PNNL - Biodefense Proteomics Research Center (24)

• MASIC: A software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features | Abstract
  Monroe ME, Shaw JL, Daly DS, Adkins JN, Smith RD.
  Comput Biol Chem2008 Jun;32(3):215-7 - PMID: 18440872
   


• DAnTE: A statistical tool for quantitative analysis of -omics data | Abstract
  Polpitiya AD, Qian WJ, Jaitly N, Petyuk VA, Adkins JN, Camp DC II, Anderson GA, Smith RD.
  Bioinformatics2008 May 3;Epub: - PMID: 18453552
   


• A computational strategy to analyze label-free temporal bottom-up proteomics data | Abstract
  Du X, Callister SJ, Mauer NP, Adkins JN, Alexandridis RA, Zeng Y, Roh JH, Smith WE, Donohue TJ, Kaplan S, Smith RD, Lipton MS.
  J Proteome Res2008 Apr 29;EPub: - PMID: 18442284
   


• Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags | Abstract
  Shen Y, Tolic N, Hixson KK, Purvine SO, Pasa-Tolic L, Qian WJ, Adkins, JN, Moore RJ, Smith RD.
  Anal Chem.2008 Mar 15;80(6):1871-82 - PMID: 18271604
   


• DeconMSn: a softweare tool for accurate parent ion monoisotopic mass determination for tandem mass spectra | Abstract
  Mayampurath AM, Jaitly N, Purvine SO, Monroe ME, Auberry KJ, Adkins JN, Smith RD.
  Bioinformatics2008 Feb 26;Epub: - PMID: 18304935
   


• Comparative bacterial proteomics: analysis of the core genome concept | Abstract
  Callister SJ, McCue LA, Turse JE, Monroe ME, Auberry KJ, Smith RD, Adkins JN, Lipton MS.
  PLos ONE2008 Feb 6;3(2):e1542 - PMID: 18253490
   


• Comparative proteomics of human monkeypox and vaccinia intracellular mature and extracellular enveloped virions | Abstract
  Manes NP, Estep RD, Mottaz HM, Moore RJ, Clauss TR, Monroe ME, Du X, Adkins JN, Wong SW, Smith RD.
  J Proteome Res2008 Jan 19;Epub: - PMID: 18205298
   


• Proteomics analysis of the causative agent of typhoid fever | Abstract
  Ansong C, Yoon H, Norbeck AD, Gustin JK, McDermott JE, Mottaz HM, Rue J, Adkins JN, Heffron F, Smith RD.
  J Proteome Res2008 Jan 1;Epub: - PMID: 18166006
   


• Proteogenomics: needs and roles to be filled by proteomics in genome annotation | Abstract
  Ansong C, Purvine SO, Adkins JN, Lipton MS, Smith RD.
  Brief Funct Genomic Proteomic2008 Jan;7(1):50-62 - PMID: 18334489
   


• Ion funnel trap interface for orthogonal time-of-flight mass spectrometry | Abstract
  Ibrahim Y, Belov ME, Tolmachev AV, Prior DC, Smith RD.
  Anal Chem2007 Oct 15;79(20):7845-52 - PMID: 17850113
   


• Ionization and transmission efficiency in an electrospray ionization-mass spectrometry interface | Abstract
  Page JS, Kelly RT, Tang K, Smith RD.
  J Am Soc Mass Spectrom2007 Sep;18(9):1582-90 - PMID: 17627841
   


• VIPER: an advanced software package to support high-throughput LC-MS peptide identification | Abstract
  Monroe ME, Tolic N, Jaitly N, Shaw JL, Adkins JN, Smith RD.
  Bioinformatics2007 Aug 1;23(15):2021-3 - PMID: 17545182
   


• PQuad - a visual analysis platform for proteomic data exploration of microbial organisms | Abstract
  Webb-Robertson BJ, Peterson, ES, Singhal M, Klicker KR, Oehmen CS, Adkins JN, Havre SL.
  Bioinformatics2007 Jul 1;23(13):1705-7 - PMID: 17483503
   


• Targeted protein degradation by salmonella under phagosome-mimicking culture conditions investigated using comparative peptidomics | Abstract | Supplemental
  Manes NP, Gustin JK, Rue J, Mottaz HM, Purvine SO, Norbeck AD, Monroe ME, Zimmer JS, Metz TO, Adkins, JN, Smith RD, Heffron F.
  Mol Cell Proteomics2007 Apr;6(4):717-27 - PMID: 17228056
   


• MicroSPE-nanoLC-ESI-MS/MS using 10-microm-i.d. silica-based monolithic columns for proteomics | Abstract
  Luo Q, Page JS, Tang K, Smith RD.
  Anal Chem2007 Jan 15;79(2):540-5 - PMID: 17222018
   


• Mass measurement accuracy in analyses of highly complex mixtures based upon multidimensional recalibration | Abstract
  Tolmachev AV, Monroe ME, Jaitly N, Petyuk VA, Adkins JN, Smith RD.
  Anal Chem2006 Dec 15;78(24):8374-85 - PMID: 17165830
   


• Chemically etched open tubular and monolithic emitters for nanoelectrospray ionization mass spectrometry | Abstract
  Kelly RT, Page JS, Luo Q, Moore RJ, Orton DJ, Tang K, and Smith RD.
  Anal Chem2006 Nov 15;78(22):7796-801 - PMID: 17105173
   


• Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline | Abstract
  Jaitly N, Monroe ME, Petyuk VA, Clauss TR, Adkins JN, Smith RD.
  Anal Chem2006 Nov 1;78(21):7397-409 - PMID: 17073405
   


• Proteomic analysis of salmonella entericar serovar typhimurium isolated from RAW 264.7 macrophages: Identification of a novel protein that contributes to the replication of serovar typhimurium inside macrophages | Abstract | Supplemental
  Shi L, Adkins JN, Coleman JR, Schepmoes AA, Dohnkova A, Mottaz HM, Norbeck AD, Purvine SO, Manes NP, Smallwood HS, Wang H, Forbes J, Gros P, Uzzau S, Rodland KD, Heffron F, Smith RD, and Squier TC.
  J Biol Chem2006 Sep 29;281(39):29131-40 - PMID: 16893888
   


• Analysis of the Salmonella typhimurium proteome through environmental response towards infectious conditions | Abstract
  Adkins JN, Mottaz HM, Norbeck AD, Gustin JK, Rue J, Clauss TRW, Purvine SO, Rodland K, Heffron F, Smith RD.
  Mol Cell Proteomics2006 Aug;5(8):1450-61 - PMID: 16684765
   


• Ultra-sensitive and quantitative characterization of proteomes | Abstract
  Smith RD, Tang K, Shen Y.
  Mol Biosyst2006 May;2(5):221-30 - PMID: 16880940
   


• The utility of accurate mass and LC elution time information in the analysis of complex proteomes | Abstract
  Norbeck AD, Monroe ME, Adkins JN, Anderson KK, Daly DS, Smith RD.
  J Am Soc Mass Spectrom2005 Aug;16(8):1239-49 - PMID: 15979333
   


• Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information | Abstract
  Petritis K, Kangas LJ, Yan B, Monroe ME, Strittmatter EF, Qian WJ, Adkins JN, Moore RJ, Xu Y, Lipton MS, Camp DG 2nd, Smith RD.
  Anal Chem2005 Jul 15;78(14):5026-39 - PMID: 16841926
   


• Ultrasensitive and quantitative analyses from combined separations-mass spectrometry for the characterization of proteomes | Abstract
  Smith RD, Shen Y, Tang K.
  Acc Chem Res2004 Apr;37(4):269-78 - PMID: 15096064