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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.
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.
Webb-Robertson B-JM, Matzke MM, Metz TO, McDermott JE, Walker H, Rodland KD, Pounds JG, Waters KM.  2013.  Sequential projection pursuit principal component analysis--dealing with missing data associated with new -omics technologies.. Biotechniques.
Zhang Q, Fillmore TL, Schepmoes AA, Clauss TRW, Gritsenko MA, Mueller PW, Rewers M, Atkinson MA, Smith RD, Metz TO.  2013.  Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes.. J Exp Med.
Ansong C, Wu S, Meng D, Liu X, Brewer HM, Kaiser BLDeathera, Nakayasu ES, Cort JR, Pevzner P, Smith RD et al..  2013.  Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions.. Proc Natl Acad Sci U S A.
2012
Shi T, Fillmore TL, Sun X, Zhao R, Schepmoes AA, Hossain M, Xie F, Wu S, Kim J-S, Jones N et al..  2012.  Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum.. Proc Natl Acad Sci U S A.
Chauvignè-Hines LM, Anderson LN, Weaver HM, Brown JN, Koech PK, Nicora CD, Hofstad BA, Smith RD, Wilkins MJ, Callister SJ et al..  2012.  Suite of activity-based probes for cellulose-degrading enzymes.. J Am Chem Soc.
2011
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.
2010
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.
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
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.
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.
Monroe ME, Shaw JL, Daly DS, Adkins JN, Smith RD.  2008.  MASIC: a software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features.. Comput Biol Chem.
2007
Ding J, Sorensen CM, Zhang Q, Jiang H, Jaitly N, Livesay EA, Shen Y, Smith RD, Metz TO.  2007.  Capillary LC coupled with high-mass measurement accuracy mass spectrometry for metabolic profiling.. Anal Chem.
Manes NP, Gustin JK, Rue J, Mottaz HM, Purvine SO, Norbeck AD, Monroe ME, Zimmer JSD, Metz TO, Adkins JN et al..  2007.  Targeted protein degradation by Salmonella under phagosome-mimicking culture conditions investigated using comparative peptidomics.. Mol Cell Proteomics.
Monroe ME, Tolić N, Jaitly N, Shaw JL, Adkins JN, Smith RD.  2007.  VIPER: an advanced software package to support high-throughput LC-MS peptide identification.. Bioinformatics.
2006
Metz TO, Jacobs JM, Gritsenko MA, Fontès G, Qian W-J, Camp DG, Poitout V, Smith RD.  2006.  Characterization of the human pancreatic islet proteome by two-dimensional LC/MS/MS.. J Proteome Res.
2005
Shen Y, Zhang R, Moore RJ, Kim J, Metz TO, Hixson KK, Zhao R, Livesay EA, Udseth HR, Smith RD.  2005.  Automated 20 kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000-1500 and capabilities in proteomics and metabolomics.. Anal Chem.
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.
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