[Psidev-ms-dev] Mascot parameters

[Fabio C. <frc...@gm...>]

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.

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.

Could anybody help me?

Thanks, Fabio.