Re: re-posting iPROPHET

[Bernt]

Hi David,
The speed of your reply is amazing, especially judging from the time
over at your side. I wonder if it's because you are kept awake by your
baby!!

From the way you put it, I gather that it means I have to do Xtandem
and Mascot searches from the same set of mzXML files! Is that correct?
I can't figure out how I can get the spectra to be referred by the
same name in both searches with any other way. If that's the case, it
would be a problem because Mascot doesn't accept mzXML schema above
2.0. And I can't find a version of trapper which can convert .d files
to mzXML 2.0 format.

As for specifying the IPROPHET option to the ProteinProphet command, I
think this is easily done at the command line? In petunia, the only
place I can find such a combination is in the <analyze peptides> page.

I guess I won't be able to analyse Xtandem with Mascot searches using
Iprophet anytime soon then, unless Mascot decides one day to accept
mzXML 3.0 or trapper can be modified to convert to mzXML 2.0. Is the
2.0 schema very different from the 3.0 one?

Good night!

Bernard