Thanks for your recommendations David.

I added decoys to my data base and I am still getting 0 probabilities for 
all of the hits. I am attaching my X! Tandem search parameters xml, could 
you please kindly do me a big favor and check it to see if there is 
anything suspicious there which might cause the issue? I am using Trypsin 
enzyme and TMT 10 plex of K and TMT 10plex of N term fixed residue 
modification.

Sincerely,

*Ali*



On Monday, October 3, 2016 at 5:57:39 PM UTC-4, David Shteynberg wrote:
>
> I highly recommend you start employing decoys in your search databases.  I 
> noticed you are not combining together the runs in the analysis.  If the 
> data was generated and searched in the same way it should be analysed 
> together for better statistical power.  I suggest you combine the results 
> from all your runs and filter by the spectrum names later.  Try this:
>
> InteractParser ./ALL.interact.xml ./*.tandem.pep.xml -S -Etrypsin
> PeptideProphetParser ./ALL.interact.xml ACCMASS PPM NOICAT MINPROB=0
>
>
> -David
>
> On Mon, Oct 3, 2016 at 2:39 PM, Ali <sma.ban...@gmail.com <javascript:>> 
> wrote:
>
>> Hi David
>>
>> Thanks for your reply. I don't think so, it is not just one set, as I 
>> said almost a third of my search results are returned with zero 
>> probabilities. All of the searches are done with the same setting and using 
>> the same database. The fact that for some of the searched files I am 
>> getting zero probabilities and some of them are just fine is a bit strange. 
>> I don't have decoys in my data base. If it helps, I can send you one of the 
>> search results with or without PeptideProphet probabilities.
>>
>> Sincerely,
>> Ali
>>
>>
>>
>> On Monday, October 3, 2016 at 4:19:05 PM UTC-4, David Shteynberg wrote:
>>>
>>> Is it possible there are no correct results in that set?  Common 
>>> pitfalls are incorrect search parameters (e.g. wrong mods enabled or 
>>> disabled) and wrong database.  If you have decoys in your database these 
>>> can be utilized for a more accurate mixture model generation using options 
>>> "DECOY=<your decoy prefix>  DECOYPROBS NONPARAM" in additions to the 
>>> options you already have enabled.
>>>
>>> -David
>>>
>>> On Mon, Oct 3, 2016 at 10:39 AM, Ali <sma.ban...@gmail.com> wrote:
>>>
>>>> Hi
>>>>
>>>> I am using PeptideProphet on my X!Tandem search results. There are ~150 
>>>> experiments and PeptideProphet works fine on most of them but for ~50 
>>>> experiments, PeptideProphet returns zero probability for all of the 
>>>> peptides. Can some one please tell me what might be the issue?
>>>>
>>>> *More Info:*
>>>> I am using TPP v4.8 on Linux. PeptideProphet does not show an error 
>>>> when it produces zero probability for all of the search results.
>>>> This is what I'm doing:
>>>> -search with X!Tandem
>>>> -Tandem2XML ./100.tandem.xml ./100.tandem.pep.xml
>>>> -InteractParser ./100.interact.xml ./100.tandem.pep.xml -S -Etrypsin
>>>> -PeptideProphetParser ./100.interact.xml ACCMASS PPM NOICAT MINPROB=0
>>>>
>>>>
>>>> Thank you very much,
>>>> *Ali*
>>>>
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>>>
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Attachment: input100.xml
Description: XML document

Attachment: default_no_k.xml
Description: XML document

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