[spctools-discuss] Malformed XML generated by Peptide Prophet
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) Tax_Id=10118 [Rattus sp] num_tol_term=2 peptide_prev_aa=K peptide_next_aa=D/ Should the gamma entry should be ltgammagt ?? 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. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
Re: [spctools-discuss] Re: How to use ASAPRatio to do SILAC quantification from Spectrum Mill Identifications or the latest X!Tandem?
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 detected much less peptides as other search programs. Is this a general result or data-dependent issue? Best regards, John On Wed, Apr 14, 2010 at 4:23 AM, dctrud dct...@ccmp.ox.ac.uk wrote: John, The TPP doesn't support the analysis of Spectrum Mill results. SEQUEST, Mascot, X!Tandem (native/k-score), ProbID, SpectraST, Phenyx, OMSSA, MyriMatch, Inspect, and YABSE are all possibilities though. To use Mascot you can try converting the mzXML files to MGF for Mascot using the TPPs MzXML2Search tool and specifying a value for the -I parameter, which filters out peaks lower than a set intensity. For example: MzXML2Search -mgf -I20 my.mzXML ... will generate an mgf file from my.mzXML which exclude peaks with an intensity less than 20. This will dramatically reduce the size of the mgf file since QTOF data tends to include a lot of very low intensity noise peaks. The value you use for the cut-off depends on the instrument. Set it to something that looks reasonable for getting rid of the lowest level noise, but not useful signal. For our Agilent 6520 (ADC based) we use 20, for a Waters QTOF (TDC based) we use 3. A caveat is that direct mzXML to MGF to Mascot doesn't give great results in our hands with data from the 6520 QTOF. Mascot benefits a lot from the spectrum processing (such as de-isotoping) that is performed when exporting an MGF from MassHunter (or indeed Mascot Distiller). On the other hand, OMSSA and X!Tandem (native scoring) work extremely well for us with spectra from the mzXML. We routinely analyse 6520 data using OMSSA + X!Tandem native, with iProphet to combine the results, and use ASAPRatio successfully for quantitation. DT On Apr 13, 9:13 pm, John gux2...@gmail.com wrote: I want to use ASAPRatio incorporated in TPP suite. However, we do not have Sequest and Our Mascot currently cannot read the XML files generated by TPP because of the huge size of mzXML file after converting Agilent Q-TOF data (.d) to mzXML file. I am trying to use X!Tandem in TPP suite to do database search. However, I noticed that the X!Tandem incorporated in TPP is an old version. Can I incorporate the latest X!Tandem in TPP? Can I use the latest X!Tandem to do the database searching and output the data into a format that TPP can read for further SILAC quantification? How Can I convert Spectrum Mill search result to the format TPP can read and to perform SILAC quantification? -- 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. -- Guoqiang Xu 9609 66th Ave, #5C Rego Park, NY 11374 Mobile: 607-351-8481 -- 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.
Re: [spctools-discuss] Malformed XML generated by Peptide Prophet
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|MRXRgamma 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 ltgammagt ?? 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.comspctools-discuss%2bunsubscr...@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.
[spctools-discuss] Re: Malformed XML generated by Peptide Prophet
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, 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|MRXRgamma 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 ltgammagt ?? 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.comspctools-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.
