There are multiple MS approaches that can be applied to yield accurate quantitation. However, each approach comes with distinct trade-offs.62 Label-free methods can provide relative quantification in simple mixtures. In complex mixtures, isotopic labelling should be employed, which allows multiplexing of samples. For instance, stable isotope labelling with amino acids in cell culture (SILAC) is based on metabolic labelling of proteins in vitro with amino acids containing heavy (e.g. 13C) stable isotopes. Fully labelled SILAC mice have also been generated.72 Methods for protein labelling are based on the use of isobaric tags, such as isobaric tags for relative and absolute quantitation (iTRAQ) or tandem mass tag (TMT).73 Isobaric tags have the same chemical structure but different isotope substitutions. When samples are labelled with different tags, they can be subsequently mixed in equal portions, and the protein abundance from the different samples can be assessed by comparing the abundance of peptides labelled with the different tags in a single LC-MS/MS run. Although these tagging methods overcome issues such as technical reproducibility of LC-MS/MS runs, labelling is only introduced after protein digestion and therefore, unlike SILAC, isobaric tags do not allow for in vivo or in vitro labelling but have been used for quantitative comparisons using tissue samples.74,75