Gash, I just downloaded the tutorial data, followed the steps, and can see the Pep3D images as well as spectra in the Comet spectrum viewer. So something went wrong for you somewhere. Reasons why the images might not show up are: 1. error with software install; not likely given that you're able to generate the pep.xml files through the TPP interface. 2. gnuplot not working for whatever reason. 3. data not placed in the right place (within c:\inetpub\wwwroot\) as specified in instructions. 4. stars were not aligned. Hard to diagnose your problem without a lot more information; I'll try to help though. Email me off list with: exact full path to the directory that contains the mzXML/pep.xml files and search results subfolders. The full URL for any one of the Comet spectrum links that open and don't show the spectrum.
The links in the Protein column that lead to the error about not being able to open the /dbase/IPI/ipi.HUMAN.fasta.v2.31 file is unfortunately expected behavior as the reference to the database location in the files still point to their original unix file locations. One intermediate quick fix is change the line entry in the sequest.params file from database_name = /dbase/IPI/ipi.HUMAN.fasta.v2.31 to database_name = c:\Inetpub\wwwroot\ISB\data\Tutorial\dbase\ipi.HUMAN.fasta.v2.31 and start over from the 'Creating pepXML Files' step. Or grab the fixed tutorial data linked below. For completeness, I'd also update the database links in all .out files too if were going to distribute this tutorial data. If someone at Insilicos wants to update the download file, the following self extracting archive has database paths updated in all files: http://proteomicsresource.washington.edu/dist/tutorial.exe - Jimmy On Mon, Mar 28, 2011 at 10:27 AM, Gash <[email protected]> wrote: > Dear all, > > I am a freshman in bio-informatics and just start to use TPP. I have > just installed TPP v4.4 together with its GUI interface (Petunia) on > my Windows 7 laptop and went through the tutorial on the SPC Tools > Wiki. > > Interestingly, when following the tutorial, many things did not work > properly in Petunia. For example, after having generated the pepXML > and tried to generate Pep3D image in the PepXML Viewer, the Pep3D > Image for LC-ESI-MS Data did not display - a broken image link was > presented on the pane. The similar situation happened when I tried to > use COMET Spectrum View and CID Spectrum Display as well - everything > was listed properly; however, no image was displayed. > > Additionally, when clicking a protein index in the "protein" column in > the PepXML viewer, the COMET Sequence Viewer did not display any > useful information such as protein serial no, observed peptides, and > in-silico digestion, instead an error message "Error - cannot open/ > dbase/IPI/ ipi.HUMAN.fasta.v2.31 (No such file or directory)" was > presented. > > As I have strictly followed the SPC's tutorial, I was wondering > whether I had done something wrong or everyone else encountered the > same issue as I did... If so, PLEASE, can you help me out and > enlighten me how to resolve these issues! > > Many thanks in advance, > Gash > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > 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. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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.
