A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics

被引：588

作者：

Cox, Juergen ^{[1
]}

Matic, Ivan ^{[1
]}

Hilger, Maximiliane ^{[1
]}

Nagaraj, Nagarjuna ^{[1
]}

Selbach, Matthias ^{[2
]}

Olsen, Jesper V. ^{[1
]}

Mann, Matthias ^{[1
]}

机构：

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

[2] Max Delbruck Ctr Mol Med, Dept Cell Signalling & Mass Spectrometry, Berlin, Germany

来源：

NATURE PROTOCOLS | 2009年 / 4卷 / 05期

关键词：

HIGH-RESOLUTION; MASS ACCURACY; CELL-CULTURE; AMINO-ACIDS; IDENTIFICATION; CONFIDENCE; DATABASE; SEARCH;

D O I：

10.1038/nprot.2009.36

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high-resolution mass spectrometry (MS) data. Currently, Thermo LTQ-Orbitrap and LTQ-FT-ICR instruments are supported and Mascot is used as a search engine. This protocol explains step by step how to use MaxQuant on stable isotope labeling by amino acids in cell culture (SILAC) data obtained with double or triple labeling. Complex experimental designs, such as time series and drug-response data, are supported. A standard desktop computer is sufficient to fulfill the computational requirements. The workflow has been stress tested with more than 1,000 liquid chromatography/mass spectrometry runs in a single project. In a typical SILAC proteome experiment, hundreds of thousands of peptides and thousands of proteins are automatically and reliably quantified. Additional information for identified proteins, such as Gene Ontology, domain composition and pathway membership, is provided in the output tables ready for further bioinformatics analysis. The software is freely available at the MaxQuant home page.

引用

页码：698 / 705

页数：8

共 30 条

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

Aebersold, R ;

Mann, M .

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

[2] 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

[3] The Universal Protein Resource (UniProt) [J].

Bairoch, Amos ;

Bougueleret, Lydie ;

Altairac, Severine ;

Amendolia, Valeria ;

Auchincloss, Andrea ;

Puy, Ghislaine Argoud ;

Axelsen, Kristian ;

Baratin, Delphine ;

Blatter, Marie-Claude ;

Boeckmann, Brigitte ;

Bollondi, Laurent ;

Boutet, Emmanuel ;

Quintaje, Silvia Braconi ;

Breuza, Lionel ;

Bridge, Alan ;

Saux, Virginie Bulliard-Le ;

decastro, Edouard ;

Ciampina, Luciane ;

Coral, Danielle ;

Coudert, Elisabeth ;

Cusin, Isabelle ;

David, Fabrice ;

Delbard, Gwennaelle ;

Dornevil, Dolnide ;

Duek-Roggli, Paula ;

Duvaud, Severine ;

Estreicher, Anne ;

Famiglietti, Livia ;

Farriol-Mathis, Nathalie ;

Ferro, Serenella ;

Feuermann, Marc ;

Gasteiger, Elisabeth ;

Gateau, Alain ;

Gehant, Sebastian ;

Gerritsen, Vivienne ;

Gos, Arnaud ;

Gruaz-Gumowski, Nadine ;

Hinz, Ursula ;

Hulo, Chantal ;

Hulo, Nicolas ;

Innocenti, Alessandro ;

James, Janet ;

Jain, Eric ;

Jimenez, Silvia ;

Jungo, Florence ;

Junker, Vivien ;

Keller, Guillaume ;

Lachaize, Corinne ;

Lane-Guermonprez, Lydie ;

Langendijk-Genevaux, Petra .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D190-D195

[4] Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics [J].

Blagoev, B ;

Ong, SE ;

Kratchmarova, I ;

Mann, M .

NATURE BIOTECHNOLOGY, 2004, 22 (09) :1139-1145

[5] Combined use of RNAi and quantitative proteomics to study gene function in Drosophila [J].

Bonaldi, Tiziana ;

Straub, Tobias ;

Cox, Juergen ;

Kumar, Chanchal ;

Becker, Peter B. ;

Mann, Matthias .

MOLECULAR CELL, 2008, 31 (05) :762-772

[6] Is proteomics the new genomics? [J].

Cox, Juergen ;

Mann, Matthias .

CELL, 2007, 130 (03) :395-398

[7] How Much Peptide Sequence Information Is Contained in Ion Trap Tandem Mass Spectra? [J].

Cox, Juergen ;

Hubner, Nina C. ;

Mann, Matthias .

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 2008, 19 (12) :1813-1820

[8] MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification [J].

Cox, Juergen ;

Mann, Matthias .

NATURE BIOTECHNOLOGY, 2008, 26 (12) :1367-1372

[9] Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast [J].

de Godoy, Lyris M. F. ;

Olsen, Jesper V. ;

Cox, Juergen ;

Nielsen, Michael L. ;

Hubner, Nina C. ;

Froehlich, Florian ;

Walther, Tobias C. ;

Mann, Matthias .

NATURE, 2008, 455 (7217) :1251-U60

[10] 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

← 1 2 3 →