Hello Vidya, It seems that your iProphet file might contain incorrect/incomplete file paths for the source mzXML files. What steps did you follow to generate this file? Feel free to email it to me so I can further diagnose.
As you found out, you can always just open the PeptideProphet results file in Pep3D, or the mzXML/mzML raw data. Cheers, --Luis On Wed, Oct 24, 2012 at 5:02 PM, Vidya Venkatraman <vidya.venk...@gmail.com> wrote: > Hi, > > I have received searched Xtandem data (from 1 raw file) which was also run > through peptide and protein prophet. I am trying to open the iprophet > pep.xml file through TPP in the pep3d viewer. But when i click on generate > 3d image, it errors saying could not open input file. Also, you can see how > the mzxml does not appear such that it can be selected. > > I just wanted to check on how one can import iprophet pep.xml results onto > pep3d viewer if it was searched and run through peptide prophet elsewhere. I > do have the fasta, mzxml, pep.xml, ipep.xml, prot.xml under > C:\Inetpub\wwwroot\ISB\data\data. > > Could it be the naming convention eg. the files need to have the same name? > What files does it look for or what files do i need to have for this to > work? > > Lastly, when i took the pep.xml file and ran it through peptide prophet on > the TPP gui (instead of starting with the ipep file), it does seem to work > and generate the pep3d image. > > I dont use TPP that often, so this could be something obvious. But i > appreciate any guidance on this matter. > > 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/-/OUBscjHcezwJ. > To post to this group, send email to spctools-discuss@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. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@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.
