Is there a threshold of min. peptide probability that ProteinProphet uses to pick the peptides?

[Xiao]

Dear all,

I have a question about the ProteinProphet. From the link of "More
Analysis Info" in the ProteinProphet results view window, I found the
"min peptide probability" to be 0.2. Is 0.2 the probability threshold
that ProteinProphet uses to select the peptides? If yes, can I set a
different value (if necessary)?

Thanks,

Xiao

[Luis Mendoza]

Hello Xiao,
You are correct: there is a lower limit in ProteinProphet to disregard peptides below a certain probability and assigned weight.  These values (0.2 and 0.5, respectively) are unfortunately hard-coded in the program and cannot be set by the user; in order to change them you would have to alter the code and recompile the software.
Cheers,
--Luis

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[James Go]

Hi Luis,

Is this option still hardcoded in the most up to date version of ProteinProphet?

[Luis Mendoza]

Hello James,

Yes, these values are still hard-coded.  If you wish to test alternative values, you can edit lines 958-959 and recompile:

https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/src/Validation/ProteinProphet/ProteinProphet.cpp

  MIN_WT = 0.5;
  MIN_PROB = 0.2;

Let us know if you find anything interesting!

Cheers,

--Luis

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