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Filters: Keyword is Proteomics and Author is Smith, Richard D  [Clear All Filters]
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.
Ansong C, Ortega C, Payne SH, Haft DH, Chauvignè-Hines LM, Lewis MP, Ollodart AR, Purvine SO, Shukla AK, Fortuin S et al..  2013.  Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis.. Chem Biol. 20(1):123-33.
Aylward FO, Burnum-Johnson KE, Tringe SG, Teiling C, Tremmel DM, Moeller JA, Scott JJ, Barry KW, Piehowski PD, Nicora CD et al..  2013.  Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens.. Appl Environ Microbiol. File Spectra_for_fungal_CAZy_enzymes_identified_by_1_peptide.xlsx (1.21 MB)Package icon Acromyrmex_echinatior_proteomics_samples.zip (37.24 MB)Package icon Atta_cephalotes_proteomics_samples.zip (41.97 MB)Package icon Protein_FASTA_Files.zip (71.91 MB)
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.
Ansong C, Schrimpe-Rutledge AC, Mitchell HD, Chauhan S, Jones MB, Kim Y-M, McAteer K, Kaiser BLDeathera, Dubois JL, Brewer HM et al..  2013.  A multi-omic systems approach to elucidating Yersinia virulence mechanisms.. Mol Biosyst.
Sims AC, Tilton SC, Menachery VD, Gralinski LE, Schäfer A, Matzke MM, Webb-Robertson B-JM, Chang J, Luna ML, Long CE et al..  2013.  Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells.. J Virol.
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, Deatherage BL, Hyduke D, Schmidt B, McDermott JE, Jones MB, Chauhan S, Charusanti P, Kim Y-M, Nakayasu ES et al..  2013.  Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling.. Curr Top Microbiol Immunol.
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.
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.
Bordbar A, Mo ML, Nakayasu ES, Schrimpe-Rutledge AC, Kim Y-M, Metz TO, Jones MB, Frank BC, Smith RD, Peterson SN et al..  2012.  Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation.. Mol Syst Biol.
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
Zhang Q, Monroe ME, Schepmoes AA, Clauss TRW, Gritsenko MA, Meng D, Petyuk VA, Smith RD, Metz TO.  2011.  Comprehensive identification of glycated peptides and their glycation motifs in plasma and erythrocytes of control and diabetic subjects.. J Proteome Res.
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.
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.
2010
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.
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.
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.
2009
Zhang Q, Ames JM, Smith RD, Baynes JW, Metz TO.  2009.  A perspective on the Maillard reaction and the analysis of protein glycation by mass spectrometry: probing the pathogenesis of chronic disease.. J Proteome Res.
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
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.
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.
Zhang Q, Schepmoes AA, Brock JWC, Wu S, Moore RJ, Purvine SO, Baynes JW, Smith RD, Metz TO.  2008.  Improved methods for the enrichment and analysis of glycated peptides.. Anal Chem.

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