Re: [Psidev-ms-dev] Mascot parameters

[David C. <su...@ma...>]

Hi Fabio,
This list is for psi related issues. Normally better to ask this sort of 
question by sending an email to su...@ma...

Answers in-line below:


Fabio Cerqueira wrote:
> Hi,
> 
> Does anybody there use Mascot for protein identification by MS/MS ion serch?
> I'm trying to use it for the first time, but I don't know how options to 
> choose for
> fixed and variable modifications.
> 
> Concerning the fixed modifications I'd like to indicate a C-term mass of
> 14.01570; and for the amino acids C, D, E  the masses: 160.03068,
> 129.04264, and 143.05829, respectively.
Carbamidomethyl (C)
Methyl (DE)

> 
> Concerning the variable modifications, I'd like to indicate phosphorylation,
> oxidation of methionine and loss of water in amino acids S and T.
> Phosphorylation and oxidation of methionine are easy. 


> But I don't know
> how option to choose concerning the loss of water in S and T.
Probably easiest to select an instrument type that deals with loss of 
water in the relevant ions series:

http://www.matrixscience.com/help/search_field_help.html#INSTRUMENT

Best regards,
David

> 
> Could anybody help me?
> 
> Thanks, Fabio.
> 
> 
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David Creasy
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