Comparison of Protein Quantification in a Complex Background by DIA and TMT Workflows

Brief Introduction

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.

https://www.leibniz-fli.de/research/core-facilities-services/cf-proteomics/