title: Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets.
abstract: In a typical shotgun proteomics experiment, a significant number of high-quality MS/MS spectra remain "unassigned." The main focus of this work is to improve our understanding of various sources of unassigned high-quality spectra. To achieve this, we designed an iterative computational approach for more efficient interrogation of MS/MS data. The method involves multiple stages of database searching with different search parameters, spectral library searching, blind searching for modified peptides, and genomic database searching. The method is applied to a large publicly available shotgun proteomic data set.
authors.affiliation: Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
authors.forename: Kang
authors.initials: K
authors.lastname: Ning
authors.forename: Damian
authors.initials: D
authors.lastname: Fermin
authors.forename: Alexey I
authors.initials: AI
authors.lastname: Nesvizhskii
mesh_terms: D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D013058:Mass Spectrometry / Q000592:standards*; D010455:Peptides / Q000032:analysis / Q000737:chemistry; D040901:Proteomics / Q000379:methods*
chemical_list: D010455:Peptides
references.citation: Mol Cell Proteomics. 2007 Jan;6(1):1-17
references.pmid: 17018520
references.citation: J Proteome Res. 2008 Jan;7(1):245-53
references.pmid: 18173222
references.citation: Anal Chem. 2002 Oct 15;74(20):5383-92
references.pmid: 12403597
references.citation: Genome Biol. 2006;7(4):R35
references.pmid: 16646984
references.citation: J Bacteriol. 2003 Aug;185(15):4593-602
references.pmid: 12867470
references.citation: Bioinformatics. 2008 Apr 1;24(7):1021-3
references.pmid: 18304935
references.citation: Nat Methods. 2007 Oct;4(10):787-97
references.pmid: 17901868
references.citation: Mass Spectrom Rev. 2006 Mar-Apr;25(2):235-54
references.pmid: 16284939
references.citation: Mol Cell Proteomics. 2009 Apr;8(4):857-69
references.pmid: 19106086
references.citation: Anal Chem. 2003 Nov 15;75(22):6251-64
references.pmid: 14616009
references.citation: J Proteome Res. 2008 Jan;7(1):286-92
references.pmid: 18078310
references.citation: Mol Syst Biol. 2007;3:102
references.pmid: 17437027
references.citation: Mol Cell Proteomics. 2006 Dec;5(12):2384-91
references.pmid: 17015437
references.citation: Mol Cell Proteomics. 2007 Aug;6(8):1343-53
references.pmid: 17519225
references.citation: Nucleic Acids Res. 2001 Jan 1;29(1):308-11
references.pmid: 11125122
references.citation: Proteomics. 2005 Nov;5(16):4096-106
references.pmid: 16196091
references.citation: Electrophoresis. 1999 Dec;20(18):3551-67
references.pmid: 10612281
references.citation: J Am Soc Mass Spectrom. 1994 Nov;5(11):976-89
references.pmid: 24226387
references.citation: Bioinformatics. 2006 Nov 15;22(22):2830-2
references.pmid: 16877754
references.citation: Anal Chem. 2005 Feb 15;77(4):964-73
references.pmid: 15858974
references.citation: Nat Biotechnol. 2009 Jul;27(7):633-41
references.pmid: 19561596
references.citation: Proteomics. 2006 Apr;6(7):2086-94
references.pmid: 16518876
references.citation: Nat Methods. 2008 Oct;5(10):873-5
references.pmid: 18806791
references.citation: Proteomics. 2001 May;1(5):651-67
references.pmid: 11678035
references.citation: Proteomics. 2007 Mar;7(5):655-67
references.pmid: 17295354
references.citation: Genome Res. 2007 Feb;17(2):231-9
references.pmid: 17189379
references.citation: J Bioinform Comput Biol. 2005 Jun;3(3):697-716
references.pmid: 16108090
references.citation: Mol Cell Proteomics. 2005 Aug;4(8):1194-204
references.pmid: 15937296
references.citation: Nat Biotechnol. 2005 Dec;23(12):1562-7
references.pmid: 16311586
references.citation: J Proteome Res. 2006 Aug;5(8):1843-9
references.pmid: 16889405
references.citation: Genome Res. 2002 Apr;12(4):656-64
references.pmid: 11932250
references.citation: Bioinformatics. 2004 Jun 12;20(9):1466-7
references.pmid: 14976030
references.citation: Anal Chem. 2004 Jul 15;76(14):3908-22
references.pmid: 15253624
references.citation: Anal Chem. 2003 Sep 1;75(17):4646-58
references.pmid: 14632076
references.citation: J Am Soc Mass Spectrom. 2000 May;11(5):422-6
references.pmid: 10790846
references.citation: Anal Chem. 1994 Dec 15;66(24):4390-9
references.pmid: 7847635
references.citation: Anal Chem. 2004 Jul 1;76(13):3556-68
references.pmid: 15228325
references.citation: Rapid Commun Mass Spectrom. 2003;17(20):2337-42
references.pmid: 14558135
references.citation: Anal Chem. 2005 Jul 15;77(14):4626-39
references.pmid: 16013882
references.citation: Proteomics. 2004 Jul;4(7):1985-8
references.pmid: 15221759
references.citation: Mol Cell Proteomics. 2006 Apr;5(4):652-70
references.pmid: 16352522