Selected reaction monitoring for quantitative proteomics: a tutorial

被引：1075

作者：

Lange, Vinzenz ^{[1
,2
]}

Picotti, Paola ^{[1
]}

Domon, Bruno ^{[1
]}

Aebersold, Ruedi ^{[1
,2
,3
,4
]}

机构：

[1] ETH, Inst Mol Syst Biol, Zurich, Switzerland

[2] Competence Ctr Syst Physiol & Metab Dis, Zurich, Switzerland

[3] Inst Syst Biol, Seattle, WA USA

[4] Univ Zurich, Fac Sci, Zurich, Switzerland

来源：

MOLECULAR SYSTEMS BIOLOGY | 2008年 / 4卷 / 1期

基金：

美国国家卫生研究院; 瑞士国家科学基金会;

关键词：

mass spectrometry; MRM; proteomics; quantitative; SRM;

D O I：

10.1038/msb.2008.61

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：

Systems biology relies on data sets in which the same group of proteins is consistently identified and precisely quantified across multiple samples, a requirement that is only partially achieved by current proteomics approaches. Selected reaction monitoring (SRM)-also called multiple reaction monitoring-is emerging as a technology that ideally complements the discovery capabilities of shotgun strategies by its unique potential for reliable quantification of analytes of low abundance in complex mixtures. In an SRM experiment, a predefined precursor ion and one of its fragments are selected by the two mass filters of a triple quadrupole instrument and monitored over time for precise quantification. A series of transitions (precursor/fragment ion pairs) in combination with the retention time of the targeted peptide can constitute a definitive assay. Typically, a large number of peptides are quantified during a single LC-MS experiment. This tutorial explains the application of SRM for quantitative proteomics, including the selection of proteotypic peptides and the optimization and validation of transitions. Furthermore, normalization and various factors affecting sensitivity and accuracy are discussed.

引用

页数：14

共 52 条

[21] IntAct - open source resource for molecular interaction data [J].

Kerrien, S. ;

Alam-Faruque, Y. ;

Aranda, B. ;

Bancarz, I. ;

Bridge, A. ;

Derow, C. ;

Dimmer, E. ;

Feuermann, M. ;

Friedrichsen, A. ;

Huntley, R. ;

Kohler, C. ;

Khadake, J. ;

Leroy, C. ;

Liban, A. ;

Lieftink, C. ;

Montecchi-Palazzi, L. ;

Orchard, S. ;

Risse, J. ;

Robbe, K. ;

Roechert, B. ;

Thorneycroft, D. ;

Zhang, Y. ;

Apweiler, R. ;

Hermjakob, H. .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D561-D565

[22] The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications [J].

Kirkpatrick, DS ;

Gerber, SA ;

Gygi, SP .

METHODS, 2005, 35 (03) :265-273

[23] An improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase HPLC - Its application to protein peptide mapping by off-line HPLC-MALDI MS [J].

Krokhin, OV ;

Craig, R ;

Spicer, V ;

Ens, W ;

Standing, KG ;

Beavis, RC ;

Wilkins, JA .

MOLECULAR & CELLULAR PROTEOMICS, 2004, 3 (09) :908-919

[24] Quantification of C-reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C-labeled peptide standards [J].

Kuhn, E ;

Wu, J ;

Karl, J ;

Liao, H ;

Zolg, W ;

Guild, B .

PROTEOMICS, 2004, 4 (04) :1175-1186

[25] Scoring proteomes with proteotypic peptide probes [J].

Kuster, B ;

Schirle, M ;

Mallick, P ;

Aebersold, R .

NATURE REVIEWS MOLECULAR CELL BIOLOGY, 2005, 6 (07) :577-583

[26] Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring [J].

Lange, Vinzenz ;

Malmstroem, Johan A. ;

Didion, John ;

King, Nichole L. ;

Johansson, Bjoern P. ;

Schaefer, Juliane ;

Rameseder, Jonathan ;

Wong, Chee-Hong ;

Deutsch, Eric W. ;

Brusniak, Mi-Youn ;

Buehlmann, Peter ;

Bjoerck, Lars ;

Domon, Bruno ;

Aebersold, Ruedi .

MOLECULAR & CELLULAR PROTEOMICS, 2008, 7 (08) :1489-1500

[27]

LOWRY OH, 1951, J BIOL CHEM, V193, P265

[28]

Macchi FD, 2000, METH MOL B, V159, P9

[29] eComputational prediction of proteotypic peptides for quantitative proteomics [J].

Mallick, Parag ;

Schirle, Markus ;

Chen, Sharon S. ;

Flory, Mark R. ;

Lee, Hookeun ;

Martin, Daniel ;

Raught, Brian ;

Schmitt, Robert ;

Werner, Thilo ;

Kuster, Bernhard ;

Aebersold, Ruedi .

NATURE BIOTECHNOLOGY, 2007, 25 (01) :125-131

[30] Human Proteinpedia enables sharing of human protein data [J].

Mathivanan, Suresh ;

Ahmed, Mukhtar ;

Ahn, Natalie G. ;

Hainard, Alexandre ;

Amanchy, Ramars ;

Andrews, Philip C. ;

Bader, Joel S. ;

Balgley, Brian M. ;

Bantscheff, Marcus ;

Bennett, Keiryn L. ;

Bjoerling, Erik ;

Blagoev, Blagoy ;

Bose, Ron ;

Brahmachari, Samir K. ;

Burlingame, Alma S. ;

Bustelo, Xose R. ;

Cagney, Gerard ;

Cantin, Greg T. ;

Cardasis, Helene L. ;

Celis, Julio E. ;

Chaerkady, Raghothama ;

Chu, Feixia ;

Cole, Philip A. ;

Costello, Catherine E. ;

Cotter, Robert J. ;

Crockett, David ;

DeLany, James P. ;

De Marzo, Angelo M. ;

DeSouza, Leroi V. ;

Deutsch, Eric W. ;

Dransfield, Eric ;

Drewes, Gerard ;

Droit, Arnaud ;

Dunn, Michael J. ;

Elenitoba-Johnson, Kojo ;

Ewing, Rob M. ;

Van Eyk, Jennifer ;

Faca, Vitor ;

Falkner, Jayson ;

Fang, Xiangming ;

Fenselau, Catherine ;

Figeys, Daniel ;

Gagne, Pierre ;

Gelfi, Cecilia ;

Gevaert, Kris ;

Gimble, Jeffrey M. ;

Gnad, Florian ;

Goel, Renu ;

Gromov, Pavel ;

Hanash, Samir M. .

NATURE BIOTECHNOLOGY, 2008, 26 (02) :164-167

← 1 2 3 4 5 6 →