title: A bayesian mixture model for comparative spectral count data in shotgun proteomics.
abstract: Recent developments in mass-spectrometry-based shotgun proteomics, especially methods using spectral counting, have enabled large-scale identification and differential profiling of complex proteomes. Most such proteomic studies are interested in identifying proteins, the abundance of which is different under various conditions. Several quantitative methods have recently been proposed and implemented for this purpose. Building on some techniques that are now widely accepted in the microarray literature, we developed and implemented a new method using a Bayesian model to calculate posterior probabilities of differential abundance for thousands of proteins in a given experiment simultaneously. Our Bayesian model is shown to deliver uniformly superior performance when compared with several existing methods.
authors: Department of Biological Statistics and Computational Biology, Cornell University, Comstock Hall, Ithaca, NY 14853, USA. jim.booth@cornell.edu
authors: James G
authors: JG
authors: Booth
authors: Kirsten E
authors: KE
authors: Eilertson
authors: Paul Dominic B
authors: PD
authors: Olinares
authors: Haiyuan
authors: H
authors: Yu
references: Stat Med. 2009 Nov 10;28(25):3049-67
references: 19630097
references: Bioinformatics. 2010 Feb 1;26(3):363-9
references: 20007255
references: Anal Chem. 2009 Aug 1;81(15):6317-26
references: 19586016
references: J Proteome Res. 2006 Sep;5(9):2339-47
references: 16944946
references: Mol Cell Proteomics. 2010 Feb;9(2):242-54
references: 19858499
references: J Proteome Res. 2009 Aug;8(8):3872-81
references: 19522537
references: BMC Bioinformatics. 2008 Jul 21;9:316
references: 18644148
references: Bioinformatics. 2010 Jun 15;26(12):1574-5
references: 20413636
references: Mol Cell Proteomics. 2005 Oct;4(10):1487-502
references: 15979981
references: J Proteome Res. 2010 Nov 5;9(11):5698-704
references: 20812748
references: Stat Appl Genet Mol Biol. 2004;3:Article3
references: 16646809
references: Science. 2006 Apr 14;312(5771):212-7
references: 16614208
references: Mol Cell Proteomics. 2010 Dec;9(12):2704-18
references: 20823122
references: J Am Soc Mass Spectrom. 2010 Sep;21(9):1534-46
references: 20541435
references: Mol Cell Proteomics. 2008 Dec;7(12):2373-85
references: 18644780
references: Anal Chem. 2010 Mar 15;82(6):2272-81
references: 20166708
references: J Proteome Res. 2008 Oct;7(10):4598-602
references: 18774840
references: J Proteome Res. 2007 Feb;6(2):654-61
references: 17269722
references: J Proteome Res. 2002 Jan-Feb;1(1):21-6
references: 12643522
references: J Proteome Res. 2010 Aug 6;9(8):4295-305
references: 20586475
references: Anal Chem. 2004 Jul 15;76(14):4193-201
references: 15253663
references: Nat Biotechnol. 2010 Jan;28(1):83-9
references: 20010810
references: Nat Biotechnol. 2010 Jul;28(7):710-21
references: 20622845
references: Mol Cell Proteomics. 2008 Apr;7(4):631-44
references: 18029349
references: Bioinformatics. 2008 Nov 1;24(21):2534-6
references: 18606607
references: Anal Bioanal Chem. 2007 Oct;389(4):1017-31
references: 17668192
references: Nat Biotechnol. 2007 Jan;25(1):117-24
references: 17187058