Hi

I am planning to do protein N terminal amine isotope labelling analysis (N-TAILS) to find the substrate proteome of my protease of interest. For this I have the WT and the knock down line for the protease. I plan to label the samples with TMT. Typically following tagging the N-terminal ends with TMT, people do trypsinization and remove the internal unlabelled tryptic peptides by running through a HPG-ALD column, which will capture the neo n-terminal peptides. This way one can enrich the TMT labelled N-terminal peptides, that are then analyzed by mass spec.

I was wondering if the HPG-ALD column purification is absolutely necessary or I can avoid this step? In any case if the analysis of the mass spec data is done on the labelled peptides, then it really does not matter if you have the unlabelled contaminants in your sample right?

Any suggestion would be highly appreciated.

Thanks

Sumit