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.banijam...@gmail.com> 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*
>>>>>
>>>>> --
>>>>> 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 post to this group, send email to spctools...@googlegroups.com.
>>>>> Visit this group at https://groups.google.com/group/spctools-discuss.
>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>
>>>>
>>>> --
>>> 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 post to this group, send email to spctools...@googlegroups.com.
>>> Visit this group at https://groups.google.com/group/spctools-discuss.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>> --
> 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 post to this group, send email to spctools-discuss@googlegroups.com.
> Visit this group at https://groups.google.com/group/spctools-discuss.
> For more options, visit https://groups.google.com/d/optout.
>

-- 
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 post to this group, send email to spctools-discuss@googlegroups.com.
Visit this group at https://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/d/optout.

Reply via email to