Muntel J, Kirkpatrick J, Bruderer R, Huang T, Vitek O, Ori A, and Reiter L. Journal of Proteome Research,
Here we compare the performance of the two most popular quantitative workflows employed in discovery proteomics, label-free DIA, and isobaric-labeled TMT 10-plex. Workflows were tested on the same spike-in samples, with matched instrument time and reciprocal assessment in two facilities. Both workflows delivered high proteome coverage with low missing values at the protein level. While TMT performed slightly better in coverage and quantitative precision, DIA showed higher scalability and quantitative accuracy.