Not all the proteins in PeptideProphet appear in ProteinProphet

[Soroush F]

Dear all,

I noticed that not all the proteins that exist in my PeptideProphet file will appear in the ProteinProphet output. Obviously I expect some proteins to be determined as having very low probability by the ProteinProphet, but why they don't appear in the ProteinProphet altogether? How can I keep them in the output of the ProteinProphet?

Also, I am not setting anything to be excluded in the ProteinProphet setting (which I run through TPP).

Many thanks for your help.

Soroush

[Luis Mendoza]

Hello Soroush,

ProteinProphet has baked-in defaults in the code that will skip over any peptide with (initial) probability < 0.05 (and won't use those below 0.20 post-NSP adjustment).  Do any of those peptides that point to the missing proteins violate that rule?

This is certainly something that can be changed in the code on your local copy, but it is not recommended.

Cheers,

--Luis

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[Soroush F]

Dear Luis,

Thanks so much for your insight. It is very much appreciated. 

I can see that the proteins that are not outputted in the ProteinProphet have PeptideProphet probability of <0.05. 

All the best,

Soroush

[Luis Mendoza]

Hello Soroush,

Great!  Good to verify that it is working as designed.  And you will not miss those zero probability proteins; they would just add even more time to the processing and make a larger output file, but with no gain in high quality results.

Cheers,

--Luis

To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/d8b7b05c-b808-47e7-a1bb-a4493749cfe4n%40googlegroups.com.