title: Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation.
abstract: While bacterial genome annotations have significantly improved in recent years, techniques for bacterial proteome annotation (including post-translational chemical modifications, signal peptides, proteolytic events, etc.) are still in their infancy. At the same time, the number of sequenced bacterial genomes is rising sharply, far outpacing our ability to validate the predicted genes, let alone annotate bacterial proteomes. In this study, we use tandem mass spectrometry (MS/MS) to annotate the proteome of Shewanella oneidensis MR-1, an important microbe for bioremediation. In particular, we provide the first comprehensive map of post-translational modifications in a bacterial genome, including a large number of chemical modifications, signal peptide cleavages, and cleavages of N-terminal methionine residues. We also detect multiple genes that were missed or assigned incorrect start positions by gene prediction programs, and suggest corrections to improve the gene annotation. This study demonstrates that complementing every genome sequencing project by an MS/MS project would significantly improve both genome and proteome annotations for a reasonable cost.
authors: Bioinformatics Program, University of California San Diego, La Jolla, California 92093, USA. nguta@ucsd.edu
authors: Nitin
authors: N
authors: Gupta
authors: Stephen
authors: S
authors: Tanner
authors: Navdeep
authors: N
authors: Jaitly
authors: Joshua N
authors: JN
authors: Adkins
authors: Mary
authors: M
authors: Lipton
authors: Robert
authors: R
authors: Edwards
authors: Margaret
authors: M
authors: Romine
authors: Andrei
authors: A
authors: Osterman
authors: Vineet
authors: V
authors: Bafna
authors: Richard D
authors: RD
authors: Smith
authors: Pavel A
authors: PA
authors: Pevzner
mesh_terms: D000595:Amino Acid Sequence; D003598:Cytoskeletal Proteins / Q000737:chemistry; D005136:Eye Proteins / Q000737:chemistry; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D006023:Glycoproteins / Q000737:chemistry; D013058:Mass Spectrometry / Q000379:methods*; D008954:Models, Biological; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods; D017386:Sequence Homology, Amino Acid; D020592:Shewanella / Q000235:genetics; D053719:Tandem Mass Spectrometry; D000099179:Myocilin
chemical_list: D003598:Cytoskeletal Proteins; D005136:Eye Proteins; D006023:Glycoproteins; D010455:Peptides; D020543:Proteome; D000099179:Myocilin
references: Proteomics. 2005 Aug;5(12):3120-30
references: 16038018
references: J Mass Spectrom. 2000 Apr;35(4):572-5
references: 10797654
references: Gene. 2002 Mar 20;286(2):187-201
references: 11943474
references: J Bacteriol. 1998 Jun;180(11):2936-42
references: 9603885
references: Genome Res. 2004 Aug;14(8):1447-61
references: 15289470
references: J Proteome Res. 2002 Mar-Apr;1(2):181-7
references: 12643538
references: Biomed Environ Mass Spectrom. 1990 Nov;19(11):713-20
references: 2076469
references: Nucleic Acids Res. 2005 Oct 07;33(17):5691-702
references: 16214803
references: EMBO J. 1982;1(3):311-5
references: 6325158
references: J Bacteriol. 1971 Jan;105(1):211-9
references: 5541007
references: Annu Rev Biochem. 1996;65:83-100
references: 8811175
references: J Biol Chem. 1977 May 25;252(10):3214-8
references: 16888
references: J Bacteriol. 1987 Feb;169(2):751-7
references: 3027045
references: Nucleic Acids Res. 2001 Jan 1;29(1):123-5
references: 11125067
references: Science. 2004 Apr 2;304(5667):66-74
references: 15001713
references: Mol Cell Proteomics. 2006 Dec;5(12):2384-91
references: 17015437
references: Genome Res. 2002 Aug;12(8):1210-20
references: 12176929
references: Nat Protoc. 2006;1(1):67-72
references: 17406213
references: Methods Enzymol. 1976;45:599-610
references: 13271
references: Mol Cell Proteomics. 2004 Jun;3(6):608-14
references: 15034119
references: Electrophoresis. 2000 Jun;21(11):2209-18
references: 10892731
references: J Mol Biol. 1991 Jun 5;219(3):471-80
references: 2051483
references: J Bacteriol. 2006 Jul;188(13):4601-9
references: 16788168
references: Antonie Van Leeuwenhoek. 2002 Aug;81(1-4):215-22
references: 12448720
references: Int J Pept Protein Res. 1989 Aug;34(2):118-23
references: 2807728
references: Nucleic Acids Res. 2003 Jan 1;31(1):87-9
references: 12519954
references: Anal Biochem. 1999 Feb 1;267(1):57-64
references: 9918655
references: Mass Spectrom Rev. 2001 Jul-Aug;20(4):157-71
references: 11835304
references: Electrophoresis. 1998 May;19(6):989-97
references: 9638945
references: Proteomics. 2004 Jan;4(1):59-77
references: 14730672
references: Science. 1991 Nov 29;254(5036):1374-7
references: 1962196
references: Mol Syst Biol. 2006;2:2006.0008
references: 16738554
references: J Biol Chem. 2006 Oct 6;281(40):29872-85
references: 16857666
references: Nature. 2003 Mar 13;422(6928):198-207
references: 12634793
references: Gene. 1993 May 15;127(1):79-85
references: 8486291
references: Nat Biotechnol. 2002 Nov;20(11):1118-23
references: 12368813
references: J Mol Biol. 2004 Jul 16;340(4):783-95
references: 15223320
references: Mol Biotechnol. 1997 Oct;8(2):105-22
references: 9406181
references: Genome Biol. 2006;7(4):R35
references: 16646984
references: Protein Sci. 1996 Aug;5(8):1625-32
references: 8844851
references: J Biol Chem. 1991 May 25;266(15):9746-53
references: 2033064
references: Rapid Commun Mass Spectrom. 2005;19(9):1130-8
references: 15799070
references: Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342-6
references: 4598299
references: Protein Eng. 1997 Jan;10(1):1-6
references: 9051728
references: Nat Rev Mol Cell Biol. 2006 Jun;7(6):391-403
references: 16723975
references: Chem Rev. 2002 Dec;102(12):4549-80
references: 12475201
references: J Microbiol Methods. 2006 Aug;66(2):223-33
references: 16417935
references: Nature. 1981 Oct 1;293(5831):408-11
references: 7024824
references: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W451-4
references: 15980510
references: J Bacteriol. 2003 Oct;185(19):5673-84
references: 13129938
references: J Pharm Sci. 2002 Nov;91(11):2331-45
references: 12379918
references: BMC Genomics. 2005 Sep 19;6:128
references: 16171517
references: FEBS Lett. 1979 Nov 15;107(2):359-62
references: 389663
references: Mol Gen Genet. 1989 Aug;218(2):355-7
references: 2779520
references: Mol Microbiol. 1996 Jul;21(2):331-46
references: 8858588
references: Electrophoresis. 1997 Aug;18(8):1259-313
references: 9298646
references: FEMS Microbiol Lett. 1998 Dec 15;169(2):375-82
references: 9868784
references: Mol Microbiol. 1996 Jul;21(2):347-60
references: 8858589
references: Genome Res. 2004 Jun;14(6):1188-90
references: 15173120
references: Genome Res. 2005 Aug;15(8):1118-26
references: 16077011
references: Proteomics. 2004 Jun;4(6):1527-33
references: 15174122
references: Proteomics. 2004 Jun;4(6):1534-6
references: 15174123
references: Science. 2002 May 24;296(5572):1462-6
references: 12029132
references: Genome Res. 2001 Sep;11(9):1484-502
references: 11544192
references: Nat Biotechnol. 2005 Dec;23(12):1562-7
references: 16311586
references: Proc Natl Acad Sci U S A. 1989 Nov;86(21):8247-51
references: 2682640
references: J Mol Biol. 1999 Jun 11;289(3):645-57
references: 10356335
references: OMICS. 2004 Fall;8(3):239-54
references: 15669716
references: Anal Chem. 2001 Aug 1;73(15):3576-82
references: 11510821
references: Mol Gen Genet. 1981;183(3):418-21
references: 7038376
references: FEMS Microbiol Lett. 1993 Sep 1;112(2):211-6
references: 8405963
references: Nat Rev Microbiol. 2003 Nov;1(2):127-36
references: 15035042
references: Trends Biochem Sci. 2001 Jan;26(1):54-61
references: 11165518
references: Anal Chem. 2005 Jul 15;77(14):4626-39
references: 16013882
references: EMBO J. 2002 Feb 15;21(4):769-78
references: 11847124
references: Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):2099-104
references: 15684069
references: Mol Cell Proteomics. 2006 Dec;5(12):2336-49
references: 16963780
references: Rapid Commun Mass Spectrom. 1996;10(15):1905-10
references: 9004526
references: Proteomics. 2001 May;1(5):641-50
references: 11678034
references: J Biol Chem. 1983 Apr 25;258(8):5050-5
references: 6300110
references: Bioinformatics. 2006 Jul 15;22(14):e481-8
references: 16873510
references: OMICS. 2003 Summer;7(2):171-5
references: 14506846
references: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W375-9
references: 15215414
references: Nat Biotechnol. 2007 Jan;25(1):117-24
references: 17187058
references: Anal Biochem. 1999 Apr 10;269(1):105-12
references: 10094780
references: Anal Chem. 1995 Sep 15;67(18):3202-10
references: 8686885