I tried Fmoc-SPPS with short cyclicPeptides (12 aa length, Brom-Acetyl at the start for cyclization), for the first time containing citrollin. Many of the petides show a main Peak at the MALDI MS of +40.3 the expected mass value. Anyone has an idea what this might be?
And some sequences containing homocitrullin started showing Peaks of +15.3 the expected mass. Normally Id expect oxidation but it in that case we normally observe a main Peak way Closer to +16...
Is there any lysine side chain in your sequence? If yes, did you use Alloc-Lysine? I faced this problem of +40 mass. I've not been able to figure it out yet. The mass of the sequence apart from lysine matched perfectly. The mass of an allyl group comes around 40. Also, I measured the mass after deprotection of the side chain PG except Alloc.
+40 corresponds to CH2CO minus 2H. This suggests very have inserted a CH2CO moiety into your peptide between 2 heteroatoms. The side-chain of citrulline is not-inert! It can react with coupling reagents. In your case I suspect you have converted the urea side chain to a oxazoline by reaction of the activated BrCHCOA with the oxygen of the urea followed by ring closure by attack of a urea nitrogen on the C-Br, and rearrangement of the exocyclic double bond into the ring. This gives +40 mu. An interesting reaction!
The same happened to me in a Cys-containing sequence. It turned out that the problem was the matrix we were using for the MALDI MS. It contained acetone that was forming an artefact with the peptide (the peptide synthesis was correct, but the MALDI result was showing the +40 peak), so we substituted the acetone in the matrix by methanol and solved the problem. In the attached pic you can see in black the +40 peak and and in red with the MeOH matrix.
Hope it helps!
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