Label free quantification (LFQ) and isobaric labelling quantification (ILQ) are the two most popular quantification workflows in discovery proteomics. Here we set out to objectively compare the two workflows given a fix amount of LC-MS time. For this purpose, we generated a gold standard data set comprising of a stable mouse background with biological variation spiked with a protein standard in known absolute amounts. For isobaric labelling, we chose TMT 10-plex (Werner et al. 2014), for LFQ we chose single shot data-independent acquisition (DIA). Biognosys and the FLI joined forces to share their respective expertise in both workflows. The LFQ-DIA and ILQ-TMT workflows were implemented at in both laboratories to measure all samples and evaluate the quantitative performance of both techniques given a fixed amount of instrument time.
THIS SEMINAR WILL BE OF INTEREST TO CURRENT OR FUTURE USERS OF PROTEOMIC METHODS