First, I synthesized by SPPS with Fmoc strategy the linear peptide : D-Glu(OtBu)-L-Lys(Alloc)-D-Glu(OtBu)-L-Ala-D-Glu(OtBu)-L-Lys(Alloc)-D-Glu(OtBu)-L-Ala. After cleavage from the resin (2-chlorotritylchloride resin), the linear peptide was cyclized in PyAOP/DIEA/DMF. The cyclic peptide was obtained but cyclization was not completed so some linear peptide was left. Then I deprotected all OtBu of the side chains with TFA/H2O, and I obtained a mix of 3 products : deprotected linear peptide, deprotected cyclic peptide and a product with a mass of +71 Da compared to the deprotected cyclic peptide in LC-MS (it could be a +53 Da compared to the deprotected linear peptide). I suspected that it was a problem of Alanine so I changed the 2 Ala by 2 Leu in the sequence, but I still had this +71 Da. I also changed the conditions of cyclization but this +71 Da product was still here. Could it be a reaction on the double bond of Lys(Alloc) ? Does anyone has a clue ? Thank you !
The product in question (LC-MS, MW 71) does not seem to be peptide derived as you did change Ala to Leu, nor it is an amino acid residue. Possibilities are from your reagents and protecting groups' derivatizations. The Alloc and OBut! But the sequence/fragments analysis and derived masses do not fit them either. The product, most probably, also being constant in trial deblocking and cyclization, seems to be, pyrrolidine, MW 71, if you not using a solvent of this class.
Riaz A. Khan Thank you for your answer. I think the product in question (LC-MS, MW +71) is in fact a peptide very similar to my peptides, because the retention time is extremely close to my deprotected cyclic peptide (they coelute, very difficult to separate them). Indeed the pyrrolidine has the right mass, but where would the pyrrolidine come from according to you ?
Which dipeptide has 71 mass? which aminoacid with amide group has MW71, all from your sequence?
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