Thank you very much! I really appreciate it!

On Tuesday, October 4, 2016 at 8:03:27 PM UTC-4, David Shteynberg wrote:
>
> PeptideProphet is doing it's job here by telling you that there is no 
> distinct population of correct results in this search.  I suspect your 
> search parameters are the problem.  This is orbitrap data so the charges 
> should be known, but it seems Tandem only searched 2+ and 3+ for you,  this 
> is somewhat troubling.  Tomorrow, I will check your parameters more 
> carefully to try to identify the actual problem with your search.
>
> -David
>
> On Tue, Oct 4, 2016 at 2:12 PM, Ali <sma.ban...@gmail.com <javascript:>> 
> wrote:
>
>> It appears that PeptideProphet fails, I am getting this message:
>>
>> using Accurate Mass Bins
>> using PPM mass difference
>>  (X! Tandem) (minprob 0)
>> adding Accurate Mass mixture distr
>> init with X! Tandem trypsin
>> MS Instrument info: Manufacturer: Thermo Scientific, Model: UNKNOWN, 
>> Ionization: nanoelectrospray, Analyzer: orbitrap, Detector: inductive 
>> detector
>>
>>  PeptideProphet  (TPP v4.8.0 PHILAE, Build 201608051257-exported 
>> (RedHatEnterpriseServer-x86_64)) AKeller@ISB
>>  read in 0 1+, 14418 2+, 11080 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
>> Initialising statistical models ...
>> negmean = 0.0533258
>> negmean = 1
>> negmean = 0.0376944
>> negmean = -0.2
>> negmean = -0.2
>> negmean = -0.2
>> negmean = -0.2
>> Iterations: .........10.........20.
>> WARNING: Mixture model quality test failed for charge (2+).
>> WARNING: Mixture model quality test failed for charge (3+).
>>
>> 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> 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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