Re: [spctools-discuss] Not all the proteins in PeptideProphet appear in ProteinProphet

2020-11-17 Thread 'Luis Mendoza' via spctools-discuss 
 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 9:32 PM Soroush F  wrote:

> 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 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
>>
>>
>>
>> On Mon, Nov 16, 2020 at 6:31 PM Soroush F  wrote:
>>
>>> 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
>>>
>>> --
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>>> 
>>> .
>>>
>> --
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> .
>

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Re: [spctools-discuss] Not all the proteins in PeptideProphet appear in ProteinProphet

2020-11-17 Thread 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




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

> 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
>
>
>
> On Mon, Nov 16, 2020 at 6:31 PM Soroush F  wrote:
>
>> 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
>>
>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "spctools-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to spctools-discu...@googlegroups.com.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/spctools-discuss/7f2700a6-ec5a-42b1-b6b1-835e4e48c799n%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [spctools-discuss] Not all the proteins in PeptideProphet appear in ProteinProphet

2020-11-17 Thread 'Luis Mendoza' via spctools-discuss 
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



On Mon, Nov 16, 2020 at 6:31 PM Soroush F  wrote:

> 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
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to spctools-discuss+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/7f2700a6-ec5a-42b1-b6b1-835e4e48c799n%40googlegroups.com
> 
> .
>

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