title: Microbial proteomics: a mass spectrometry primer for biologists.
abstract: It is now more than 10 years since the publication of the first microbial genome sequence and science is now moving towards a post genomic era with transcriptomics and proteomics offering insights into cellular processes and function. The ability to assess the entire protein network of a cell at a given spatial or temporal point will have a profound effect upon microbial science as the function of proteins is inextricably linked to phenotype. Whilst such a situation is still beyond current technologies rapid advances in mass spectrometry, bioinformatics and protein separation technologies have produced a step change in our current proteomic capabilities. Subsequently a small, but steadily growing, number of groups are taking advantage of this cutting edge technology to discover more about the physiology and metabolism of microorganisms. From this research it will be possible to move towards a systems biology understanding of a microorganism. Where upon researchers can build a comprehensive cellular map for each microorganism that links an accurately annotated genome sequence to gene expression data, at a transcriptomic and proteomic level.In order for microbiologists to embrace the potential that proteomics offers, an understanding of a variety of analytical tools is required. The aim of this review is to provide a basic overview of mass spectrometry (MS) and its application to protein identification. In addition we will describe how the protein complexity of microbial samples can be reduced by gel-based and gel-free methodologies prior to analysis by MS. Finally in order to illustrate the power of microbial proteomics a case study of its current application within the Bacilliaceae is given together with a description of the emerging discipline of metaproteomics.
authors: School of Biomedical Sciences, University of Ulster, Coleraine, County Londonderry, BT52 1SA, UK. g.mcmullan@ulster.ac.uk.
authors: Robert Lj
authors: RLj
authors: Graham
authors: Ciaren
authors: C
authors: Graham
authors: Geoff
authors: G
authors: McMullan
references: J Proteome Res. 2005 Sep-Oct;4(5):1789-98
references: 16212434
references: Curr Opin Struct Biol. 1998 Jun;8(3):393-400
references: 9666337
references: Anal Chem. 1991 Dec 15;63(24):1193A-1203A
references: 1789447
references: Curr Opin Biotechnol. 2003 Feb;14(1):101-9
references: 12566009
references: J Chromatogr A. 2003 Jun 6;1000(1-2):589-608
references: 12877191
references: J Am Soc Mass Spectrom. 1999 Oct;10(10):992-9
references: 10497810
references: Curr Opin Biotechnol. 2003 Feb;14(1):110-8
references: 12566010
references: Mol Cell Biol. 1999 Nov;19(11):7357-68
references: 10523624
references: Proteomics. 2001 Mar;1(3):377-96
references: 11680884
references: J Proteome Res. 2006 Sep;5(9):2465-73
references: 16944960
references: Proteomics. 2001 Feb;1(2):194-9
references: 11680866
references: Nature. 2005 Nov 24;438(7067):443-8
references: 16306982
references: Mol Cell Endocrinol. 2007 Jan 2;260-262:212-27
references: 17097803
references: FEMS Microbiol Lett. 2001 Dec 18;205(2):291-7
references: 11750818
references: Nucleic Acids Res. 2000 Nov 1;28(21):4317-31
references: 11058132
references: Anal Biochem. 1990 Feb 15;185(1):94-102
references: 2344051
references: Proteomics. 2001 Feb;1(2):223-38
references: 11680869
references: Appl Environ Microbiol. 2002 Aug;68(8):4067-73
references: 12147508
references: Proc Natl Acad Sci U S A. 1992 Jan 1;89(1):286-9
references: 1309610
references: Anal Chem. 1987 Nov 1;59(21):2621-5
references: 3688448
references: Lett Appl Microbiol. 2003;36(4):191-6
references: 12641709
references: J Biol Chem. 1975 May 25;250(10):4007-21
references: 236308
references: Anal Chem. 2002 Apr 1;74(7):1650-7
references: 12043600
references: J Am Soc Mass Spectrom. 1998 Apr;9(4):341-4
references: 9879364
references: Trends Microbiol. 2007 Jan;15(1):45-50
references: 17113776
references: Curr Opin Mol Ther. 2002 Jun;4(3):242-50
references: 12139310
references: Electrophoresis. 1999 Dec;20(18):3551-67
references: 10612281
references: J Am Soc Mass Spectrom. 1994 Nov;5(11):976-89
references: 24226387
references: Science. 2005 Jun 24;308(5730):1915-20
references: 15879173
references: Curr Opin Chem Biol. 2002 Feb;6(1):46-50
references: 11827822
references: Mol Cell Proteomics. 2004 May;3(5):456-65
references: 14762214
references: Nature. 2003 Mar 13;422(6928):198-207
references: 12634793
references: J Mol Biol. 2004 Jul 16;340(4):783-95
references: 15223320
references: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D582-5
references: 14681486
references: Anal Chem. 1988 Oct 15;60(20):2299-301
references: 3239801
references: Nat Biotechnol. 2003 Mar;21(3):255-61
references: 12610572
references: Mol Cell Proteomics. 2004 Aug;3(8):780-7
references: 15115803
references: Dis Markers. 2002;18(2):99-105
references: 12364816
references: Clin Infect Dis. 2002 Sep 1;35(Suppl 1):S58-64
references: 12173110
references: Nat Methods. 2006 Jun;3(6):420
references: 16770867
references: J Proteome Res. 2005 Mar-Apr;4(2):578-85
references: 15822937
references: J Microbiol Methods. 2002 Feb;48(2-3):117-26
references: 11777562
references: Nucleic Acids Res. 2002 Sep 15;30(18):3927-35
references: 12235376
references: Anal Chem. 2001 Apr 1;73(7):1440-8
references: 11321292
references: Electrophoresis. 1997 Oct;18(11):2071-7
references: 9420172
references: Annu Rev Biochem. 2001;70:437-73
references: 11395414
references: Curr Opin Microbiol. 2000 Jun;3(3):292-7
references: 10851159
references: Appl Environ Microbiol. 2005 Jul;71(7):4121-6
references: 16000831
references: Nat Biotechnol. 2001 Mar;19(3):242-7
references: 11231557
references: Science. 2006 Apr 14;312(5771):212-7
references: 16614208
references: Science. 1989 Oct 6;246(4926):64-71
references: 2675315
references: Mol Cell Proteomics. 2005 Jun;4(6):762-72
references: 15703444
references: J Proteome Res. 2006 Nov;5(11):3145-53
references: 17081066
references: Trends Biotechnol. 2000 Apr;18(4):151-60
references: 10740261
references: Nat Biotechnol. 2002 Mar;20(3):301-5
references: 11875433
references: Nucleic Acids Res. 2005 Oct 24;33(19):6083-9
references: 16246909
references: Proteomics. 2003 Jul;3(7):1128-44
references: 12872214
references: J Chromatogr A. 1996 Oct 25;750(1-2):3-10
references: 8938379
references: Trends Microbiol. 2006 Feb;14(2):92-7
references: 16406790
references: J Am Soc Mass Spectrom. 2004 Jul;15(7):1099-108
references: 15234368
references: Mol Cell Proteomics. 2005 Aug;4(8):1134-44
references: 15923565
references: Trends Biochem Sci. 2006 Aug;31(8):473-84
references: 16815709
references: J Immunol Methods. 2002 Apr 1;262(1-2):5-19
references: 11983215
references: Mol Cell Proteomics. 2004 Dec;3(12):1154-69
references: 15385600
references: Proteomics. 2007 Jan;7(1):82-91
references: 17146838
references: Water Sci Technol. 2006;54(1):217-26
references: 16898155
references: Bioinformatics. 2005 Mar 1;21(5):617-23
references: 15501914
references: Nat Biotechnol. 1999 Oct;17(10):994-9
references: 10504701
references: Proteomics. 2005 Nov;5(16):4161-9
references: 16196092
references: Proteomics. 2006 Jun;6(12):3636-48
references: 16705751
references: J Proteome Res. 2006 Apr;5(4):822-8
references: 16602689
references: Nucleic Acids Res. 2004 Dec 01;32(21):6292-303
references: 15576355
references: Nat Biotechnol. 1999 Jul;17(7):676-82
references: 10404161
references: BMC Microbiol. 2005 Oct 07;5:58
references: 16212653
references: Appl Environ Microbiol. 1999 Aug;65(8):3697-704
references: 10427068
references: Mass Spectrom Rev. 2005 Mar-Apr;24(2):168-200
references: 15389855
references: Exp Gerontol. 2002 May;37(5):721-34
references: 11909689
references: Protein Expr Purif. 2000 Nov;20(2):142-51
references: 11049738
references: Clin Chim Acta. 2003 Nov;337(1-2):11-21
references: 14568176
references: Proteomics. 2004 Dec;4(12):3665-85
references: 15543535
references: J Am Soc Mass Spectrom. 2004 Oct;15(10):1478-1486
references: 15465361
references: Proteomics. 2003 Aug;3(8):1637-46
references: 12923788
references: Nutrition. 2004 Jan;20(1):155-65
references: 14698031
references: Proteomics. 2006 Aug;6(16):4565-85
references: 16847875
references: Methods Biochem Anal. 2006;49:179-208
references: 16929680
references: Vaccine. 2001 Mar 21;19(17-19):2692-700
references: 11257411
references: Anal Chem. 2005 Nov 15;77(22):7455-61
references: 16285700
references: J Mass Spectrom. 2000 Jul;35(7):763-72
references: 10934430
references: J Mass Spectrom. 2000 Jan;35(1):1-12
references: 10633229
references: Trends Biotechnol. 2002 Jun;20(6):261-8
references: 12007495
references: Mol Cell Proteomics. 2005 Sep;4(9):1265-72
references: 15958392
references: Anal Chem. 2004 Jul 15;76(14):3935-43
references: 15253627
references: Proteomics. 2006 Sep;6 Suppl 2:16-21
references: 17031791
references: Biochim Biophys Acta. 2003 Mar 21;1646(1-2):1-10
references: 12637006
references: Environ Microbiol. 2004 Sep;6(9):911-20
references: 15305916
references: Proteomics. 2006 Mar;6(5):1550-62
references: 16440371
references: Proteomics. 2004 Dec;4(12):3727-50
references: 15540212
references: Clin Chem. 2006 Jul;52(7):1218-22
references: 16675505
references: Oecologia. 2005 Jan;142(3):335-43
references: 15449171
references: Rapid Commun Mass Spectrom. 2003;17(10):1056-64
references: 12720286
references: Biochem J. 2001 May 1;355(Pt 3):545-61
references: 11311115