I seem to have figured this one out myself. It appears to be a stupid Windows 7 permissions thing. Even though I have admin rights, I’m still running into issues when trying to run certain TPP commands. If I unzip the appropriate tgz file and change the msms_run_summary in the pepXML file to point to the folder with the files, I can easily see the spectra when I click the appropriate hyperlink in the Petunia interface. It occurred to me the problem might actually be an inability to run the unzip command since I was having similar permissions issues when I was trying to run idconvert on other files.I can’t say I know how to fix the permissions problems, but at least I know the process is working and I can get the result I require, albeit the long way.
If anyone else has seen this problem and has a solution, I’d be grateful. Peter On Friday, August 14, 2015 at 4:03:02 PM UTC+10, [email protected] wrote: > > Hi, > > I'm using TPP (4.8.0) to process Mascot searches (2.5.1). I can > successfully convert the *.DAT file to a pepXML, but when I open the pepXML > I cannot then select the ion2 to view the MS/MS spectra. I get the > following error; > > command "c:\Inetpub\wwwroot\..\tpp-bin\tar.exe -tzf > c:/Inetpub/wwwroot/ISB/data/IS_all_01.tgz > "*Fri_Aug_14_15-47-05_2015.spectrum1001.00000.00000.2.dta" > /dev/null" > failed: Operation not permitted > > I used an MGF for searching, but I made that from an mzXML file. The > process was WIFF -> mzML (AB data converter) -> mzXML (msconvert) -> MGF > (msconvert). I used the mzXML as I need it for later analysis. The mzXML is > not in the same directory as the DAT file during the DAT -> pepXML > conversion process, nor is it there when I click the ions2 link. Is this > relevant? > > For the above example, I can open the tgz file, get the right scan number, > open it and see mass and intensity data. So it's there. The tgz mentioned > above is also in the location stated. So why isn't this working? All > suggestions gratefully received... > > When convert the DAT to a pepXML I do a get a few error messages about > spectra not being found eg; > > Warning: could not find scan numbers of spectrum > IS_all_01.7890.7890.2File:,NativeID:scan=7890 > Set to 0000Warning: could not find scan numbers of spectrum > IS_all_01.6844.6844.2File:,NativeID:scan=6844 > Set to 0000Warning: could not find scan numbers of spectrum > IS_all_01.6857.6857.2File:,NativeID:scan=6857 > Set to 0000Warning: could not find scan numbers of spectrum > IS_all_01.6258.6258.2File:,NativeID:scan=6258 > Set to 0000Warning: could not find scan numbers of spectrum > IS_all_01.6605.6605.2File:,NativeID:scan=6605 > Set to 0000Warning: could not find scan numbers of spectrum > IS_all_01.6509.6509.2File:,NativeID:scan=6509 > Set to 0000 > > > I'm not so worried about a few failing spectra, it's more that I can't see > the spectra of the vast majority of my data. > > Thanks, > > Peter > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
