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2013
Matzke MM, Brown JN, Gritsenko MA, Metz TO, Pounds JG, Rodland KD, Shukla AK, Smith RD, Waters KM, McDermott JE et al..  2013.  A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments.. Proteomics.
Gralinski LE, Bankhead A, Jeng S, Menachery VD, Proll S, Belisle SE, Matzke M, Webb-Robertson B-JM, Luna ML, Shukla AK et al..  2013.  Mechanisms of severe acute respiratory syndrome coronavirus-induced acute lung injury.. MBio.
LaMarche BL, Crowell KL, Jaitly N, Petyuk VA, Shah AR, Polpitiya AD, Sandoval JD, Kiebel GR, Monroe ME, Callister SJ et al..  2013.  MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis.. BMC Bioinformatics.
2012
Schrimpe-Rutledge AC, Fontès G, Gritsenko MA, Norbeck AD, Anderson DJ, Waters KM, Adkins JN, Smith RD, Poitout V, Metz TO.  2012.  Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics.. J Proteome Res.
Alfaro JF, Gong C-X, Monroe ME, Aldrich JT, Clauss TRW, Purvine SO, Wang Z, Camp DG, Shabanowitz J, Stanley P et al..  2012.  Tandem mass spectrometry identifies many mouse brain O-GlcNAcylated proteins including EGF domain-specific O-GlcNAc transferase targets.. Proc Natl Acad Sci U S A.
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.
Matzke MM, Waters KM, Metz TO, Jacobs JM, Sims AC, Baric RS, Pounds JG, Webb-Robertson B-JM.  2011.  Improved quality control processing of peptide-centric LC-MS proteomics data.. Bioinformatics.
Venter E, Smith RD, Payne SH.  2011.  Proteogenomic analysis of bacteria and archaea: a 46 organism case study.. PLoS One.
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.
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)
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.
2009
Shi L, Chowdhury SM, Smallwood HS, Yoon H, Mottaz-Brewer HM, Norbeck AD, McDermott JE, Clauss TRW, Heffron F, Smith RD et al..  2009.  Proteomic investigation of the time course responses of RAW 264.7 macrophages to infection with Salmonella enterica.. Infect Immun.
Karpievitch Y, Stanley J, Taverner T, Huang J, Adkins JN, Ansong C, Heffron F, Metz TO, Qian W-J, Yoon H et al..  2009.  A statistical framework for protein quantitation in bottom-up MS-based proteomics.. Bioinformatics.
2008
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.
Zhang Q, Tang N, Schepmoes AA, Phillips LS, Smith RD, Metz TO.  2008.  Proteomic profiling of nonenzymatically glycated proteins in human plasma and erythrocyte membranes.. J Proteome Res.
2005
Shen Y, Strittmatter EF, Zhang R, Metz TO, Moore RJ, Li F, Udseth HR, Smith RD, Unger KK, Kumar D et al..  2005.  Making broad proteome protein measurements in 1-5 min using high-speed RPLC separations and high-accuracy mass measurements.. Anal Chem.
2002
Smith RD, Anderson GA, Lipton MS, Pasa-Tolic L, Shen Y, Conrads TP, Veenstra TD, Udseth HR.  2002.  An accurate mass tag strategy for quantitative and high-throughput proteome measurements.. Proteomics. 2(5):513-23.
Adkins JN, Varnum SM, Auberry KJ, Moore RJ, Angell NH, Smith RD, Springer DL, Pounds JG.  2002.  Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry.. Mol Cell Proteomics. 1(12):947-55.
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