Re: [spctools-discuss] Is there a threshold of min. peptide probability that ProteinProphet uses to pick the peptides?

['Luis Mendoza' via spctools-discuss]

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



On Wed, Dec 23, 2020 at 3:04 PM James Go  wrote:

> Hi Luis,
>
> Is this option still hardcoded in the most up to date version of
> ProteinProphet?
>
> On Tuesday, November 22, 2011 at 5:39:54 PM UTC-8 Luis wrote:
>
>> 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
>>
>>
>> On Mon, Nov 21, 2011 at 8:23 AM, Xiao  wrote:
>>
>>> 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
>>>
>>
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Re: [spctools-discuss] Is there a threshold of min. peptide probability that ProteinProphet uses to pick the peptides?

[James Go]

Hi Luis,

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

On Tuesday, November 22, 2011 at 5:39:54 PM UTC-8 Luis wrote:

> 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
>
>
> On Mon, Nov 21, 2011 at 8:23 AM, Xiao  wrote:
>
>> 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
>>
>
>> --
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>> "spctools-discuss" group.
>> To post to this group, send email to spctools...@googlegroups.com.
>> To unsubscribe from this group, send email to 
>> spctools-discu...@googlegroups.com.
>> For more options, visit this group at 
>> http://groups.google.com/group/spctools-discuss?hl=en.
>>
>>
>

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Re: [spctools-discuss] Is there a threshold of min. peptide probability that ProteinProphet uses to pick the peptides?

[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


On Mon, Nov 21, 2011 at 8:23 AM, Xiao xiaolovesli...@gmail.com wrote:

 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

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[spctools-discuss] 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

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