I actually fixed this back in February, but it's in the current ("trunk")
code and not the 4.3 release.Brian On Thu, Apr 15, 2010 at 5:34 PM, Simon Michnowicz < [email protected]> wrote: > Brian > my apologies, the pepXML file was indeed broken. Mascot2XML took a > FASTA entry like > >tr|A0N7J4|V<beta>6-N-D<beta>-N-J<beta>1.1 protein (Fragment) Tax_Id=9606 > [Homo sapiens] > > Into > <search_hit hit_rank="1" peptide="CASSSDR" peptide_prev_aa="-" > peptide_next_aa="A" protein="tr|A0N7J4|V<beta>6-N-D<beta>-N- > J<beta>1.1" num_tot_proteins="1" num_matched_ions="3" > tot_num_ions="12" calc_neutral_pep_mass="926.2242" massdiff="-0.3787" > num_tol_term="2" num_missed_cleavages="0" calc_pI="5.83" > is_rejected="0"> > > Which breaks the pepXML viewer, and I imagine xinteract. > > We have a version of Mascot2XML from TPP v4.3. Is there a more recent > version that might have a fix? > > thanks > Simon Michnowicz > > > > On Apr 16, 1:09 am, Brian Pratt <[email protected]> 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 < > > > > > > > > [email protected]> 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 [email protected] > . > > > To unsubscribe from this group, send email to > > > [email protected]<spctools-discuss%[email protected]><spctools-discuss%2Bunsubscrib > [email protected]> > > > . > > > 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 [email protected]. > To unsubscribe from this group, send email to > [email protected]<spctools-discuss%[email protected]> > . > 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 [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
