TY - JOUR
T1 - A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics
AU - Cox, Jürgen
AU - Matic, Ivan
AU - Hilger, Maximiliane
AU - Nagaraj, Nagarjuna
AU - Selbach, Matthias
AU - Olsen, Jesper V
AU - Mann, Matthias
N1 - Keywords: Chromatography, Liquid; Computational Biology; Isotope Labeling; Mass Spectrometry; Proteins; Proteomics; Software
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
U2 - 10.1038/nprot.2009.36
DO - 10.1038/nprot.2009.36
M3 - Journal article
C2 - 19373234
SN - 1754-2189
VL - 4
SP - 698
EP - 705
JO - Nature Protocols (Print Edition)
JF - Nature Protocols (Print Edition)
IS - 5
ER -