Protocol abstract
Nature Protocols 4, - 698 - 705 (2009)
Published online: 16 April 2009 | doi:10.1038/nprot.2009.36
Subject Categories: Biochemistry and protein analysis | Computational and theoretical biology | Genomics and proteomics | Spectroscopy and structural analysis
A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics
Jürgen Cox1, Ivan Matic1, Maximiliane Hilger1, Nagarjuna Nagaraj1, Matthias Selbach2, Jesper V Olsen1 & Matthias Mann1
Abstract
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.
- Department for Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Martinsried, Germany.
- Department for Cell Signalling and Mass Spectrometry, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
Correspondence to: Jürgen Cox1 e-mail: cox@biochem.mpg.de
Correspondence to: Matthias Mann1 e-mail: mmann@biochem.mpg.de
