U.S. Department of Energy

Pacific Northwest National Laboratory

Biblio

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2011
Dresang LR, Teuton JR, Feng H, Jacobs JM, Camp DG, Purvine SO, Gritsenko MA, Li Z, Smith RD, Sugden B et al..  2011.  Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes.. BMC Genomics.
Gonzalez RM, Zhang Q, Zangar RC, Smith RD, Metz TO.  2011.  Development of a fibrinogen-specific sandwich enzyme-linked immunosorbent assay microarray assay for distinguishing between blood plasma and serum samples.. Anal Biochem.
Niemann GS, Brown RN, Gustin JK, Stufkens A, Shaikh-Kidwai AS, Li J, McDermott JE, Brewer HM, Schepmoes A, Smith RD et al..  2011.  Discovery of novel secreted virulence factors from Salmonella enterica serovar Typhimurium by proteomic analysis of culture supernatants.. Infect Immun.
Kim Y-M, Metz TO, Hu Z, Wiedner SD, Kim J-S, Smith RD, Morgan WF, Zhang Q.  2011.  Formation of dehydroalanine from mimosine and cysteine: artifacts in gas chromatography/mass spectrometry based metabolomics.. Rapid Commun Mass Spectrom.
Venter E, Smith RD, Payne SH.  2011.  Proteogenomic analysis of bacteria and archaea: a 46 organism case study.. PLoS One.
Shvartsburg AA, Isaac G, Leveque N, Smith RD, Metz TO.  2011.  Separation and classification of lipids using differential ion mobility spectrometry.. J Am Soc Mass Spectrom.
Yoon H, Ansong C, McDermott JE, Gritsenko M, Smith RD, Heffron F, Adkins JN.  2011.  Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella.. BMC Syst Biol.
Rasmussen AL, Diamond DL, McDermott JE, Gao X, Metz TO, Matzke MM, Carter VS, Belisle SE, Korth MJ, Waters KM et al..  2011.  Systems virology identifies a mitochondrial fatty acid oxidation enzyme, dodecenoyl coenzyme A delta isomerase, required for hepatitis C virus replication and likely pathogenesis.. J Virol.
2010
Brown JN, Estep RD, Lopez-Ferrer D, Brewer HM, Clauss TR, Manes NP, O'Connor M, Li H, Adkins JN, Wong SW et al..  2010.  Characterization of macaque pulmonary fluid proteome during monkeypox infection: dynamics of host response.. Mol Cell Proteomics.
Petyuk VA, Mayampurath AM, Monroe ME, Polpitiya AD, Purvine SO, Anderson GA, Camp DG, Smith RD.  2010.  DtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets.. Mol Cell Proteomics.
Brown JN, Palermo RE, Baskin CR, Gritsenko M, Sabourin PJ, Long JP, Sabourin CL, Bielefeldt-Ohmann H, García-Sastre A, Albrecht R et al..  2010.  Macaque proteome response to highly pathogenic avian influenza and 1918 reassortant influenza virus infections.. J Virol. File MacaqueProteome_PeptideCrosstab.xlsx (2.02 MB)
Adkins JN, Mottaz H, Metz TO, Ansong C, Manes NP, Smith RD, Heffron F.  2010.  Performing comparative peptidomics analyses of Salmonella from different growth conditions.. Methods Mol Biol.
Sorensen CM, Ding J, Zhang Q, Alquier T, Zhao R, Mueller PW, Smith RD, Metz TO.  2010.  Perturbations in the lipid profile of individuals with newly diagnosed type 1 diabetes mellitus: lipidomics analysis of a Diabetes Antibody Standardization Program sample subset.. Clin Biochem.
Angel TE, Luft BJ, Yang X, Nicora CD, Camp DG, Jacobs JM, Smith RD.  2010.  Proteome analysis of Borrelia burgdorferi response to environmental change.. PLoS One.
Diamond DL, Syder AJ, Jacobs JM, Sorensen CM, Walters K-A, Proll SC, McDermott JE, Gritsenko MA, Zhang Q, Zhao R et al..  2010.  Temporal proteome and lipidome profiles reveal hepatitis C virus-associated reprogramming of hepatocellular metabolism and bioenergetics.. PLoS Pathog.
2008
Zhang Q, Petyuk VA, Schepmoes AA, Orton DJ, Monroe ME, Yang F, Smith RD, Metz TO.  2008.  Analysis of non-enzymatically glycated peptides: neutral-loss-triggered MS(3) versus multi-stage activation tandem mass spectrometry.. Rapid Commun Mass Spectrom.
Metz TO, Qian W-J, Jacobs JM, Gritsenko MA, Moore RJ, Polpitiya AD, Monroe ME, Camp DG, Mueller PW, Smith RD.  2008.  Application of proteomics in the discovery of candidate protein biomarkers in a diabetes autoantibody standardization program sample subset.. J Proteome Res.
Ding J, Sorensen CM, Jaitly N, Jiang H, Orton DJ, Monroe ME, Moore RJ, Smith RD, Metz TO.  2008.  Application of the accurate mass and time tag approach in studies of the human blood lipidome.. J Chromatogr B Analyt Technol Biomed Life Sci.
Polpitiya AD, Qian W-J, Jaitly N, Petyuk VA, Adkins JN, Camp DG, Anderson GA, Smith RD.  2008.  DAnTE: a statistical tool for quantitative analysis of -omics data.. Bioinformatics.
Petyuk VA, Jaitly N, Moore RJ, Ding J, Metz TO, Tang K, Monroe ME, Tolmachev AV, Adkins JN, Belov ME 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.. Anal Chem.
Metz TO, Page JS, Baker ES, Tang K, Ding J, Shen Y, Smith RD.  2008.  High Resolution Separations and Improved Ion Production and Transmission in Metabolomics.. Trends Analyt Chem.

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