Unbiased Statistical Analysis for Multi-Stage Proteomic Search Strategies

被引：44

作者：

Everett, Logan J. ^{[1
]}

Bierl, Charlene ^{[1
]}

Master, Stephen R. ^{[1
]}

机构：

[1] Univ Penn, Dept Pathol & Lab Med, Stellar Chance Labs 613A, Philadelphia, PA 19104 USA

来源：

JOURNAL OF PROTEOME RESEARCH | 2010年 / 9卷 / 02期

关键词：

Proteomics; Mass Spectrometry; Peptide Identification; Bioinformatics; FALSE DISCOVERY RATES; POSTTRANSLATIONAL MODIFICATIONS; PROTEIN IDENTIFICATIONS; PEPTIDE IDENTIFICATIONS; TANDEM; DATABASE; MODEL; ALGORITHMS; SEQUENCES; MS/MS;

D O I：

10.1021/pr900256v

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

"Multi-stage" search strategies have become widely accepted for peptide identification and are implemented in a number of available software packages. We describe limitations of these strategies for validation and decoy-based statistical analyses and demonstrate these limitations using a set of control sample spectra. We propose a solution that corrects the statistical deficiencies and describe its implementation using the open-source software XITandem.

引用

页码：700 / 707

页数：8

共 25 条

[1] False discovery rates and related statistical concepts in mass spectrometry-based proteomics [J].

Choi, Hyungwon ;

Nesvizhskii, Alexey I. .

JOURNAL OF PROTEOME RESEARCH, 2008, 7 (01) :47-50

[2] Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics [J].

Choi, Hyungwon ;

Nesvizhskii, Alexey I. .

JOURNAL OF PROTEOME RESEARCH, 2008, 7 (01) :254-265

[3] A method for reducing the time required to match protein sequences with tandem mass spectra [J].

Craig, R ;

Beavis, RC .

RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 2003, 17 (20) :2310-2316

[4] TANDEM: matching proteins with tandem mass spectra [J].

Craig, R ;

Beavis, RC .

BIOINFORMATICS, 2004, 20 (09) :1466-1467

[5]

Creasy DM, 2002, PROTEOMICS, V2, P1426, DOI 10.1002/1615-9861(200210)2:10<1426::AID-PROT1426>3.0.CO

[6]

2-5

[7] Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry [J].

Elias, Joshua E. ;

Gygi, Steven P. .

NATURE METHODS, 2007, 4 (03) :207-214

[8] AN APPROACH TO CORRELATE TANDEM MASS-SPECTRAL DATA OF PEPTIDES WITH AMINO-ACID-SEQUENCES IN A PROTEIN DATABASE [J].

ENG, JK ;

MCCORMACK, AL ;

YATES, JR .

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 1994, 5 (11) :976-989

[9] A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes [J].

Fenyö, D ;

Beavis, RC .

ANALYTICAL CHEMISTRY, 2003, 75 (04) :768-774

[10] Prediction of error associated with false-positive rate determination for peptide identification in large-scale proteomics experiments using a combined reverse and forward peptide sequence database strategy [J].

Huttlin, Edward L. ;

Hegeman, Adrian D. ;

Harms, Amy C. ;

Sussman, Michael R. .

JOURNAL OF PROTEOME RESEARCH, 2007, 6 (01) :392-398

← 1 2 3 →