Label-free liquid chromatography-based quantitative proteomics. Challenges and recent developments

Recent innovations in liquid chromatography-mass spectrometry (LC-MS) based methods have facilitated comparative and functional proteomic analyses of large numbers of proteins derived from complex samples without any need for protein or peptide labelling. Here we discuss the features of label-free LC-based proteomics techniques. We first summarize recent methods used for quantitative protein analyses by MS techniques. The major challenges faced by label-free LC-MS based approaches are discussed; these include sample preparation, peptide separation, data mining and quantification. Absolute quantification, kinetic approaches and database search algorithms are also addressed. We focus on the ExpressionE SystemTM (Waters, Manchester, UK), a relatively new platform allowing label-free quantification of peptides for which mass and retention time have been accurately measured. Enhancing the power of this method will require developments in both separation technology and bioinformatics/statistical analysis