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Jon Jacobs
Biomedical scientist

Dr. Jon Jacobs is a biomedical scientist who leads the Cell Signaling and Communications team. Jacobs has more than 19 years of experience in proteomics and protein chemistry. As a staff scientist for Pacific Northwest National Laboratory, Jacobs studies the application of advanced proteomic approaches toward answering both clinical and fundamental biological questions relevant to the Biological and Environmental Research program, sponsored by the U.S. Department of Energy’s Office of Science and the National Institutes of Health. Jacobs serves as the associate resource director of the Proteomics Research Resource for Integrative Biology, which is a national user facility that designs and develops proteomic technologies for use in the biomedical community. He also supports the OHSU/PNNL PMedIC program through creating and building collaborative projects and programs. His article on blood plasma proteomics measurements for the discovery of new candidate biomarkers for various diseases was recognized as one of top 20 most cited articles of all time published by the Journal of Proteome Research. His most recent research includes nutritional markers and proteome in patients undergoing treatment for pulmonary tuberculosis, system-wide investigation of alcoholic hepatitis disease progression and treatment, omics analysis supporting the Acute to Chronic Pain Signature consortium, and nanoscale proteome spatial mapping of SIV/HIV infected tissue.

Discipline and Skills

  • Mass spectrometry
  • Protein chemistry
  • Proteomics

Education

  • PhD in Biochemistry, Montana State University, 2002
  • BS in Chemistry, Doctor of Philosophy, Brigham Young University, 1996

Affiliations and Professional Service

  • Washington State University Tri-Cities, Richland, WA. Adjunct Faculty, Department of Biological Science (2003–2008)
  • PLoS ONE Editorial Board, Academic Editor (2014–present) 
  • Ad hoc peer reviewer for NIH/NIAID, Special Emphasis Panel member (2014–present)

Patents

  • Jacobs, J.M., Burnum-Johnson, K.E., Baker, E.M., Smith, R.D., Gritsenko, M.A., Orton, D. Biomarkers for liver fibrosis. 2017 U.S. Patent 9,651,563
  • Jacobs, J.M., Burnum-Johnson, K.E., Baker, E.M., Smith, R.D., Gritsenko, M.A., Orton, D. Biomarkers for liver fibrosis. 2015 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.

Publications

2020

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. Proteomic assessment of serum biomarkers of longevity in older men. Aging Cell (2020) epub.

Tsai, CF, Smith, JS, Eiger, DS, Martin, K, Liu, T, Smith, RD, Shi, T, Rajagopal, S,  Jacobs, JM. Mass spectrometry-based proteomics for analysis of hydrophilic phosphopeptides. Book Chapter, Methods in Molecular Biology.(2020)

Deatherage Kaiser BL, Jacobs JM, Schepmoes AA, Brewer HM, Webb-Robertson BM, Valtier S, Bebarta VS, Adkins JN Assessment of the Utility of the Oral Fluid and Plasma Proteomes for Hydrocodone Exposure.. J Med Toxicol. (2020) Jan;16(1):49-60.

 

2019

Nagarajan A, Zhou M, Nguyen AY, Liberton M, Kedia K, Shi T, Piehowski P, Shukla A, Fillmore TL, Nicora C, Smith RD, Koppenaal DW, Jacobs JM, Pakrasi HB. Proteomic Insights into Phycobilisome Degradation, A Selective and Tightly Controlled Process in The Fast-Growing Cyanobacterium Synechococcus elongatus UTEX 2973. Biomolecules. (2019) Aug 16;9(8).

Tsai CF, Smith JS, Krajewski K, Zhao R, Moghieb AM, Nicora CD, Xiong X, Moore RJ, Liu T, Smith RD, Jacobs JM, Rajagopal S, Shi T. Tandem Mass Tag Labeling Facilitates Reversed-Phase Liquid Chromatography-Mass Spectrometry Analysis of Hydrophilic Phosphopeptides. Anal Chem. (2019) Sep 17;91(18):11606-11613.

Nielson CM, Jacobs JM, Orwoll ES. Proteomic studies of bone and skeletal health outcomes. Bone. (2019) Sep;126:18-26.

Moghieb A, Tesfay L, Nie S, Gritsenko M, Fillmore TL, Jacobs JM, Smith RD, Torti FM, Torti SV, Shi T, Ansong C. A Targeted Mass Spectrometric Assay for Reliable Sensitive Hepcidin Quantification. Sci Rep. (2019) May 13;9(1):7264.

Zhang P, Gaffrey MJ, Zhu Y, Chrisler WB, Fillmore TL, Yi L, Nicora CD, Zhang T, Wu H, Jacobs JM, Tang K, Kagan J, Srivastava S, Rodland KD, Qian WJ, Smith RD, Liu T, Wiley HS, Shi T. Carrier-assisted single-tube processing approach for targeted proteomics analysis of low numbers of mammalian cells. Anal Chem. (2019) Jan 15;91(2):1441-145.

Stevens SL, Liu T, Bahjat FR, Petyuk VA, Schepmoes AA, Sontag RL, Gritsenko MA, Wu C, Wang S, Shukla AK, Jacobs JM, Smith RD, Rodland KD, Alexander West G, Kohama SG, Glynn C, Stenzel-Poore MP. Preconditioning in the Rhesus Macaque Induces a Proteomic Signature Following Cerebral Ischemia that Is Associated with Neuroprotection. Transl Stroke Res. (2019) Aug;10(4):440-448.

 

2018

Orwoll ES, Wiedrick J, Jacobs J, Baker ES, Piehowski P, Petyuk V, Gao Y, Shi T, Smith RD, Bauer DC, Cummings SR, Nielson CM, Lapidus J; Osteoporotic Fractures in Men Study (MrOS) Research Group. High-throughput serum proteomics for the identification of protein biomarkers of mortality in older men. Aging Cell. (2018) Apr;17(2).

Kedia K, Wendler JP, Baker ES, Burnum-Johnson KE, Jarsberg LG, Stratton KG, Wright AT, Piehowski PD, Gritsenko MA, Lewinsohn DM, Sigal GB, Weiner MH, Smith RD, Jacobs JM, Nahid P.Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis. Tuberculosis. (2018) Sep;112:52-61.

 

2017

Sigal GB, Segal MR, Mathew A, Jarlsberg L, Wang M, Barbero S, Small N, Haynesworth K, Davis JL, Weiner M, Whitworth WC, Jacobs J, Schorey J, Lewinsohn DM, Nahid P. Biomarkers of Tuberculosis Severity and Treatment Effect: A Directed Screen of 70 Host Markers in a Randomized Clinical Trial. EBioMedicine. (2017) Nov;25:112-121.

Amie J. Eisfeld, Peter J. Halfmann, Jason P. Wendler, Jennifer E. Kyle, Kristin E. Burnum-Johnson, Zuleyma Peralta, Tadashi Maemura, Kevin B. Walters, Tokiko Watanabe, Satoshi Fukuyama, Makoto Yamashita, Jon M. Jacobs, Young-Mo Kim, Cameron P. Casey, Kelly G. Stratton, Bobbie-Jo Webb-Robertson, Marina A. Gritsenko, Matthew E. Monroe, Karl K. Weitz, Anil K. Shukla, Mingyuan Tian, Gabriele Neumann, Jennifer L. Reed, Harm van Bakel, Thomas O. Metz, Richard D. Smith, Katrina M. Waters, Alhaji N’jai, Foday Sahr, and Yoshihiro Kawaoka. Human Ebola Virus Disease Pathogenesis Revealed by Multi-Platform ‘Omics Analysis. Cell Host Microbe. (2017) Dec 13;22(6):817-829.e8.

Nielson CM, Wiedrick J, Shen J, Jacobs J, Baker ES, Baraff A, Piehowski P, Lee CG, Baratt A, Petyuk V, McWeeney S, Lim JY, Bauer DC, Lane NE, Cawthon PM, Smith RD, Lapidus J, Orwoll ES; Osteoporotic Fractures in Men (MrOS) Study Research Group. Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics. J Bone Miner Res. (2017) Jul;32(7):1559-1567.

Liberton M, Chrisler WB, Nicora CD, Moore RJ, Smith RD, Koppenaal DW, Pakrasi HB, Jacobs JM. Phycobilisome truncation causes widespread proteome changes in Synechocystis sp. PCC 6803. PLoS One. (2017) Mar 2;12(3):e0173251.

 

2016

Oxford KL, Wendler JP, McDermott JE, White Iii RA, Powell JD, Jacobs JM, Adkins JN, Waters KM. “The landscape of viral proteomics and its potential to impact human health.” Expert Rev Proteomics. (2016) Jun;13(6):579-91.

Velásquez C, Cheng E, Shuda M, Lee-Oesterreich PJ, Pogge von Strandmann L, Gritsenko MA, Jacobs JM, Moore PS, Chang Y. Mitotic protein kinase CDK1 phosphorylation of mRNA translation regulator 4E-BP1 Ser83 may contribute to cell transformation. Proc Natl Acad Sci U S A. (2016) Jul 26;113(30):8466-71.

Hiras J, Wu YW, Deng K, Nicora CD, Aldrich JT, Frey D, Kolinko S, Robinson EW, Jacobs JM, Adams PD, Northen TR, Simmons BA, Singer SW.Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis.MBio. (2016) Aug 23;7(4).

Nakayasu, E.S., Nicora, C.D., Sims, A.C., Burnum-Johnson, K.E., Kim, Y.M., Kyle, J.E., Matzke, M.M., Shukla, A.K., Chu, R.K., Schepmoes, A.A., Jacobs, J.M., Baric,R.S., Webb-Robertson, B.J., Smith, R.D., Metz, T.O. “MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses” (2016) Volume 1 Issue 3 e00043-16.

Oxford KL, Wendler JP, McDermott JE, White Iii RA, Powell JD, Jacobs JM, Adkins JN, Waters KM. “The landscape of viral proteomics and its potential to impact human health.” Expert Rev Proteomics. (2016) Jun;13(6):579-91.

Velásquez C, Cheng E, Shuda M, Lee-Oesterreich PJ, Pogge von Strandmann L, Gritsenko MA, Jacobs JM, Moore PS, Chang Y. Mitotic protein kinase CDK1 phosphorylation of mRNA translation regulator 4E-BP1 Ser83 may contribute to cell transformation. Proc Natl Acad Sci U S A. (2016) Jul 26;113(30):8466-71.

Nielson CM, Jones KS, Chun RF, Jacobs JM, Wang Y, Hewison M, Adams JS, Swanson CM, Lee CG, Vanderschueren D, Pauwels S, Prentice A, Smith RD, Shi T, Gao Y, Schepmoes AA, Zmuda JM, Lapidus J, Cauley JA, Bouillon R, Schoenmakers I, Orwoll ES; Osteoporotic Fractures in Men (MrOS) Research Group. “Free 25-Hydroxyvitamin D: Impact of Vitamin D Binding Protein Assays on Racial-Genotypic Associations.”J Clin Endocrinol Metab. (2016) May;101(5):2226-34.

Nielson CM, Jones KS, Bouillon R; Osteoporotic Fractures in Men (MrOS) Research Group, Chun RF, Jacobs J, Wang Y, Hewison M, Adams JS, Swanson CM, Lee CG, Vanderschueren D, Pauwels S, Prentice A, Smith RD, Shi T, Gao Y, Zmuda JM, Lapidus J, Cauley JA, Schoenmakers I, Orwoll ES. “Role of Assay Type in Determining Free 25-Hydroxyvitamin D Levels in Diverse Populations.” N Engl J Med. (2016) Apr 28;374(17):1695-6.

Liberton M, Saha R, Jacobs JM, Nguyen AY, Gritsenko MA, Smith RD, Koppenaal DW, Pakrasi HB. “Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium.” Mol Cell Proteomics. (2016) Jun;15(6):2021-32.

 

2015

Yu, J., Liberton, M., Cliften, P.F., Head, R.D., Jacobs, J.M., Smith, R.D., Koppenaal, D.W., Brand, J.J., Pakrasi, H.B. “Synechococcus elongatus UTEX 2973, a fast growing cyanobacterial chassis for biosynthesis using light and CO2” (2015) Scientific Reports 5:8132.

 

2014

Welkie, D., Zhang, X., Markillie, M.L., Taylor, R., Orr, G., Jacobs, J.M., Bhide, K., Thimmapuram, J., Gritsenko, M., Mitchell, H., Smith, R.D., Sherman, L.A. “Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light–dark cycle” (2014) BMC Genomics 15:1185.

Aevermann, B.D., Pickett, B.E., Kumar, S., Klem, E.B., Agnihothram, S., Askovich, P.S., Bankhead, A. 3rd, Bolles, M., Carter, V., Chang, J., Clauss, T.R., Dash, P., Diercks, A.H., Eisfeld, A.J., Ellis, A., Fan, S., Ferris, M.T., Gralinski, L.E., Green, R.R., Gritsenko, M.A., Hatta, M., Heegel, R.A., Jacobs, J.M., Jeng, S., Josset, L., Kaiser, S.M., Kelly, S., Law, G.L., Li, C., Li, J., Long, C., Luna, M.L., Matzke, M., McDermott, J., Menachery, V., Metz, T.O., Mitchell, H., Monroe, M.E., Navarro, G., Neumann, G., Podyminogin, R.L., Purvine, S.O., Rosenberger, C.M., Sanders, C.J., Schepmoes, A.A., Shukla, A.K., Sims, A., Sova, P., Tam, V.C., Tchitchek, N., Thomas, P.G., Tilton, S.C., Totura, A., Wang, J., Webb-Robertson, B.J., Wen, J., Weiss, J.M., Yang, F., Yount, B., Zhang, Q., McWeeney, S., Smith, R.D., Waters, K.M., Kawaoka, Y., Baric, R., Aderem, A., Katze, M.G., Scheuermann, R.H. “A comprehensive collection of systems biology data characterizing the host response to viral infection.” (2014) Sci Data 1:140033.

Guo, J., Nguyen, A.Y., Dai, Z., Su, D., Gaffrey, M.J., Moore, R.J., Jacobs, J.M., Monroe, M.E., Smith, R.D., Koppenaal, D.W., Pakrasi, H.B., Qian, W.J. “Proteome-wide Light/Dark Modulation of Thiol Oxidation in Cyanobacteria Revealed by Quantitative Site-Specific Redox Proteomics.” (2014) Mol Cell Proteomics. 13:3270-85.

Govey, P.M., Jacobs, J.M., Tilton, S.C., Loiselle, A.E., Zhang, Y., Freeman, W.M., Waters, K.M., Karin, N.J., Donahue, H.J. “Integrative transcriptomic and proteomic analysis of osteocytic cells exposed to fluid flow reveals novel mechano-sensitive signaling pathways.” (2014) J Biomech. 47, 1838-45.

Dominy, S.S., Brown, J.N., Ryder, M.I., Gritsenko, M., Jacobs, J.M., Smith, R.D. “Proteomic Analysis of Saliva in HIV-Positive Heroin Addicts Reveals Proteins Correlated with Cognition.” (2014) PLoS One. 9:e89366.

Baker, E.S., Burnum-Johnson, K.E., Jacobs, J.M., Diamond, D.L., Brown, R.N., Ibrahim, Y.M., Orton, D.J., Piehowski, P.D., Purdy, D.E., Moore, R.J., Danielson, W.F., Monroe, M.E., Crowell, K.L., Slysz, G.W., Gritsenko, M.A., Sandoval, J.D., Lamarche, B.L., Matzke, M.M., Webb-Robertson, B.J., Simons, B.C., McMahon, B.J., Bhattacharya, R., Perkins, J.D., Carithers, R.L., Strom,S., Self, S.G., Katze, M.G., Anderson, G.A., Smith, R.D. “Advancing the high throughput identification of liver fibrosis protein signatures using multiplexed ion mobility spectrometry.” (2014) Mol Cell Proteomics. 13, 1119-27.

 

2013

Wang, J., Webb-Robertson, B.J., Matzke, M.M., Varnum, S.M., Brown, J.N., Riensche, R.M., Adkins, J.N., Jacobs, J.M., Hoidal, J.R., Scholand, M.B., Pounds, J.G., Blackburn, M.R., Rodland, K.D., McDermott, J.E. “A semiautomated framework for integrating expert knowledge into disease marker identification.” (2013) Dis Markers. 35, 513-23.

Price, R.W., Peterson, J., Fuchs, D., Angel, T.E., Zetterberg, H., Hagberg, L., Spudich, S., Smith, R.D., Jacobs, J.M., Brown, J.N., Gisslen, M. “Approach to cerebrospinal fluid (CSF) biomarker discovery and evaluation in HIV infection.” (2013) J Neuroimmune Pharmacol. 8:1147-58.

 

2012

Angel, T.E., Jacobs, J.M., Smith, R.P., Pasternack, M.S., Elias, S., Gritsenko, M.A., Shukla, A., Gilmore, E.C., McCarthy, C., Camp, D.G. 2nd, Smith, R.D., Warren, H.S. “Cerebrospinal Fluid Proteome of Patients with Acute Lyme Disease.” (2012)  J. Proteome Res. 11:4814-4822.

Brown, J.N., Ortiz, G.M., Angel, T.E., Jacobs, J.M., Gritsenko, M., Chan, E.Y., Purdy, D.E., Murnane, R.D., Larsen, K., Palermo, R.E., Shukla, A.K., Clauss, T.R., Katze, M.G., McCune, J.M., Smith, R.D. “Morphine produces immunosuppressive effects in nonhuman primates at the proteomic and cellular levels.” (2012) Mol Cell Proteomics. 11:605-18.

Angel, T.E., Jacobs, J.M., Spudich, S.S., Gritsenko, M.A., Fuchs, D., Liegler, T., Zetterberg, H., Camp, D.G. 2nd, Price, R.W., Smith, R.D. “The cerebrospinal fluid proteome in HIV infection: change associated with disease severity.” (2012) Clin Proteomics. 9:3.

Diamond, D.L., Krasnoselski, A., Burnum, K.E., Susnow, N., Webb-Robertson, B.J., McDermott, J.E.,  Yeh, M.M.,Strom, S.,Proll, S.C., Belisle, S.E., Rasmussen, A.L., Walters, K.A., Jacobs, J.M., Gritsenko, M.A., Bhattacharya, R., Perkins, J.D., Carithers

Jr., R.L., Liou, I.W., Waters, K.M., Smith, R.D., Larson, A.M.,  Katze, M.G. “Proteome Profiles Correlate with Rapidly Progressive Fibrosis in Hepatitis C Virus Infected Liver Transplant Recipients” (2012) Hepatology, 56:28-38.

Aryal UK, Stöckel J, Welsh EA, Gritsenko MA, Nicora CD, Koppenaal DW, Smith RD, Pakrasi HB, Jacobs JM. “Dynamic Proteome Analysis of Cyanothece sp. ATCC 51142 under Constant Light.” (2012) J Proteome Res. 11:609.

 

2011

Webb-Robertson BJ, Matzke MM, Jacobs JM, Pounds JG, Waters KM “A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors.”. Proteomics. (2011) 11:4736-41.

Dresang LR, Teuton JR, Feng H, Jacobs JM, Camp DG 2nd, Purvine SO, Gritsenko MA, Li Z, Smith RD, Sugden B, Moore PS, Chang Y. “Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes.” (2011) BMC Genomics. 12:625.

Aryal UK, Stöckel J, Krovvidi RK, Gritsenko MA, Monroe ME, Moore RJ, Koppenaal DW, Smith RD, Pakrasi HB, Jacobs JM. “Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles.” (2011) BMC Syst Biol. 1:194.

Matzke MM, KM Waters, TO Metz, JM Jacobs, A Sims, R Baric, JG Pounds, and BJM Webb-Robertson. "Improved Quality Control Processing of Peptide-centric LCMS Proteomics Data." (2011) Bioinformatics. 27:2866.

Stöckel J, Jacobs JM, Elvitigala TR, Liberton M, Welsh EA, Polpitiya AD, Gritsenko MA, Nicora CD, Koppenaal DW, Smith RD, Pakrasi HB. “Diurnal rhythms result in significant changes in the cellular protein complement in the cyanobacterium Cyanothece 51142.” (2011) PLoS One. 6:e16680.

Teeguarden JG, Webb-Robertson BJ, Waters KM, Murray AR, Kisin ER, Varnum SM, Jacobs JM, Pounds JG, Zanger RC, Shvedova AA. “Comparative proteomics and pulmonary toxicity of instilled single-walled carbon nanotubes, crocidolite asbestos, and ultrafine carbon black in mice.” (2011) Toxicol Sci. 120:123-35.

Waters KM, Jacobs JM, Gritsenko MA, Karin NJ. “Regulation of gene expression and subcellular protein distribution in MLO-Y4 osteocytic cells by lysophosphatidic acid: Relevance to dendrite outgrowth.” (2011) Bone. 48:1328-35.

Wang Y, Yang F, Fu Y, Huang X, Wang W, Jiang X, Gritsenko MA, Zhao R, Monore ME, Pertz OC, Purvine SO, Orton DJ, Jacobs JM, Camp DG 2nd, Smith RD, Klemke RL. “Spatial phosphoprotein profiling reveals a compartmentalized ERK switch governing neurite growth and retraction.” (2011) J Biol Chem.  286:18190-201.

 

2010

Angel TE, Luft BJ, Yang X, Nicora CD, Camp DG 2nd, Jacobs JM, Smith RD. “Proteome analysis of Borrelia burgdorferi response to environmental change.” (2010) PLoS One. 5:e13800.

Zhang X, Monroe ME, Chen B, Chin MH, Heibeck TH, Schepmoes AA, Yang F, Petritis BO, Camp DG 2nd, Pounds JG, Jacobs JM, Smith DJ, Bigelow DJ, Smith RD, Qian WJ. “Endogenous 3,4-dihydroxyphenylalanine and dopaquinone modifications on protein tyrosine: links to mitochondrially derived oxidative stress via hydroxyl radical.” (2010) Mol Cell Proteomics. 9:1199-208.

Webb-Robertson BJ, McCue LA, Waters KM, Matzke MM, Jacobs JM, Metz TO, Varnum SM, Pounds JG. “Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-Based Proteomics Data.” (2010) J Proteome Res. 9:5748-56.

Brown JN, Palermo RE, Baskin CR, Gritsenko M, Sabourin PJ, Long JP, Sabourin CL, Bielefeldt-Ohmann H, García-Sastre A, Albrecht R, Tumpey TM, Jacobs JM, Smith RD, Katze MG. “Macaque proteome response to highly pathogenic avian influenza and 1918 reassortant influenza virus infections.” (2010) J Virol. 84:12058-68.

Wegener KM, Singh AK, Jacobs JM, Elvitigala TR, Welsh EA, Keren N, Gritsenko MA, Ghosh BK, Camp DG 2nd, Smith RD, Pakrasi HB. “Global proteomics reveal an atypical strategy for carbon/nitrogen assimilation by a cyanobacterium under diverse environmental perturbations.” (2010) Mol Cell Proteomics. 9:2678-89.

Diamond DL, Snyder AJ, Jacobs JM, Sorensen CM, Walters KA, Proll SC, McDermott JE, Gritsenko MA, Zhang Q, Zhao R, Metz TO, Camp DG 2nd, Waters KM, Smith RD, Rice CM, Katze MG. “Temporal proteome and lipidome profiles reveal hepatitis C virus-associated reprogramming of hepatocellular metabolism and bioenergetics.” (2010) PLoS Pathog. 6:e1000719

 

2009

Chan EY, Sutton JN, Jacobs JM, Bondarenko A, Smith RD, Katze MG “Dynamic host energetics and cytoskeletal proteomes in human immunodeficiency virus type 1-infected human primary CD4 cells: analysis by multiplexed label-free mass spectrometry” (2009) J. Virol. 83:9283-95.

 

2008

Wegener, K.M., Welsh, E.A., Thornton, L.E., Keren, N., Jacobs, J.M., Hixson, K.K., Monroe, M.E., Camp, D.G. 2nd, Smith, R.D., Pakrasi, H.B. “High sensitivity proteomics assisted discovery of a novel operon involved in the assembly of photosystem II, a membrane protein complex.” (2008) J Biol Chem. 283: 27829-27837.

Welsh, E.A., Liberton, M., Stöckel, J., Loh, T., Elvitigala, T., Wang, C., Wollam, A., Fulton, R.S., Clifton, S.W., Jacobs, J.M., Aurora, R., Ghosh, B.K., Sherman, L.A., Smith, R.D., Wilson, R.K., Pakrasi, H.B. “The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle.” (2008) Proc Natl Acad Sci USA 105:15094-15099.

Ding, S.J., Wang, Y., Jacobs, J.M., Qian, W.J., Yang, F., Tolmachev, A.V., Du, X., Wang, W., Moore, R.J., Monroe, M.E., Purvine, S.O., Waters, K., Heibeck, T.H., Adkins, J.N., Camp, D.G. 2nd, Klemke, R.L., Smith, R.D. “Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis Applying Dual-Step (18)O Labeling Coupled with Immobilized Metal-Ion Affinity Chromatography.” (2008) J. Proteome Res. 7:4215-4224.

Dumortier, J., Streblow, D.N., Moses, A.V., Jacobs, J.M., Kreklywich, C.N., Camp, D., Smith, R.D., Orloff, S.L., Nelson, J.A. “Human Cytomegalovirus Secretome Contains Factors That Induce Angiogenesis and Wound Healing” (2008) J. Virol. 82:6524-6535.

Jacobs JM, Waters KM, Kathmann LE, Camp DG 2nd, Wiley HS, Smith RD, Thrall BD. “The Mammary Epithelial Cell Secretome and its Regulation by Signal Transduction Pathways” (2008) J.Proteome Res. 7:558-569.

Metz TO, Qian WJ, Jacobs JM, Gritsenko MA, Moore RJ, Polpitiya AD, Monroe ME, Camp DG 2nd, Mueller PW, Smith RD. “Application of Proteomics in the Discovery of Candidate Protein Biomarkers in a Diabetes Autoantibody Standardization Program Sample Subset” (2008) J.Proteome Res.7: 698-707.

Pasa-Tolic L., J. M. Jacobs, W.-J. Qian and R. D. Smith “Quantitative Proteomics using Nano-LC with High Accuracy Mass Spectrometry, in: Clinical Proteomics (J. E. Van Eyk and M. J. Dunn, Eds.),”, Wiley-VCH Verlag GmbH & Co. KGaA, Chapter 7, 89-100 (2008).

 

2007

Wilkinson RA, Evans JR, Jacobs JM, Slunaker D, Pincus SH, Pinter A, Parkos CA, Burritt JB, Teintze M. “Peptides Selected from a Phage Display Library with an HIV-Neutralizing Antibody Elicit Antibodies to HIV gp120 in Rabbits, But Not to the Same Epitope”  AIDS Research and Human Retroviruses. (2007) 23(11): 1416-1427.

Dutta D, Sundaram SK, Teeguarden JG, Riley BJ, Fifield LS, Jacobs JM, Addleman SR, Kaysen GA, Moudgil BM, Weber TJ. “Adsorbed Proteins Influence the Biological Activity and Molecular Targeting of Nanomaterials. (2007) Toxicol Sci. 100, 303-315.

Wang Y, S Ding, W Wang, JM Jacobs, DG Camp, II, RD Smith, and RL Klemke.  "Methods for Pseudopodia Purification and Proteomic Analysis." (2007).   Science STKE 400, 14.

Wang Y, Ding SJ, Wang W, Jacobs JM, Qian WJ, Moore RJ, Yang F, Camp DG 2nd, Smith RD, Klemke RL. “Profiling Signaling Polarity in Chemotactic Cells” (2007) Proc Natl Acad Sci USA 104, 8328-8333.

Diamond DL, Jacobs JM, Paeper B, Proll SC, Gritsenko MA, Carithers RL Jr, Larson AM, Yeh MM, Camp DG 2nd, Smith RD, Katze MG. “Proteomic Profiling of Human Liver Biopsies: Hepatitis C Virus-Induced Fibrosis and Mitochondrial Dysfunction” (2007) Hepatology 46 (3):649-657.

Metz T, Q Zhang, JS Page, Y Shen, SJ Callister, JM Jacobs, and RD Smith."The future of liquid chromatography-mass spectrometry in metabolic profiling and metabolomic studies for biomarker discovery."  (2007)   Biomarkers in Medicine 1(1):159-185.

 

2006

Metz, T.O., Jacobs, J.M., Gritsenko, M.A., Fontès, G., Qian, W.J., Camp II, D.G., Poitout, V., Smith, R.D. "Characterization of the Human Pancreatic Islet Proteome by Two- Dimensional LC/MS/MS" (2006)  J. Proteome Res. 5, 3345-3354.

Baas, T., Baskin, C.R., Diamond, D.L., García-Sastre, A., Bielefeldt-Ohmann, H., Tumpey, T.M., Thomas, M.J., Carter, V.S., Teal, T.H., Van Hoeven, N., Proll, S., Jacobs, J.M., Caldwell, Z.R., Gritsenko, M.A., Hukkanen, R.R., Camp II, D.G., Smith, R.D, Katze, M.G. “An Integrated Molecular Signature of Disease: Analysis of Influenza Virus-Infected Macaques through Functional Genomics and Proteomics” (2006) J. Virol. 80, 10813-10828.

Jacobs, J.M., Smith, R.D. (2006) “Proteomic Analyses using High Efficiency Separations and Accurate Mass Measurements” Chapter 20 in Separations in Proteomics, pp. 355-377. Dekker Publishing.

Qian WJ, Jacobs JM, Liu T, Camp DG 2nd, Smith RD."Advances and Challenges in Liquid Chromatography-Mass Spectrometry Based Proteomic Profiling for Clinical Applications" (2006) Mol. Cell. Proteomics, 5, 1727-1744.

Diamond DL, Proll SC, Jacobs JM, Chan EY, Camp DG 2nd, Smith RD, Katze MG. “HepatoProteomics: Appling proteomic technologies to the study of liver function and disease”. (2006) Hepatology 44, 299-308.

 

2005

Qian, W.J., Monroe, M.E., Liu, T., Jacobs, J.M., Anderson, G.A., Shen, Y., Camp II, D.G., Moore, R.J., Anderson, D.J., Zhang, R., Davis, R.W., Tompkins, R.G., Smith, R.D.  “Quantitative Proteome Analysis of Human Plasma Following in vivo Lipopolysaccharide Administration using 16O/18O Labeling and the Accurate Mass and Time Tag Approach”  (2005) Mol. Cell. Proteomics 4, 700-709.

Adkins, J.N., Monroe, M.E., Auberry, K.J., Shen, Y., Jacobs, J.M., Camp, D.G., Vitzthum, F., Rodland, K.D., Smith, R.D., Pounds, J.G. “A Proteomic Study of HUPOs Plasma Proteome Project Pilot Samples using an Accurate Mass and Time Tag Strategy” (2005) Proteomics 5, 3454-3466.

Jacobs, J.M., Adkins, J.N., Qian, W.J., Liu, T., Shen, Y., Camp, D.G., Smith, R.D. “Utilizing Human Blood Plasma for Proteomic Biomarker Discovery” (2005) J. Proteome Res. 4, 1073-1085.

Shen, Y., Kim, J.K., Strittmatter, E.F., Jacobs, J.M., Camp, D.G., Fang, R., Tolić, N., Moore, R.J., Smith, R.D. “Characterization of the human blood plasma proteome” (2005) Proteomics 5, 4034-4045.

Jacobs, J.M., Diamond, D.L., Chan, E.Y., Gritsenko, M.A., Qian, W.J., Stastna, M., Baas, T., Camp, D.G., Carithers, R.L., Smith, R.D., Katze, M.G.  “Proteome Analysis of Liver Cells Expressing a Full- Length Hepatitis C Virus (HCV) Replicon and Biopsies of Post-Transplanted Liver from HCV-Infected Patients.” (2005) J. Virol. 12, 7558-7569.

Qian, W.J., Jacobs, J.M., Camp, D.G., Monroe, M.E., Moore, R.J., Gritsenko, M.A., Calvano, S.E., Lowry, S.F., Xiao, W., Moldawer, L.L., Davis, R.W., Tompkins, R.G., Smith, R.D.  "Comparative Proteome Analyses of Human Plasma Following Lipopolysaccharide Treatment Using Mass Spectrometry." (2005) Proteomics 5, 572-584.

Liu, T., Qian, W.J., Chen, W.U., Jacobs, J.M., Moore, R.J., Anderson, D.J., Gritsenko, M.A., Monroe, M.E., Thrall, B.D., Camp, D.G., Smith, R.D. “Improved Proteome Coverage by Using High Efficiency Cysteinyl-peptide Enrichment: The Human Mammary Epithelial Cell Proteome” (2005) Proteomics 5, 1263-1273.

Jacobs, J.M., Monroe, M.E., Qian, W.J., Shen, Y., Anderson, G.A., Smith, R.D. “Ultra-sensitive, high throughput, and quantitative proteomic measurements.” (2005) International Journal of Mass Spectrometry 240, 195-212.

Jacobs, J.M., Yang, X., Luft, B.J., Dunn, J.J., Camp, D.G., Smith, R.D. “Proteomic Analysis of Lyme Disease: Global Protein Comparison of Three Strains of Borrelia Burgdorferi” (2005) Proteomics 5, 1446-1453.

Qian, W.J., Liu, T., Monroe, M.E., Strittmatter, E.F., Jacobs, J.M., Kangas, L.J., Petritis, K., Camp, D.G., Smith, R.D. “Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis:  The human proteome” (2005) J. Proteome Res. 4, 53-62.

2004

Jacobs, J.M., Mottaz, H.M., Yu, L.R., Anderson, D.J., Moore, R.J., Chen, W.U., Auberry, K.J., Strittmatter, E.F., Monroe, M.E., Thrall, B.D., Camp, D.G., Smith, R.D. “Multidimensional proteome analysis of human mammary epithelial cells.” (2004) J. Proteome Res. 3, 68-75.

Shen, Y., Jacobs, J.M., Camp, D.G., Fang, R., Moore, R.J., Xiao, W., Davis, R.W., Tompkins, R.G., Smith, R.D. “Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome.” (2004) Anal. Chem. 76, 1134-1144.

Strittmatter, E.F., Kangas, L.J., Petritis, K., Mottaz, H.M., Anderson, G.A., Shen, Y., Jacobs, J.M., Camp, D.G., Smith, R.D.  "Application of peptide retention time information in a discriminant function for peptide identification by tandem mass spectrometry."  (2004) J. Proteome Res. 3(4):760-769.

2003

Jacobs, J.M., Bailey, B.W., Burritt, J.B., Morrison, S.G., Morrison, R.P., Dratz, E.A., Jesaitis, A.J., Teintze, M. QSYP peptide sequence is selected from phage display libraries by bovine IgG contaminants in monoclonal antibody preparations. (2003) Biotechniques 34, 132-141.