An overview of label-free quantitation methods in proteomics by mass spectrometry

Protein quantification represents an important extension to identification proteomics, enabling the comparison of protein expression across different samples or treatments. Comparative protein quantification by mass spectrometry typically employs stable isotope incorporation, but recently, comparative quantification of label-free LC(n)-MS proteomics data has emerged as an alternative approach. In this chapter, we provide an overview of the different approaches for extracting quantitative data from label-free LC(n)-MS experiments. The computational procedure for recovering the quantitative information is outlined. Examples of statistical tests used to evaluate the relevance of results are also provided.