Hi,
Following the fractionation of a few variants of the same protein under investigation that can be separated by reversed phase HPLC, it was noted that the reduced tryptic peptide mapping results obtained for the individual variants revealed a few differences between them (overall, the resulting peptide maps were largely similar).
Upon closer inspection of the data, the differences observed are mainly caused by differences in digestion efficiency: in one variant a certain peptide sequence gets cleaved completely, while in another the same peptide sequence is observed containing a missed cleavage.
What could be the reason for this type of difference, given that the conditions used for the experiment we're denaturing (i.e. reduction, alkylation, etc.)?
Thanks for your suggestions!
... "in one variant a certain peptide sequence gets cleaved completely, while in another the same peptide sequence is observed containing a missed cleavage.."
Are you sure that the peptide sequences under consideration are completely identical in both samples? Or do you have variants with altered arginine and lysine positions which determine the attack by trypsin.
Peter
Hi Peter,
Thanks for your suggestion; I hadn't looked at the data that closely, I must admit. But it is a good idea to dive into some of the MS/MS data, indeed!
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