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Topic: Wrong fragment ion calculation for C-amide peptides

I'm using mMass 5.3.0
When calculating the list of fragments for a peptide containing C-terminal amide (eg. AAHPEEDDGGQPRPPGR-NH2, checked with some others, the result is similar), modification is only in a16 and b16 fragments (should NOT be in any b-ion), and is not in ANY of y-type fragments (should be in ALL of them) and M-type (unfragmented peptide).

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Re: Wrong fragment ion calculation for C-amide peptides

Hi,
unfortunately, you are right. Until I release a new version, you can use this workaround: just define your terminal modification as a regular modification on terminal amino acid. So in your example ( AAHPEEDDGGQPRPPGR ) apply Amide on Arginine R17 instead of using C-terminus.

Thanks for report!

martin

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Re: Wrong fragment ion calculation for C-amide peptides

Thank you, Martin. The workaround you suggested works fine, but I hope the new version will come soon