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
On Tue, Nov 17, 2020 at
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
On Tuesday, November 17, 2020 at 2:42:17 PM UTC-5 Luis wrote:
> Hello
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
