StPeter SIn displays all --n/a-- in protXML viewer (TPP v. 5.2.0)

[Jason Winget]

Hi folks, I was running the tutorial for DISCO using the new TPP version and decided to also look at the results with StPeter.

Everything seemed to run fine, and I can see the <StPeterQuant> blocks in the resulting protXML file with values. When I view these with the Petunia protXML viewer, however, all the results show "-- n/a --" in the StPeter SIn column.

This is true before or after filtering the results and also when ordering by descending StPeter_Quant. I also tried switching the quantification display between text and graphical bars to no effect.

[Jason Winget]

I should probably add that I use the -d flag, so the attributes are dSIn instead of SIn. I wonder if that's the issue and it has to do with how the reader parses the <StPeterQuant> attributes...

[Eric Deutsch]

Hi Jason, I have no solution yet, but I have one more data point. It seemed to work well when I used all the default TPPGUI settings. But then in another run when I fiddled with several of the settings, I had a similar result as you describe. So I think there is a bug in one of the settings that needs to be found and fixed. I have not had time to follow up. It would be interesting to see if it works for you with all default settings. And then figure out which setting is causing the issue. I can’t look at it today, but let me know if you find something a little more specific.

 

Thanks,

Eric

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[Jason]

Ok, I can confirm that running StPeter without the -d flag displays fine in the viewer, so I suspect it's just an attribute naming issue. The default attribute is named "Sin" but if you set the -d flag it's named "dSIn" 

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[Luis Mendoza]

Hi Jason,

Thanks for the report.  It seems that the ProtXMLViewer has not been updated to handle dSIn.  I'll update this soon and send you a patch.  And will be included with our next release, 5.2.1.

--Luis

[Luis Mendoza]

Hi Jason,

I have uploaded a patched version of the viewer here: 

https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v0.0%20%28Development%29/

Simply download the ProtXMLViewer.pl file, and place it under C:\TPP\cgi-bin\   (or wherever you have TPP installed), while making a backup of the file you have, just in case.

Let us know how it goes, and if you find anything else that needs out attention.

Cheers,

--Luis

[Jason]

Thanks Luis!