MaxQuant for in-depth analysis of large SILAC datasets

Abstract

Proteomics experiments can generate very large volumes of data, in particular in situations where within one experimental design many samples are compared to each other, possibly in combination with pre-fractionation of samples prior to LC-MS analysis. Here we provide a step-by-step protocol explaining how the current MaxQuant version can be used to analyze large SILAC-labeling datasets in an efficient way. © 2014 Springer Science+Business Media New York.