Dear Group,
I am running a Peptide Prophet search but xinteract breaks. The error
message is :
Syntax error parsing XML.not well-formed (invalid token)
The offending line (in a peptide-xml file) is
alternative_protein protein=tr|Q78E99|MRXRgamma
protein_descr=homolog protein (Fragment)
Hi DT,
Thank you very much for the great suggestion.
I have not tried OMSSA too much. I will try to use these two software
and ASAPRatio for the quantification.
By the way, do you have any publications which described the way you
did the quantification?
As for Mascot, recently, I kind of
The defect is really somewhere upstream - whatever created the pepxml files
that went into xinteract should have escaped those characters.
On Wed, Apr 14, 2010 at 11:25 PM, Simon Michnowicz
simon.michnow...@gmail.com wrote:
Dear Group,
I am running a Peptide Prophet search but xinteract
Brian,
the pepXML was created using Mascot2XML. The pepXML file that was
input to xinteract does not contain the entry
tr|Q78E99|MRXRgamma
My understanding is that xinteract opens the database mentioned in the
pepXML file to extract information.
Regards
Simon Michnowicz
On Apr 16, 1:09 am,
