MaxQuant for in-depth analysis of large SILAC datasets

Methods Mol Biol. 2014;1188:351-64. doi: 10.1007/978-1-4939-1142-4_24.


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.

MeSH terms

  • Amino Acids / chemistry*
  • Cells, Cultured
  • Chromatography, Liquid
  • Computational Biology / methods*
  • Isotope Labeling / methods*
  • Mass Spectrometry
  • Proteomics / methods*
  • Software*
  • Statistics as Topic / methods*
  • User-Computer Interface


  • Amino Acids