HI Joe, That seems to have resolved the problem. The issue seems to have been there in the pepxml itself so I went back and redit the .dat to pepxml conversion with the edited fasta file and now I saw that the pepxml viewer actually loaded. Using this pepxml file, the peptide and protein prophet works.
If I run into any further issues, I will post back. Thanks so much, Vidya On Friday, November 30, 2012 8:04:00 PM UTC-5, [email protected] wrote: > > Vidya, > > I noticed that you happen to have the string "<alpha>" in some of your > sequence definition lines in your database. These are showing up in your > interact.pep.xml and causing the parser to fail. Now we should be escaping > anything that looks like xml in the sequence definition its possible we > missed it somewhere. Could you try just removing the "<>" from the > descriptions in the fasta file and rerunning? The four lines are: > > >tr|Q9UMA4|Q9UMA4_HUMAN IFN-<alpha>2 protein (Fragment) OS=Homo sapiens > GN=IFN-<alpha>2 PE=2 SV=1 > >tr|A0N7E2|A0N7E2_HUMAN V<alpha>13 protein (Fragment) OS=Homo sapiens > GN=V<alpha>13 PE=2 SV=1 > >tr|A0N7E4|A0N7E4_HUMAN V<alpha>1 protein (Fragment) OS=Homo sapiens > GN=V<alpha>1 PE=2 SV=1 > > > -Joe > > > On Fri, Nov 30, 2012 at 4:21 PM, Vidya Venkatraman > <[email protected]<javascript:> > > wrote: > >> Hi Joe, >> >> Thanks for your quick response. I have put all the remaining output files >> into dropbox now. Please take a look and let me know if you need any other >> information. >> >> Vidya >> >> >> >> On Friday, November 30, 2012 6:44:45 PM UTC-5, >> [email protected]: >> >>> Hi Vidya, >>> >>> Thanks for providing such great detail on the issue and I'm sorry it >>> isn't working for you. We're taking a look at what you posted and there is >>> an error indicating invalid XML formatting in one of your files. >>> Unfortunately this is one of the ones that you haven't posted to dropbox. >>> Any chance you can upload the following file from your system (from the >>> "not working" case)? >>> >>> C:/Inetpub/wwwroot/ISB/data/**data/interact.pep.xml" >>> >>> Thanks, >>> Joe >>> >>> On Fri, Nov 30, 2012 at 3:04 PM, Vidya Venkatraman >>> <[email protected]>wrote: >>> >>>> Hi, >>>> >>>> I have encountered an issue wherein if I try to convert a mascot .dat >>>> file to pepxml, it does the conversion and when I try to use this pepxml >>>> to run peptideprophet and proteinprophet, it fails. >>>> >>>> I tried to check if .dat to pepxml conversion worked properly, but >>>> realised that when I click on the pepxml, nothing loads on the pepxml >>>> viewer and I also saw that usually there is an index file that is created >>>> and in this case, it did not create the index file as well. Just to make >>>> sure the .dat file is good, i was also able to open it up on Scaffold and >>>> see some proteins. >>>> >>>> This is the link to the shared dropbox folder called "TPP" >>>> https://www.dropbox.com/sh/**4unsley0gir7jve/7D3-XANnj8<https://www.dropbox.com/sh/4unsley0gir7jve/7D3-XANnj8> >>>> >>>> I have 2 folders there, one called "working files" where I tested a >>>> .dat file (from same samle, different fraction) conversion to pepxml and >>>> ran peptide and protein prophet and it worked successfully. The other >>>> folder called "not working files" has the .dat file which failed to run >>>> peptide and protein prophet. Also attached are .mzxml, .pepxml, the log of >>>> conversion from .dat to .pepxml and errorlog of conversion from pepxml to >>>> peptide and protein prophet along with screenshots. I have also included >>>> the fasta file I used in the "Fasta" folder. >>>> >>>> Can you anyone guide me as to what could have gone wrong? >>>> >>>> Thanks in advance, >>>> Vidya >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "spctools-discuss" group. >>>> To view this discussion on the web visit https://groups.google.com/d/** >>>> msg/spctools-discuss/-/_**OXYGwHUJmQJ<https://groups.google.com/d/msg/spctools-discuss/-/_OXYGwHUJmQJ> >>>> . >>>> To post to this group, send email to spctools...@googlegroups.**com. >>>> To unsubscribe from this group, send email to spctools-discu...@** >>>> googlegroups.com. >>>> >>>> For more options, visit this group at http://groups.google.com/** >>>> group/spctools-discuss?hl=en<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 view this discussion on the web visit >> https://groups.google.com/d/msg/spctools-discuss/-/sR6TGOvkegwJ. >> >> To post to this group, send email to >> [email protected]<javascript:> >> . >> To unsubscribe from this group, send email to >> [email protected] <javascript:>. >> 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 view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/W_YfMRu4e8EJ. 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.
