Dear all,

I'm working on the finer details of my experimental design, and have some questions regarding bridging channels for TMT based experiments.

I have two conditions to test, across nine biological replicates, in order to run as one 18-plex TMT-pro experiment.

I am aware of the use of one or more bridging channels being used with pooled samples to combine multiple TMT mixtures, however a colleague has mentioned that a bridging channel should also be considered for normalisation if only one set is used.

Does anyone have any experience using a bridging channel for normalisation in a single mixture? Is it worth sacrificing one or more biological replicates for?

I will be using MSstatsTMT for normalisation and summarisation.

Sam