Hello everyone,
I have been getting warnings of the following type from Tandem2XML when processing all-15N search results:
WARNING: Unknown modification 'C' (-18.0236) for scan 58137.
WARNING: Unknown modification 'Q' (-18.0236) for scan 66445.
The all-15N search uses modified residues as well as modified NH3 mass specification, as detailed here. However, Tandem2XML simply uses hard-coded masses for the default special Tandem modifications, such as pyrolidone, etc:
// Special X! Tandem n-terminal AA variable modifications
ModSpecData modSpec;
modSpec.symbol = '^';
modSpec.comment = "X! Tandem n-terminal AA variable modification";
modSpec.aa = 'E';
modSpec.mass = -18.0106;
addModSpec(modSpec, true);
modSpec.aa = 'Q';
modSpec.mass = -17.0265;
addModSpec(modSpec, true);
if ((long) modsStatic['C'].mass == 57)
{
modSpec.aa = 'C';
modSpec.mass = -17.0265;
addModSpec(modSpec, true);
}
// deal with quick acetyl
modSpec.aa = '[';
modSpec.mass = 42.0106;
addModSpec(modSpec, true);
I think these masses should be following the definitions provided by the user for specific isotopic labeling requirements (2H, 15N, ...) and not taken as fixed values.
Does this sound valid to the developers and would a fix be appropriate?
Thank you,
Farshad