Tandem Mass Tags for Comparative and Discovery Proteomics

Relative or comparative proteomics provides valuable insights about the altered protein abundances across different biological samples in a single (labeled) or series (label-free) of LC–MS measurement(s). Chemical labeling of peptides using isobaric mass tags for identification and quantification of different proteomes simultaneously has become a routine in the so-called discovery proteomics in the past decade. One of the earliest isobaric tags-based technologies is TMT (tandem mass tags), which relies on the comparison of the unique “reporter ions” intensities for relative peptide/protein quantification. This differential labeling approach has evolved over time with respect to its multiplexing capability, i.e., from just 2 samples (TMTduplex) to 10 samples (TMT10plex) and a nowadays of up to 16 samples (TMTpro 16plex). Here, we describe a straightforward protocol to perform relatively deep proteome quantitative analyses using TMT10plex.