Bioinformatics analysis of mass spectrometry-based proteomics data sets

被引：115

作者：

Kumar, Chanchal ^{[1
]}

Mann, Matthias ^{[1
]}

机构：

[1] Max Planck Inst Biochem, Dept Prote & Signal Transduct, D-82152 Martinsried, Germany

来源：

FEBS LETTERS | 2009年 / 583卷 / 11期

关键词：

Quantitative mass spectrometry; Computational proteomics; Bioinformatics; Systems biology; SILAC; MaxQuant; QUANTITATIVE PROTEOMICS; PROTEIN-INTERACTION; BIOMARKER DISCOVERY; ABSOLUTE PROTEIN; GENE ONTOLOGY; CELL-CULTURE; AMINO-ACIDS; GENOME-WIDE; IN-VIVO; EXPRESSION;

D O I：

10.1016/j.febslet.2009.03.035

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：

Proteomics has made tremendous progress, attaining throughput and comprehensiveness so far only seen in genomics technologies. The consequent avalanche of proteome level data poses great analytical challenges for downstream interpretation. We review bioinformatic analysis of qualitative and quantitative proteomic data, focusing on current and emerging paradigms employed for functional analysis, data mining and knowledge discovery from high resolution quantitative mass spectrometric data. Many bioinformatics tools developed for microarrays can be reused in proteomics, however, the uniquely quantitative nature of proteomics data also offers entirely novel analysis possibilities, which directly suggest and illuminate biological mechanisms. (C) 2009 Federation of European Biochemical Societies. Published by Elsevier B. V. All rights reserved.

引用

页码：1703 / 1712

页数：10

共 99 条

[1] In-depth analysis of the adipocyte proteome by mass spectrometry and bioinformatics [J].

Adachi, Jun ;

Kumar, Chanchal ;

Zhang, Yanling ;

Mann, Matthias .

MOLECULAR & CELLULAR PROTEOMICS, 2007, 6 (07) :1257-1273

[2] The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins [J].

Adachi, Jun ;

Kumar, Chanchal ;

Zhang, Yanling ;

Olsen, Jesper V. ;

Mann, Matthias .

GENOME BIOLOGY, 2006, 7 (09)

[3] Mass spectrometry-based proteomics [J].

Aebersold, R ;

Mann, M .

NATURE, 2003, 422 (6928) :198-207

[4] Gene prioritization through genomic data fusion [J].

Aerts, S ;

Lambrechts, D ;

Maity, S ;

Van Loo, P ;

Coessens, B ;

De Smet, F ;

Tranchevent, LC ;

De Moor, B ;

Marynen, P ;

Hassan, B ;

Carmeliet, P ;

Moreau, Y .

NATURE BIOTECHNOLOGY, 2006, 24 (05) :537-544

[5] Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling [J].

Alizadeh, AA ;

Eisen, MB ;

Davis, RE ;

Ma, C ;

Lossos, IS ;

Rosenwald, A ;

Boldrick, JG ;

Sabet, H ;

Tran, T ;

Yu, X ;

Powell, JI ;

Yang, LM ;

Marti, GE ;

Moore, T ;

Hudson, J ;

Lu, LS ;

Lewis, DB ;

Tibshirani, R ;

Sherlock, G ;

Chan, WC ;

Greiner, TC ;

Weisenburger, DD ;

Armitage, JO ;

Warnke, R ;

Levy, R ;

Wilson, W ;

Grever, MR ;

Byrd, JC ;

Botstein, D ;

Brown, PO ;

Staudt, LM .

NATURE, 2000, 403 (6769) :503-511

[6] Organellar proteomics: turning inventories into insights [J].

Andersen, Jens S. ;

Mann, Matthias .

EMBO REPORTS, 2006, 7 (09) :874-879

[7] Nucleolar proteome dynamics [J].

Andersen, JS ;

Lam, YW ;

Leung, AKL ;

Ong, SE ;

Lyon, CE ;

Lamond, AI ;

Mann, M .

NATURE, 2005, 433 (7021) :77-83

[8] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[9] The impact of microRNAs on protein output [J].

Baek, Daehyun ;

Villen, Judit ;

Shin, Chanseok ;

Camargo, Fernando D. ;

Gygi, Steven P. ;

Bartel, David P. .

NATURE, 2008, 455 (7209) :64-U38

[10] Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics [J].

Baerenfaller, Katja ;

Grossmann, Jonas ;

Grobei, Monica A. ;

Hull, Roger ;

Hirsch-Hoffmann, Matthias ;

Yalovsky, Shaul ;

Zimmermann, Philip ;

Grossniklaus, Ueli ;

Gruissem, Wilhelm ;

Baginsky, Sacha .

SCIENCE, 2008, 320 (5878) :938-941

← 1 2 3 4 5 6 7 8 9 10 →