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 <javascript:>> 
> 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*
>>>>>>>>
>>>>>>>> -- 
>>>>>>>> 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-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 <javascript:>.
>> To post to this group, send email to spctools...@googlegroups.com 
>> <javascript:>.
>> 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