Mascot2xml and user-defined modifications

[xiaoj...@gmail.com]

Dear David,

Can Mascot2xml handle user-defined modifications? I used Mascot to
search a dataset and defined deamidation of N (not of NQ as listed in
Mascot). When I tried to convert the results in dat file, I received
an error message saying modification not recognized. In the dat file,
I can clearly see the definition of deamidation of N.

Any suggestions?

Thanks!

Xiaojun

[David Shteynberg]

Hi Xiaojun,

Actually, Mascot2XML can only handle Mascot standard modifications at
this point. New modifications must be added to the code
(src/common/ResidueMass class) and the binary must be recompiled to
work. We have plans to implement automatic parsing and inclusion of
user-defined modifications directly from the Mascot modifications config
file at some point in the future, but we are only at the planning stages
for adding this part.

Cheers,
-David

[Mark Shifman]

Hi Xiaojun

It is not hard to add the modifications and recompile (although it can
be tedious if some of
the modifications were put into Mascot differently ie with an underscore
instead of a - etc).
you can find the modifications that are already in mascot at
http://www.unimod.org/mod_file/mod_file

However, I do look forward to having some automatic procedure for
getting the modifications
since i seem to get bit every time I upgrade to a new version.

mas