitigala, E.A. Welsh, N.S. Keren, and M.A. Gritsenko, et al. 2010. "Global Proteomics Reveal An Atypical Strategy for Carbon/Nitrogen Assimilation by a Cyanobacterium Under Diverse Environmental Perturbations." Molecular & Cellular Proteomics. MCP 9, no. 12:2678-89. PNNL-SA-67041. doi:10.1074/mcp.M110.000109
  • Zhang X., M.E. Monroe, B. Chen, M.H. Chin, T.H. Heibeck, A.A. Schepmoes, and F. Yang, et al. 2010. "Endogenous 3, 4- Dihydroxyphenylalanine and Dopaquinone Modifications on Protein Tyrosine: links to mitochondrially derived oxidative stress via hydroxyl radical." Molecular & Cellular Proteomics. MCP 9, no. 6:1199-1208. PNNL-SA-65899. 


  • Chan E.Y., J.N. Sutton, J.M. Jacobs, A. Bondarenko, R.D. Smith, and M.G. Katze. 2009. "Dynamic Host Energetics and Cytoskeletal Proteomes in HIV-1 -Infected Human Primary CD4 Cells: Analysis by Multiplexed Label-free Mass Spectrometry." Journal of Virology 83, no. 18:9283-9295. PNWD-SA-8677. 


  • 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
  • Dumortier J., D.N. Streblow, A.V. Moses, J.M. Jacobs, C.N. Kreklywich, D.G. Camp, and R.D. Smith, et al. 2008. "Human Cytomegalovirus Secretome Contains Factors That Induce Angiogenesis and Wound Healing." Journal of Virology 82, no. 13:6524-6535. PNNL-SA-60994. doi:10.1128/JVI.00502-08
  • Jacobs J.M., K.M. Waters, L.E. Kathmann, D.G. Camp, H.S. Wiley, R.D. Smith, and B.D. Thrall. 2008. "The Mammary Epithelial Cell Secretome and its Regulation by Signal Transduction Pathways." Journal of Proteome Research 7, no. 2:558-569. PNNL-SA-56310. doi:10.1021/pr0704377
  • Metz T.O., W. Qian, J.M. Jacobs, M.A. Gritsenko, R.J. Moore, A.D. Polpitiya, and M.E. Monroe, et al. 2008. "Application of proteomics in the discovery of candidate protein biomarkers in a Diabetes Autoantibody Standardization Program sample subset." Journal of Proteome Research 7, no. 2:698-707. PNNL-SA-56533. doi:10.1021/pr700606w
  • Pasa-Tolic L., J.M. Jacobs, W. Qian, and R.D. Smith. 2008. "Quantitative Proteomics using Nano-LC with High Accuracy Mass Spectrometry." In Clinical Proteomics: From Diagnosis to Therapy, edited by JE Van Eyk and MJ Dunn. 89-100. Weinheim:Wiley-VCH. PNNL-SA-51867. 
  • Wegener K.M., E.A. Welsh, L.E. Thornton, N.S. Keren, J.M. Jacobs, K.K. Hixson, and M.E. Monroe, et al. 2008. "High Sensitivity Proteomics Assisted Discovery of a Novel Operon Involved in the Assembly of Photosystem II, a Membrane Protein Complex." Journal of Biological Chemistry 283, no. 41:27829-27837. PNNL-SA-57538. doi:10.1074/jbc.M803918200
  • Welsh E.A., M.L. Liberton, J. Stockel, T. Loh, T.R. Elvitigala, C. Wang, and A. Wollam, et al. 2008. "The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle." Proceedings of the National Academy of Sciences of the United States of America 105, no. 39:15094-15099. PNNL-SA-56846. doi:10.1073/pnas.0805418105


  • Diamond D.L., J.M. Jacobs, B. Paeper, S. Proll, M.A. Gritsenko, R.L. Carithers, Jr., and A.M. Larson, et al. 2007. "Proteomic Profiling of Human Liver Biopsies: Hepatitis C Virus-Induced Fibrosis and Mitochondrial Dysfunction." Hepatology 46, no. 3:649-657. PNWD-SA-7685. doi:10.1002/hep.21751
  • Dutta D., S.K. Sundaram, J.G. Teeguarden, B.J. Riley, L.S. Fifield, J.M. Jacobs, and R.S. Addleman, et al. 2007. "Adsorbed Proteins Influence the Biological Activity and Molecular Targeting of Nanomaterials." Toxicological Sciences 100, no. 1:303-315. PNNL-SA-55139. doi:10.1093/toxsci/kfm217
  • Metz T.O., Q. Zhang, J.S. Page, Y. Shen, S.J. Callister, J.M. Jacobs, and R.D. Smith. 2007. "The future of liquid chromatography-mass spectrometry in metabolic profiling and metabolomic studies for biomarker discovery." Biomarkers in Medicine 1, no. 1:159-185. PNNL-SA-53806. 
  • Wang Y., S. Ding, W. Wang, F. Yang, J.M. Jacobs, D.G. Camp, and R.D. Smith, et al. 2007. "Methods for Pseudopodia Purification and Proteomic Analysis." Sciences STKE Signal Transduction Knowledge Environment 2007, no. 400:p14. PNNL-SA-56168. 
  • Wang Y., S. Ding, W. Wang, J.M. Jacobs, W. Qian, R.J. Moore, and F. Yang, et al. 2007. "Profiling Signaling Polarity in Chemotactic Cells." Proceedings of the National Academy of Sciences of the United States of America 104, no. 20:8328-8333. PNNL-SA-51866. doi:10.1073/pnas.0701103104


  • Baas T., C.R. Baskin, D.L. Diamond, A. Garcia-Sastre, H. Bielefeldt-Ohmann, T.M. Tumpey, and M.J. Thomas, et al. 2006. "Integrated Molecular Signature of Disease: Analysis of Influenza Virus-Infected Macaques through Functional Genomics and Proteomics." Journal of Virology80, no. 21:10813 (16 pages). PNWD-SA-7379. doi:10.1128/JVI.00851-06
  • Diamond D.L., S. Proll, J.M. Jacobs, E.Y. Chan, D.G. Camp, R.D. Smith, and M.G. Katze. 2006. "HepatoProteomics: Applying Proteomic Technologies to the Study of Liver Function and Disease." Hepatology 44, no. 2:299-308. PNWD-SA-7378. 
  • Jacobs J.M., and R.D. Smith. 2006. "Proteomic Analyses Using High-Efficiency Separations and Accurate Mass Measurements." In Separation Methods in Proteomics, edited by GB Smejkal and A Lazareu. 363-385. Boca Raton, Florida:CRC Taylor & Francis. PNNL-SA-42439. 
  • Metz T.O., J.M. Jacobs, M.A. Gritsenko, G. Fontes, W. Qian, D.G. Camp, and V.J. Poitout, et al. 2006. "Characterization of the Human Pancreatic Islet Proteome by Two-Dimensional LC/MS/MS." Journal of Proteome Research 5, no. 12:3345-3354. PNNL-SA-49730. doi:10.1021/pr060322n
  • Qian W., J.M. Jacobs, T. Liu, D.G. Camp, and R.D. Smith. 2006. "Advances and Challenges in Liquid Chromatography-Mass Spectrometry-Based Proteomics Profiling for Clinical Applications." Molecular & Cellular Proteomics. MCP 5, no. 10:1727-1744. PNWD-SA-7399. doi:10.1074/mcp.M600162-MCP200


  • 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
  • Jacobs J.M., D.L. Diamond, E.Y. Chan, M.A. Gritsenko, W. Qian, M. Stastna, and T. Baas, et al. 2005. "Proteome Analysis of Liver Cells Expressing a Full- Length Hepatitis C Virus (HCV) Replicon and Biopsy Specimens of Posttransplantation Liver from HCV-Infected Patients." Journal of Virology 79, no. 12:7558-7569. PNWD-SA-6678. 
  • 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
  • Jacobs J.M., M.E. Monroe, W. Qian, Y. Shen, G.A. Anderson, and R.D. Smith. 2005. "Ultra-Sensitive, High Throughput and Quantitative Proteomics Measurements." International Journal of Mass Spectrometry 240, no. 3:195-212. PNNL-SA-42919. 
  • Jacobs J.M., X. Yang, B.J. Luft, J.J. Dunn, D.G. Camp, and R.D. Smith. 2005. "Proteomic Analysis of Lyme Disease: Global Protein Comparison of Three Strains of Borrelia burgdorferi." Proteomics 5, no. 5:1446-1453. PNNL-SA-42921. 
  • Liu T., W. Qian, W.U. Chen, J.M. Jacobs, R.J. Moore, D.J. Anderson, and M.A. Gritsenko, et al. 2005. "Improved Proteome Coverage by Using High Efficiency Cysteinyl-peptide Enrichment: The Human Mammary Epithelial Cell Proteome." Proteomics 5, no. 5:1263-1273. PNNL-SA-42468. 
  • Qian W., J.M. Jacobs, D.G. Camp, M.E. Monroe, R.J. Moore, M.A. Gritsenko, and S.E. Calvano, et al. 2005. "Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry." Proteomics 5, no. 2:572-584. PNNL-SA-40692. doi:10.1002/pmic.200400942
  • Qian W., M.E. Monroe, T. Liu, J.M. Jacobs, G.A. Anderson, Y. Shen, and R.J. Moore, et al. 2005. "Quantitative Proteome Analysis of Human Plasma Following in vivo Lipopolysaccharide Administration using O-16/O-18 Labeling and the Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics. MCP 4, no. 5:700-709. PNNL-SA-44302. 
  • Qian W., T. Liu, M.E. Monroe, E.F. Strittmatter, J.M. Jacobs, L.J. Kangas, and K. Petritis, et al. 2005. "Probability-Based Evaluation of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis: The Human Proteome." Journal of Proteome Research4, no. 1:53-62. PNNL-SA-42815. 
  • Shen Y., J. Kim, E.F. Strittmatter, J.M. Jacobs, D.G. Camp, R. Fang, and N. Tolic, et al. 2005. "Characterization of the human blood plasma proteome." Proteomics 5, no. 15:4034-4045. PNWD-SA-6708. 


  • Jacobs J.M., H.M. Mottaz, L. Yu, D.J. Anderson, R.J. Moore, W.U. Chen, and K.J. Auberry, et al. 2004. "Multidimensional Proteome Analysis of Human Mammary Epithelial Cells." Journal of Proteome Research 3, no. 1:68-75. PNWD-SA-6087. 
  • Shen Y., J.M. Jacobs, D.G. Camp, R. Fang, R.J. Moore, R.D. Smith, and W. Xiao, et al. 2004. "Ultra-High-Efficiency Strong Cation Exchange LC/RPLC/MS/MS for High Dynamic Range Characterization of the Human Plasma Proteome." Analytical Chemistry 76, no. 4:1134-1144. PNNL-SA-39155. 
  • Strittmatter E.F., L.J. Kangas, K. Petritis, H.M. Mottaz, G.A. Anderson, Y. Shen, and J.M. Jacobs, et al. 2004. "Application of Peptide LC Retention Time Information in a Discriminant Function for Peptide Identification by Tandem Mass Spectrometry." Journal of Proteome Research 3, no. 4:760-769. PNNL-SA-40693.