Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets.
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.
Ning
Kang
K
Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
Fermin
Damian
D
Nesvizhskii
Alexey I
AI
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*
D010455:Peptides
Mol Cell Proteomics. 2007 Jan;6(1):1-17
17018520
J Proteome Res. 2008 Jan;7(1):245-53
18173222
Anal Chem. 2002 Oct 15;74(20):5383-92
12403597
Genome Biol. 2006;7(4):R35
16646984
J Bacteriol. 2003 Aug;185(15):4593-602
12867470
Bioinformatics. 2008 Apr 1;24(7):1021-3
18304935
Nat Methods. 2007 Oct;4(10):787-97
17901868
Mass Spectrom Rev. 2006 Mar-Apr;25(2):235-54
16284939
Mol Cell Proteomics. 2009 Apr;8(4):857-69
19106086
Anal Chem. 2003 Nov 15;75(22):6251-64
14616009
J Proteome Res. 2008 Jan;7(1):286-92
18078310
Mol Syst Biol. 2007;3:102
17437027
Mol Cell Proteomics. 2006 Dec;5(12):2384-91
17015437
Mol Cell Proteomics. 2007 Aug;6(8):1343-53
17519225
Nucleic Acids Res. 2001 Jan 1;29(1):308-11
11125122
Proteomics. 2005 Nov;5(16):4096-106
16196091
Electrophoresis. 1999 Dec;20(18):3551-67
10612281
J Am Soc Mass Spectrom. 1994 Nov;5(11):976-89
24226387
Bioinformatics. 2006 Nov 15;22(22):2830-2
16877754
Anal Chem. 2005 Feb 15;77(4):964-73
15858974
Nat Biotechnol. 2009 Jul;27(7):633-41
19561596
Proteomics. 2006 Apr;6(7):2086-94
16518876
Nat Methods. 2008 Oct;5(10):873-5
18806791
Proteomics. 2001 May;1(5):651-67
11678035
Proteomics. 2007 Mar;7(5):655-67
17295354
Genome Res. 2007 Feb;17(2):231-9
17189379
J Bioinform Comput Biol. 2005 Jun;3(3):697-716
16108090
Mol Cell Proteomics. 2005 Aug;4(8):1194-204
15937296
Nat Biotechnol. 2005 Dec;23(12):1562-7
16311586
J Proteome Res. 2006 Aug;5(8):1843-9
16889405
Genome Res. 2002 Apr;12(4):656-64
11932250
Bioinformatics. 2004 Jun 12;20(9):1466-7
14976030
Anal Chem. 2004 Jul 15;76(14):3908-22
15253624
Anal Chem. 2003 Sep 1;75(17):4646-58
14632076
J Am Soc Mass Spectrom. 2000 May;11(5):422-6
10790846
Anal Chem. 1994 Dec 15;66(24):4390-9
7847635
Anal Chem. 2004 Jul 1;76(13):3556-68
15228325
Rapid Commun Mass Spectrom. 2003;17(20):2337-42
14558135
Anal Chem. 2005 Jul 15;77(14):4626-39
16013882
Proteomics. 2004 Jul;4(7):1985-8
15221759
Mol Cell Proteomics. 2006 Apr;5(4):652-70
16352522