The TPP is not tested to work with ProteomeDiscoverer pepXML.  Sure you can
send me a sample file, but it may take some time to implement support for
this type of data.  Comet is open source and easy to use out of the box.
Why don't you try that route?

-David

On Wed, Oct 12, 2016 at 3:24 PM, Ali <sma.banijam...@gmail.com> wrote:

> Dear David
>
> Thank you very much! You were right, the problem was with X!Tandem. I
> decided do the searches with Proteome Discoverer. I exported the results to
> pep.xml (from .msf) using PD but now the results don't work with
> PeptideProphet. I can open them in PepXMLViewer but as I said in another
> post just now, I am having problem with processing them with PeptideProphet
> and InteractParser. Do you have experience with these files? I can send you
> a sample of the pepxml files for you.
>
> Sincerely,
>
> Ali
>
> On Wednesday, October 12, 2016 at 6:12:57 PM UTC-4, David Shteynberg wrote:
>>
>> Hi Ali,
>>
>> I searched your data with Comet and PeptideProphet got valid PSMs in the
>> analysis that failed to produce correct results from your GPM-version of
>> tandem on the same data.  The problem in your dataset is the Tandem
>> search.  Attached are the comet parameters I used to search your data.
>>
>>
>> -David
>>
>>
>>
>> On Wed, Oct 5, 2016 at 9:36 PM, Ali <sma.ban...@gmail.com> wrote:
>>
>>> I sent the link to your email. Thank you very much!
>>>
>>> On Wednesday, October 5, 2016 at 9:21:04 PM UTC-4, David Shteynberg
>>> wrote:
>>>>
>>>> I cannot tell from the search parameters if there is a problem.  The
>>>> only issue I saw was that you didn't enable isotopic offsets, which are
>>>> sometimes helpful.   If you send me a sample mzML file and possibly the
>>>> search results in pep.xml along with the database I can troubleshoot
>>>> further.  One question, you said you are selecting 2+ 3+ and 4+, why are
>>>> only 2+ and 3+ in this dataset?  Does any other dataset in your analysis
>>>> contain 4+?
>>>>
>>>> -David
>>>>
>>>> On Wed, Oct 5, 2016 at 6:16 PM, Ali <sma.ban...@gmail.com> wrote:
>>>>
>>>>> Hi David
>>>>>
>>>>> We are only collecting 2+, 3+ and 4+ data. I am working on the
>>>>> cluster, so I am using the GPM version and we were unable to install the
>>>>> k-score plugin therefore I am using the X! Tandem native scoring for the
>>>>> searches.
>>>>>
>>>>> If you mean combining all of the search results with xinteract and
>>>>> then using PeptideProphet (as you instructed), I have not yet done so
>>>>> because I wanted to make sure that we are getting results from the
>>>>> individual searches. Is there an issue in my search parameters which is
>>>>> responsible for the problem?
>>>>>
>>>>> Many Thanks,
>>>>> Ali
>>>>>
>>>>> On Wednesday, October 5, 2016 at 7:06:19 PM UTC-4, David Shteynberg
>>>>> wrote:
>>>>>>
>>>>>> Hi Ali,
>>>>>>
>>>>>>
>>>>>> Are you setting your instrument to collect only 2+ and 3+ data?  Are
>>>>>> you using the tandem bundled with TPP or the GPM version of tandem?  Have
>>>>>> you tried to process all your runs in one file?
>>>>>>
>>>>>> Thanks,
>>>>>> -David
>>>>>>
>>>>>>
>>>>>> On Wed, Oct 5, 2016 at 11:39 AM, Ali <sma.ban...@gmail.com> wrote:
>>>>>>
>>>>>>> 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> 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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