converting prot.xml to tsv/something else

[Emma Whittington]

Hi,

I am running TPP 6.2.0 via a singularity image. I have been using the EXCELXX option in ProteinProphet to a tab-separated file. However, that is for some reason not working at the moment (tried today and yesterday). I tried to also use ProtXMLViewer.pl but it doesn't seem to exist in the singularity image. How else can I convert the prot.xml files? 

Thank you! 

[Luis Mendoza]

Hi Emma,

The ProtXMLViewer is under the cgi-bin/ directory of the image.  However, the version in 6.2.0 does not have the command-line capability of exporting protXML to TSV.  We introduced this feature in 6.3.0, and will be available once we produce the related image.  (well, after fixing some bugs and releasing 6.3.3, soon).

Do note that if using the viewer interactively, you can export to TSV via the File & Info tab of ProtXMLViewer.

We can gladly help convert a few files for you if you are able to share those; just contact me directly if so.

Thanks,

--Luis

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[Emma Whittington]

Thank you. 

A co-worker with a windows machine tried the ProtXMLViewer with the GUI. However, I'm confused that the output doesn't include a total number or number of unique peptides or something similar - just "tot indep spectra" and "percent share of spectrum ids". Is there a good way to get this information? 

All the best, 

Emma