ProtXML viewer doesn't display iProphet results, another clue

[Brian Hampton]

Hi,

Using a Ubuntu install of TPP4.6.1 the ProtXML viewer will only display the first protein hit from an iProphet result.  However, I discovered today that if I check "hide" for peptides, then it displays the entire result set.  It will export to Excel the results with any setting.

Maybe this clue will help troubleshoot for a solution..

Thanks in advance,

Brian

[ChargedPeptide]

I have this problem as well, however hiding the peptides did not fix the issue. :(

I'll be having a look at the prot.xml later tonight.

[christine...@qimr.edu.au]

Hi,

same problem here with TPP4.6.2. Has anybody solved this?

Thanks,
Christine

[Luis Mendoza]

Hello everyone,

Can you send us a couple of screenshots so we can see what you mean by "only display the first protein hit"?  I have not been able to replicate this in Windows or Linux.

Thanks,

--Luis

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[christine...@qimr.edu.au]

Hi Luis,

Thanks for your answer. Pls find attached 2 screenshots (default view, only the 1st protein hit; and when "peptides hide" is checked, all protein hits)  and web server error.log
Let me know if you need something else.

Regards,

Christine

[Dave Trudgian]

This is the same outcome I had with a problem in 4.2.0 back in 2009:

https://groups.google.com/forum/#!searchin/spctools-discuss/xsltproc/spctools-discuss/47vHn08zLjU/7amlOxqjrCoJ

Maybe the problem, and fix is similar - I remember modifying the code to make it work, but don't have it handy to check back what I did. Don't have a 4.6.2 installation to check either. I will try to find out what I did...

[Dave Trudgian]

Ahh, the fix back then was this:

https://groups.google.com/forum/#!searchin/spctools-discuss/xslt/spctools-discuss/0h73qbqbqes/CFRakqDIQeAJ

Probably more important was that I now remember that running the xslt translation through Xalan (rather than xsltproc) gave a nice error message that indicated exactly what the problem was. Maybe that'd work this time? Happy to look if anyone wants to send me a .prot.xml file.

DT

[Christine]

Thanks Dave. This works!

So as the script is not exactly as it was in 2009, I moved the line from line 4546 to line 4545 (protxml2html.pl, v4.6.2):
print XSL '<xsl:param name="mypep"/>';

That means this line should be before (instead of after):
    print XSL '<xsl:variable name="PepMass"><xsl:if test="@calc_neutral_pep_mass"><xsl:value-of select="@calc_neutral_pep_mass"/></xsl:if></xsl:variable>';


Cheers,
Christine

[Joseph Slagel]

Christine,

Thanks for pointing this out and I'm glad to say this change is already in the trunk.  Back in April I spent a little time running the pepxml  files TPP produces through a XML validator to ensure that what we produced was valid XML and matched the pepXML schema.  Needless to say we had to make a few adjustments to both the standard and the code and this was one of those changes.  It'll be going out in the 4.6.3 release which should be announced very soon.

-Joe