Jessie, The spectral viewer tries to read the spectra in .mzXML, .mzML, .dta or collection of .dta compressed into a .tgz archive. So it doesn't assume your data is in a .tgz file, that was just one of the attempts it went through to try and access the underlying spectral data to display and you saw the error message when that attempt failed. It does not support mzXML files in a .tgz archive so that won't work as you found out.
Just based on the error message, try either of the following and see if you get any further trying to visualize that particular spectrum: 1. place your mzXML or mzML file as c:/MSGFDB/output/orbivelos/A1A2merged.mzXML 2. create a .dta file as c:/MSGFDB/output/orbivelos/A1A2merged/A1A2merged.00003.00003.2.dta If either don't work, which is a likely scenario, my guess is that the created pep.xml file is writing some element or attribute that either isn't strictly correct or doesn't conform to the expected format. In the error message about the .tgz archive, it's trying to look for a .dta file in the archive with a base name "A1A2merged" but the .tgz archive itself has a different base name "A1A2mergedmzXML" and that mismatch indicates a problem with your created pep.xml file. Check your pep.xml file. I think you want the base_name attribute to be something like: <msms_run_summary base_name="c:/MSGFDB/output/orbivelos/A1A2merged" <search_summary base_name="./A1A2merged" Good luck - Jimmy On Thu, Aug 2, 2012 at 10:00 AM, Jesse <jgme...@ucsd.edu> wrote: > Hi everyone, > > I am trying to trick TPP into letting me use it to view annotated spectra > from a currently unsupported search algorithm, MS-GFDB (which is an > excellent tool by the way). I was able to use a script I found online, > msgfdb2pepxml.py, to make the pepxml file and it does load using the TPP > pepXML viewer, but when I try to click on the ions to see a spectra I get > the following message: > > command "c:\Inetpub\wwwroot\..\tpp-bin\tar.exe -tzf > c:/MSGFDB/output/orbivelos/A1A2mergedmzXML.tgz > "*A1A2merged.00003.00003.2.dta" > /dev/null" failed: Operation not permitted > Error - cannot read spectrum; tried direct .dta, from mzXML/mzData and from > .tgz > > First of all, my data is not in a .tgz file so I am confused why it assumes > this. Second, even if I put the mzXML into that directory as a .tgz > compressed file, it fails. Do I need to use dta files for this feature? > Otherwise does anyone know a good method for quickly viewing annotated > spectra? > > Thanks in advance! Best regards, > Jesse > > -- > 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/-/Jqh4daWrBVoJ. > 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.
