Challenges and opportunities in proteomics data analysis

被引:79
作者
Domon, Bruno
Aebersold, Ruedi
机构
[1] Univ Zurich, Fac Sci, CH-8049 Zurich, Switzerland
[2] Inst Mol Syst Biol, Seattle, WA 98103 USA
关键词
PROTEIN IDENTIFICATION DATA; MASS-SPECTROMETRY; STATISTICAL-MODEL; PEPTIDE; SYSTEM;
D O I
10.1074/mcp.R600012-MCP200
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Accurate, consistent, and transparent data processing and analysis are integral and critical parts of proteomics workflows in general and for biomarker discovery in particular. Definition of common standards for data representation and analysis and the creation of data repositories are essential to compare, exchange, and share data within the community. Current issues in data processing, analysis, and validation are discussed together with opportunities for improving the process in the future and for defining alternative workflows.
引用
收藏
页码:1921 / 1926
页数:6
相关论文
共 20 条
[1]   Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins [J].
Anderson, L ;
Hunter, CL .
MOLECULAR & CELLULAR PROTEOMICS, 2006, 5 (04) :573-588
[2]   Protein identification by mass spectrometry - Issues to be considered [J].
Baldwin, MA .
MOLECULAR & CELLULAR PROTEOMICS, 2004, 3 (01) :1-9
[3]   Reporting protein identification data - The next generation of guidelines [J].
Bradshaw, RA ;
Burlingame, AL ;
Carr, S ;
Aebersold, R .
MOLECULAR & CELLULAR PROTEOMICS, 2006, 5 (05) :787-788
[4]   The need for guidelines in publication of peptide and protein identification data - Working group on publication guidelines for peptide and protein identification data [J].
Carr, S ;
Aebersold, R ;
Baldwin, M ;
Burlingame, A ;
Clauser, K ;
Nesvizhskii, A .
MOLECULAR & CELLULAR PROTEOMICS, 2004, 3 (06) :531-533
[5]   Open source system for analyzing, validating, and storing protein identification data [J].
Craig, R ;
Cortens, JP ;
Beavis, RC .
JOURNAL OF PROTEOME RESEARCH, 2004, 3 (06) :1234-1242
[6]  
Desiere F, 2005, GENOME BIOL, V6
[7]  
DONON B, 2006, IN PRESS P 54 ASMS C
[8]   Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations [J].
Elias, JE ;
Haas, W ;
Faherty, BK ;
Gygi, SP .
NATURE METHODS, 2005, 2 (09) :667-675
[9]  
Kearney P, 2003, J Bioinform Comput Biol, V1, P183, DOI 10.1142/S021972000300023X
[10]   Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search [J].
Keller, A ;
Nesvizhskii, AI ;
Kolker, E ;
Aebersold, R .
ANALYTICAL CHEMISTRY, 2002, 74 (20) :5383-5392