Next-generation proteomics: towards an integrative view of proteome dynamics

被引：533

作者：

Altelaar, A. F. Maarten ^{[1
,2
,3
]}

Munoz, Javier ^{[1
,2
,3
]}

Heck, Albert J. R. ^{[1
,2
,3
]}

机构：

[1] Univ Utrecht, Bijvoet Ctr Biomol Res, NL-3584 CH Utrecht, Netherlands

[2] Univ Utrecht, Utrecht Inst Pharmaceut Sci, NL-3584 CH Utrecht, Netherlands

[3] Netherlands Prote Ctr, NL-3584 CH Utrecht, Netherlands

来源：

NATURE REVIEWS GENETICS | 2013年 / 14卷 / 01期

关键词：

PLURIPOTENT STEM-CELLS; MULTIPLEXED QUANTITATIVE PROTEOMICS; SPECTROMETRY-BASED PROTEOMICS; GENE-EXPRESSION SIGNATURES; DNA-SEQUENCE DIFFERENCES; CHEMICAL CROSS-LINKING; SCALE DATA SETS; MASS-SPECTROMETRY; SACCHAROMYCES-CEREVISIAE; SYSTEMS BIOLOGY;

D O I：

10.1038/nrg3356

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Next-generation sequencing allows the analysis of genomes, including those representing disease states. However, the causes of most disorders are multifactorial, and systems-level approaches, including the analysis of proteomes, are required for a more comprehensive understanding. The proteome is extremely multifaceted owing to splicing and protein modifications, and this is further amplified by the interconnectivity of proteins into complexes and signalling networks that are highly divergent in time and space. Proteome analysis heavily relies on mass spectrometry (MS). MS-based proteomics is starting to mature and to deliver through a combination of developments in instrumentation, sample preparation and computational analysis. Here we describe this emerging next generation of proteomics and highlight recent applications.

引用

页码：35 / 48

页数：14

共 156 条

[1] A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease [J].

Addona, Terri A. ;

Shi, Xu ;

Keshishian, Hasmik ;

Mani, D. R. ;

Burgess, Michael ;

Gillette, Michael A. ;

Clauser, Karl R. ;

Shen, Dongxiao ;

Lewis, Gregory D. ;

Farrell, Laurie A. ;

Fifer, Michael A. ;

Sabatine, Marc S. ;

Gerszten, Robert E. ;

Carr, Steven A. .

NATURE BIOTECHNOLOGY, 2011, 29 (07) :635-U119

[2] Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma [J].

Addona, Terri A. ;

Abbatiello, Susan E. ;

Schilling, Birgit ;

Skates, Steven J. ;

Mani, D. R. ;

Bunk, David M. ;

Spiegelman, Clifford H. ;

Zimmerman, Lisa J. ;

Ham, Amy-Joan L. ;

Keshishian, Hasmik ;

Hall, Steven C. ;

Allen, Simon ;

Blackman, Ronald K. ;

Borchers, Christoph H. ;

Buck, Charles ;

Cardasis, Helene L. ;

Cusack, Michael P. ;

Dodder, Nathan G. ;

Gibson, Bradford W. ;

Held, Jason M. ;

Hiltke, Tara ;

Jackson, Angela ;

Johansen, Eric B. ;

Kinsinger, Christopher R. ;

Li, Jing ;

Mesri, Mehdi ;

Neubert, Thomas A. ;

Niles, Richard K. ;

Pulsipher, Trenton C. ;

Ransohoff, David ;

Rodriguez, Henry ;

Rudnick, Paul A. ;

Smith, Derek ;

Tabb, David L. ;

Tegeler, Tony J. ;

Variyath, Asokan M. ;

Vega-Montoto, Lorenzo J. ;

Wahlander, Asa ;

Waldemarson, Sofia ;

Wang, Mu ;

Whiteaker, Jeffrey R. ;

Zhao, Lei ;

Anderson, N. Leigh ;

Fisher, Susan J. ;

Liebler, Daniel C. ;

Paulovich, Amanda G. ;

Regnier, Fred E. ;

Tempst, Paul ;

Carr, Steven A. .

NATURE BIOTECHNOLOGY, 2009, 27 (07) :633-U85

[3] Benchmarking stable isotope labeling based quantitative proteomics [J].

Altelaar, A. F. Maarten ;

Frese, Christian K. ;

Preisinger, Christian ;

Hennrich, Marco L. ;

Schram, Andree W. ;

Timmers, H. Th. Marc ;

Heck, Albert J. R. ;

Mohammed, Shabaz .

JOURNAL OF PROTEOMICS, 2013, 88 :14-26

[4] Trends in ultrasensitive proteomics [J].

Altelaar, A. F. Maarten ;

Heck, Albert J. R. .

CURRENT OPINION IN CHEMICAL BIOLOGY, 2012, 16 (1-2) :206-213

[5] Database independent proteomics analysis of the ostrich and human proteome [J].

Altelaar, A. F. Maarten ;

Navarro, Danny ;

Boekhorst, Jos ;

van Breukelen, Bas ;

Snel, Berend ;

Mohammed, Shabaz ;

Heck, Albert J. R. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2012, 109 (02) :407-412

[6]

Andersen J, 2010, DANCING TIMES, V100, P55

[7] Performance Characteristics of a New Hybrid Quadrupole Time-of-Flight Tandem Mass Spectrometer (TripleTOF 5600) [J].

Andrews, Genna L. ;

Simons, Brigitte L. ;

Young, J. Bryce ;

Hawkridge, Adam M. ;

Muddiman, David C. .

ANALYTICAL CHEMISTRY, 2011, 83 (13) :5442-5446

[8] Proteomic snapshot of the EGF-induced ubiquitin network [J].

Argenzio, Elisabetta ;

Bange, Tanja ;

Oldrini, Barbara ;

Bianchi, Fabrizio ;

Peesari, Raghunath ;

Mari, Sara ;

Di Fiore, Pier Paolo ;

Mann, Matthias ;

Polo, Simona .

MOLECULAR SYSTEMS BIOLOGY, 2011, 7

[9] Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae [J].

Babu, Mohan ;

Vlasblom, James ;

Pu, Shuye ;

Guo, Xinghua ;

Graham, Chris ;

Bean, Bjoern D. M. ;

Burston, Helen E. ;

Vizeacoumar, Franco J. ;

Snider, Jamie ;

Phanse, Sadhna ;

Fong, Vincent ;

Tam, Yuen Yi C. ;

Davey, Michael ;

Hnatshak, Olha ;

Bajaj, Navgeet ;

Chandran, Shamanta ;

Punna, Thanuja ;

Christopolous, Constantine ;

Wong, Victoria ;

Yu, Analyn ;

Zhong, Gouqing ;

Li, Joyce ;

Stagljar, Igor ;

Conibear, Elizabeth ;

Wodak, Shoshana J. ;

Emili, Andrew ;

Greenblatt, Jack F. .

NATURE, 2012, 489 (7417) :585-+

[10] Instant spectral assignment for advanced decision tree-driven mass spectrometry [J].

Bailey, Derek J. ;

Rose, Christopher M. ;

McAlister, Graeme C. ;

Brumbaugh, Justin ;

Yu, Pengzhi ;

Wenger, Craig D. ;

Westphall, Michael S. ;

Thomson, James A. ;

Coon, Joshua J. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2012, 109 (22) :8411-8416

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