Brian Pratt responded: |
2019-03-28 17:32 |
Hi Richard,
What does your Peptide Settings > Modifications tab look like? You probably have some settings there that you don't actually want.
Thanks for using the Skyline support board!
Brian Pratt
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Brendan MacLean responded: |
2019-03-28 20:11 |
Yeah. That C[+57] is Carbamidomethyl (C). If you don't want that, you can uncheck this modification in the Peptide Settings - Modifications tab, but if I may ask how did you treat your Cysteines? We don't usually see completely unmodified Cysteine. Usually it is either Carbamidomethyl (C) [+57] or Carboxymethyl (C) [+58].
If you are sure you have bare unmodified Cysteine though, then it is easy enough to uncheck that modification.
--Brendan
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Richard Lam responded: |
2019-04-01 10:41 |
I just performed traditional protein digestion protocol, i.e. reduction by DTT, alkylation by IAA, then digestion by trypsin.
Do you think I should consider Carbamidomethyl (C) [+57] and/or Carboxymethyl (C) [+58] modifications? Thanks!
Regards,
Richard
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Mike MacCoss responded: |
2019-04-01 15:00 |
Hi Richard,
It depends. Are you alkylating with iodoacetamide or iodoacetic acid? Alkylating with iodoacetamide results in carbamidomethyl cysteine [+57] and alkylating with iodoacetic acid results in caboxymethyl [+58]. BTW, most people these days use iodoacetamide.
I hope this helps,
Mike
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Richard Lam responded: |
2019-04-02 12:48 |
Got it. I am using iodoacetamide. Thanks for the clarification.
Regards,
Richard
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