Improved sequence tag generation method for peptide identification in tandem mass spectrometry.
The sequence tag-based peptide identification methods are a promising alternative to the traditional database search approach. However, a more comprehensive analysis, optimization, and comparison with established methods are necessary before these methods can gain widespread use in the proteomics community. Using the InsPecT open source code base ( Tanner et al., Anal. Chem. 2005, 77, 4626- 39 ), we present an improved sequence tag generation method that directly incorporates multicharged fragment ion peaks present in many tandem mass spectra of higher charge states. We also investigate the performance of sequence tagging under different settings using control data sets generated on five different types of mass spectrometers, as well as using a complex phosphopeptide-enriched sample. We also demonstrate that additional modeling of InsPecT search scores using a semiparametric approach incorporating the accuracy of the precursor ion mass measurement provides additional improvement in the ability to discriminate between correct and incorrect peptide identifications. The overall superior performance of the sequence tag-based peptide identification method is demonstrated by comparison with a commonly used SEQUEST/PeptideProphet approach.
Cao
Xia
X
Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA.
Nesvizhskii
Alexey I
AI
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D030562:Databases, Protein; D029721:Drosophila Proteins / Q000032:analysis / Q000235:genetics; D004331:Drosophila melanogaster; D008970:Molecular Weight; D010455:Peptides / Q000032:analysis*; D040901:Proteomics / Q000379:methods; D012680:Sensitivity and Specificity; D053719:Tandem Mass Spectrometry / Q000379:methods*
D029721:Drosophila Proteins; D010455:Peptides
Mol Cell Proteomics. 2005 Aug;4(8):1180-8
15911534
Mol Cell Proteomics. 2007 Sep;6(9):1638-55
17533153
Anal Chem. 2005 Feb 15;77(4):964-73
15858974
Anal Chem. 2003 Dec 1;75(23):6415-21
14640709
Rapid Commun Mass Spectrom. 2003;17(20):2310-6
14558131
Anal Chem. 2007 Feb 15;79(4):1393-400
17243770
Anal Chem. 2003 Sep 1;75(17):4646-58
14632076
Methods Mol Biol. 2007;367:87-119
17185772
J Proteome Res. 2004 Sep-Oct;3(5):958-64
15473683
Anal Chem. 2005 Sep 15;77(18):5800-13
16159109
J Proteome Res. 2008 Jan;7(1):286-92
18078310
Anal Chem. 2003 Mar 15;75(6):1307-15
12659190
Mol Cell Proteomics. 2008 Jan;7(1):71-87
17872894
Proteomics. 2003 Aug;3(8):1434-40
12923768
Anal Chem. 2002 Oct 15;74(20):5383-92
12403597
J Proteome Res. 2008 Aug;7(8):3373-81
18563926
Electrophoresis. 1999 Dec;20(18):3551-67
10612281
J Am Soc Mass Spectrom. 1994 Nov;5(11):976-89
24226387
J Proteome Res. 2005 Jul-Aug;4(4):1287-95
16083278
Nat Methods. 2007 Oct;4(10):787-97
17901868
Proteomics. 2006 Oct;6(19):5117-31
16955515
J Proteome Res. 2005 Mar-Apr;4(2):546-54
15822933
J Proteome Res. 2002 May-Jun;1(3):211-5
12645897
J Bioinform Comput Biol. 2005 Jun;3(3):697-716
16108090
Anal Chem. 2005 Aug 1;77(15):4870-82
16053300
Anal Chem. 2001 Jun 1;73(11):2594-604
11403305
J Comput Biol. 1999 Fall-Winter;6(3-4):327-42
10582570
Rapid Commun Mass Spectrom. 1997;11(9):1067-75
9204580
Drug Discov Today. 2006 Jul;11(13-14):595-600
16793527
Mass Spectrom Rev. 2006 Mar-Apr;25(2):235-54
16284939
J Bioinform Comput Biol. 2006 Dec;4(6):1329-52
17245817
J Proteome Res. 2008 Jan;7(1):96-103
17711323
Anal Chem. 1994 Dec 15;66(24):4390-9
7847635
J Proteome Res. 2008 Jan;7(1):254-65
18159924
Rapid Commun Mass Spectrom. 2003;17(20):2337-42
14558135
Anal Chem. 2005 Jul 15;77(14):4626-39
16013882
Proteomics. 2003 Aug;3(8):1597-610
12923784
Mol Cell Proteomics. 2006 Apr;5(4):652-70
16352522