Brian, the pepXML was created using Mascot2XML. The pepXML file that was input to xinteract does not contain the entry "tr|Q78E99|MRXR<gamma>"
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, Brian Pratt <brian.pr...@insilicos.com> wrote: > 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 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|MRXR<gamma>" > > protein_descr="homolog protein (Fragment) Tax_Id=10118 [Rattus sp]" > > num_tol_term="2" peptide_prev_aa="K" peptide_next_aa="D"/> > > > Should the <gamma> entry should be <gamma> ?? > > Is there an easy fix to this problem? > > Thanks > > Simon Michnowicz > > > -- > > You received this message because you are subscribed to the Google Groups > > "spctools-discuss" group. > > To post to this group, send email to spctools-disc...@googlegroups.com. > > To unsubscribe from this group, send email to > > spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2Bunsubscrib > > e...@googlegroups.com> > > . > > For more options, visit this group at > >http://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
