Quantitative Proteomics by Metabolic Labeling of Model Organisms

被引:111
作者
Gouw, Joost W.
Krijgsveld, Jeroen
Heck, Albert J. R. [1 ]
机构
[1] Univ Utrecht, Biomol Mass Spectrometry & Prote Grp, Bijvoet Ctr Biomol Res, NL-3584 CH Utrecht, Netherlands
关键词
EFFICIENT PROTEIN IDENTIFICATION; DESORPTION/IONIZATION MASS-SPECTROMETRY; REVEALS POSTTRANSCRIPTIONAL REGULATION; SITE-SPECIFIC PHOSPHORYLATION; CELL-CULTURE SILAC; STABLE-ISOTOPE; DROSOPHILA-MELANOGASTER; ARABIDOPSIS-THALIANA; SACCHAROMYCES-CEREVISIAE; IN-VIVO;
D O I
10.1074/mcp.R900001-MCP200
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
In the biological sciences, model organisms have been used for many decades and have enabled the gathering of a large proportion of our present day knowledge of basic biological processes and their derailments in disease. Although in many of these studies using model organisms, the focus has primarily been on genetics and genomics approaches, it is important that methods become available to extend this to the relevant protein level. Mass spectrometry-based proteomics is increasingly becoming the standard to comprehensively analyze proteomes. An important transition has been made recently by moving from charting static proteomes to monitoring their dynamics by simultaneously quantifying multiple proteins obtained from differently treated samples. Especially the labeling with stable isotopes has proved an effective means to accurately determine differential expression levels of proteins. Among these, metabolic incorporation of stable isotopes in vivo in whole organisms is one of the favored strategies. In this perspective, we will focus on methodologies to stable isotope label a variety of model organisms in vivo, ranging from relatively simple organisms such as bacteria and yeast to Caenorhabditis elegans, Drosophila, and Arabidopsis up to mammals such as rats and mice. We also summarize how this has opened up ways to investigate biological processes at the protein level in health and disease, revealing conservation and variation across the evolutionary tree of life. Molecular & Cellular Proteomics 9: 11-24, 2010.
引用
收藏
页码:11 / 24
页数:14
相关论文
共 150 条
[1]   The genome sequence of Drosophila melanogaster [J].
Adams, MD ;
Celniker, SE ;
Holt, RA ;
Evans, CA ;
Gocayne, JD ;
Amanatides, PG ;
Scherer, SE ;
Li, PW ;
Hoskins, RA ;
Galle, RF ;
George, RA ;
Lewis, SE ;
Richards, S ;
Ashburner, M ;
Henderson, SN ;
Sutton, GG ;
Wortman, JR ;
Yandell, MD ;
Zhang, Q ;
Chen, LX ;
Brandon, RC ;
Rogers, YHC ;
Blazej, RG ;
Champe, M ;
Pfeiffer, BD ;
Wan, KH ;
Doyle, C ;
Baxter, EG ;
Helt, G ;
Nelson, CR ;
Miklos, GLG ;
Abril, JF ;
Agbayani, A ;
An, HJ ;
Andrews-Pfannkoch, C ;
Baldwin, D ;
Ballew, RM ;
Basu, A ;
Baxendale, J ;
Bayraktaroglu, L ;
Beasley, EM ;
Beeson, KY ;
Benos, PV ;
Berman, BP ;
Bhandari, D ;
Bolshakov, S ;
Borkova, D ;
Botchan, MR ;
Bouck, J ;
Brokstein, P .
SCIENCE, 2000, 287 (5461) :2185-2195
[2]   Mass spectrometry-based proteomics [J].
Aebersold, R ;
Mann, M .
NATURE, 2003, 422 (6928) :198-207
[3]   Nucleolar proteome dynamics [J].
Andersen, JS ;
Lam, YW ;
Leung, AKL ;
Ong, SE ;
Lyon, CE ;
Lamond, AI ;
Mann, M .
NATURE, 2005, 433 (7021) :77-83
[4]   The versatile worm:: genetic and genomic resources for Caenorhabditis elegans research [J].
Antoshechkin, Igor ;
Sternberg, Paul W. .
NATURE REVIEWS GENETICS, 2007, 8 (07) :518-532
[5]   Quantitative proteomics as a new piece of the systems biology puzzle [J].
Bachi, Angela ;
Bonaldi, Tiziana .
JOURNAL OF PROTEOMICS, 2008, 71 (03) :357-367
[6]   Quantitative mass spectrometry in proteomics: a critical review [J].
Bantscheff, Marcus ;
Schirle, Markus ;
Sweetman, Gavain ;
Rick, Jens ;
Kuster, Bernhard .
ANALYTICAL AND BIOANALYTICAL CHEMISTRY, 2007, 389 (04) :1017-1031
[7]   Prevention of amino acid conversion in SILAC experiments with embryonic stem cells [J].
Bendall, Sean C. ;
Hughes, Chris ;
Stewart, Morag H. ;
Doble, Brad ;
Bhatia, Mickie ;
Lajoie, Gilles A. .
MOLECULAR & CELLULAR PROTEOMICS, 2008, 7 (09) :1587-1597
[8]   Quantitative phosphoproteomics of early elicitor signaling in Arabidopsis [J].
Benschop, Joris J. ;
Mohammed, Shabaz ;
O'Flaherty, Martina ;
Heck, Albert J. R. ;
Slijper, Monique ;
Menke, Frank L. H. .
MOLECULAR & CELLULAR PROTEOMICS, 2007, 6 (07) :1198-1214
[9]   Drosophila, the golden bug, emerges as a tool for human genetics [J].
Bier, E .
NATURE REVIEWS GENETICS, 2005, 6 (01) :9-23
[10]   Hydroponic isotope labelling of entire plants (HILEP) for quantitative plant proteomics; an oxidative stress case study [J].
Bindschedler, Laurence V. ;
Palmblad, Magnus ;
Cramer, Rainer .
PHYTOCHEMISTRY, 2008, 69 (10) :1962-1972