Is TMT labeling compatible with PTMScan®?

We understand some customers choose to pursue TMT labeling for PTMScan proteomics analysis, but we do not have a defined protocol for this method. However, there are two questions we can address:

 

1) We know that labs have succeeded in performing this experiment by enriching for the PTM peptides first then labeling second. This is critical for UbiScan and ubiquitin remant in particular because the TMT label is now on the K-e-GG remnant and the antibody won't be able to bind if the labeling is performed first.

 

2) We have recently found that to recover the TMT peptides efficiently from the stage tip C-18 desalting step you need to use 50% ACN/ 0.15% TFA (an increase from 40%). The TMT label makes the peptides more hydrophobic and the increase in ACN helps elute them from the C-18.

Last updated: March 20, 2024