TMT proteomics input

Dear mixOmics team,

Thank you for developing such a fantastic tool!

Our lab is trying to use DIABLO to integrate transcriptomics, proteomics & metabolomics on 18 samples (2 cell types x 3 conditions (control vs treatment A, B) x 3 replicates). We are a bit stuck at the input of proteomics data. Because they were performed with TMT labeling, we have abundance ratios between different samples (treatment A/control), not peak value intensity/abundance per condition.

We tried to consult the proteomics facility. The reply was also that we should use the abundance ratios for any downstream data analysis due to the TMT plexes set up.

Hence, we wondered if “feeding” the abundance ratios of proteins to the script is correct. If this is the case, are there different pre-processing steps (as these values are ratios) we should follow in addition to those mentioned in the vignette?

Thank you & looking forward to your reply!

Warm wishes,