During the MS3 analysis for more accurate TMT quantifications, 5 fragment ions were co-isolated using synchronous precursor selection using a window of 2 Th and further fragmented using HCD collision energy of 55%. The fragments were then analysed in the orbitrap with a resolution of 60,000. The AGC target was set to 1.0 e5 and the maximum injection time was set to 105 ms.
