Proteomics data validation: why all must provide data

被引:30
作者
Martens, Lennart [1 ]
Hermjakob, Henning [1 ]
机构
[1] European Bioinformat Inst, EMBL Outstn, PRIDE Project, Proteom Serv Team,Sequence Database Grp, Cambridge, England
关键词
D O I
10.1039/b705178f
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The field of proteomics has gained considerable momentum over the last years as new technologies and better instrumentation allowed the field to mature from what resembled a cottage industry into a high-throughput means to identify, characterize and quantify hundreds of proteins. The identifications and (relative) quantitation values obtained are often controversial however, as various techniques and different software platforms are used in the many laboratories worldwide. This Opinion attempts to shed some light on some of the underlying issues, and proposes certain guidelines authors can adhere to in order to allow others to validate their findings.
引用
收藏
页码:518 / 522
页数:5
相关论文
共 24 条
[1]   Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project [J].
Adamski, M ;
Blackwell, T ;
Menon, R ;
Martens, L ;
Hermjakob, H ;
Taylor, C ;
Omenn, GS ;
States, DJ .
PROTEOMICS, 2005, 5 (13) :3246-3261
[2]  
[Anonymous], 2007, NAT BIOTECHNOL, V25, P262
[3]   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
[4]   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
[5]  
Desiere F, 2005, GENOME BIOL, V6
[6]   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
[7]   ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats [J].
Falkner, J. A. ;
Falkner, J. W. ;
Andrews, P. C. .
BIOINFORMATICS, 2007, 23 (02) :262-263
[8]   Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering [J].
Flikka, K ;
Martens, L ;
Vandekerckhoe, J ;
Gevaert, K ;
Eidhammer, I .
PROTEOMICS, 2006, 6 (07) :2086-2094
[9]   Preprocessing of tandem mass spectrometric data to support automatic protein identification [J].
Gentzel, M ;
Köcher, T ;
Ponnusamy, S ;
Wilm, M .
PROTEOMICS, 2003, 3 (08) :1597-1610
[10]   The HUPO proteomics standards initiative - Overcoming the fragmentation of proteomics data [J].
Hermjakob, Henning .
PROTEOMICS, 2006, :34-38