Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-12 Thread Ali
Hi David!

I played with the fragment mass tolerance but I am still having the issue. 
However I searched the problematic files with TPP's X!Tandem (instead of 
GPM's) and it worked perfectly with Peptide Prophet! Is there a linux 
version of it which I can use on the cluster or is it just usable inside 
the TPP's GUI? and why do I usually get Internal Server Error when I select 
Tandem as the pipeline?

Many Thanks,
Ali

On Wednesday, October 12, 2016 at 6:41:55 PM UTC-4, David Shteynberg wrote:
>
> 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  
> 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  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  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  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  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, 

Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-12 Thread Ali
Thanks David!

Let me try lowering fragment mass error. I will let you know about the 
outcome.

Well, we already had the Proteome Discoverer results and we really want to 
create the spectral library asap, so I was given those results to use 
instead of X!Tandem. and I have never worked with comet. I have to figure 
out how it works first.

I will upload the ProteomeDiscoverer pep.xml in the folder that you have 
it's link, if you had a few minutes just take a look at it. May be it 
needed a few tweaks to work with PeptideProphet.

Thanks so much,
Ali

On Wednesday, October 12, 2016 at 6:41:55 PM UTC-4, David Shteynberg wrote:
>
> 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  
> 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  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  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  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  wrote:
>
>> It appears that PeptideProphet fails, I am getting this message:
>>
>> using Accurate Mass Bins
>> using PPM mass difference
>>  (X! Tandem) (minprob 0)
>> adding 

Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-12 Thread David Shteynberg
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  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  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  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  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  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 

Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-12 Thread Ali
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  
> 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  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  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  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 

Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-12 Thread David Shteynberg
My suspicion regarding the Tandem failure is the fragment mass tolerance.
I am observing fragment mass differences of much less than 0.05 daltons,
yet your Tandem search uses 0.5 daltons as the tolerance.  Could GPM-tandem
be having a problem there?  Can you try to lower the fragment mass
tolerance and redo the search?  Can you employ comet in your pipeline?

-David

On Wed, Oct 12, 2016 at 3:12 PM, David Shteynberg <
david.shteynb...@systemsbiology.org> 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  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  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  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  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 

Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-12 Thread David Shteynberg
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  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  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  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  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  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 

Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-05 Thread Ali
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  
> 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  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  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  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 

Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-05 Thread Ali
How can I send you these files? Can I upload them on the cloud and send you 
the link?

I am not doing the mass spec so I don't know the details of each 
experiments but some of them have all three charges and some of them only 
have 2+ and 3+. Here is an example of similar issue for a file with three 
charges:

PeptideProphet  (TPP v4.8.0 PHILAE, Build 201608051257-exported 
(RedHatEnterpriseServer-x86_64)) AKeller@ISB
 read in 0 1+, 5857 2+, 2812 3+, 406 4+, 0 5+, 0 6+, and 0 7+ spectra.
negmean = 0.0533258
negmean = 1
negmean = 0.901666
negmean = -0.2
negmean = -0.2
negmean = -0.2
negmean = -0.2
WARNING: Mixture model quality test failed for charge (2+).
WARNING: Mixture model quality test failed for charge (3+).
WARNING: Mixture model quality test failed for charge (4+).


Thanks,
Ali



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  
> 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  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  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  wrote:

Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-05 Thread David Shteynberg
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  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  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  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  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 

Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-05 Thread Ali
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  
> 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  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  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=  DECOYPROBS NONPARAM" in additions to the 
>>> options you already have enabled.
>>>
>>> -David
>>>
>>> On Mon, Oct 3, 2016 at 10:39 AM, Ali  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 

Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-05 Thread David Shteynberg
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  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  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  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=  DECOYPROBS NONPARAM" in additions to the
>> options you already have enabled.
>>
>> -David
>>
>> On Mon, Oct 3, 2016 at 10:39 AM, Ali  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 

Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-05 Thread Ali
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  
> 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  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=  DECOYPROBS NONPARAM" in additions to the 
> options you already have enabled.
>
> -David
>
> On Mon, Oct 3, 2016 at 10:39 AM, Ali  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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>> Groups "spctools-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, 
>> send an email to spctools-discu...@googlegroups.com.
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>> For more options, visit https://groups.google.com/d/optout.
>>
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Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-04 Thread David Shteynberg
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  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  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=  DECOYPROBS NONPARAM" in additions to the
 options you already have enabled.

 -David

 On Mon, Oct 3, 2016 at 10:39 AM, Ali  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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> 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.
>

 --
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>>> Groups "spctools-discuss" group.
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>>> an email to spctools-discu...@googlegroups.com.
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>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>> --
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Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-04 Thread Ali
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  
> 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=  DECOYPROBS NONPARAM" in additions to the 
>>> options you already have enabled.
>>>
>>> -David
>>>
>>> On Mon, Oct 3, 2016 at 10:39 AM, Ali  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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 Groups "spctools-discuss" group.
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 Visit this group at https://groups.google.com/group/spctools-discuss.
 For more options, visit https://groups.google.com/d/optout.

>>>
>>> -- 
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>> "spctools-discuss" group.
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>> email to spctools-discu...@googlegroups.com .
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>> .
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>>
>
>

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Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-04 Thread Ali
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  
> 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=  DECOYPROBS NONPARAM" in additions to the 
>>> options you already have enabled.
>>>
>>> -David
>>>
>>> On Mon, Oct 3, 2016 at 10:39 AM, Ali  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.
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 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.

>>>
>>> -- 
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>> "spctools-discuss" group.
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>> email to spctools-discu...@googlegroups.com .
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>> .
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>>
>
>

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input100.xml
Description: XML document


default_no_k.xml
Description: XML document


Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-03 Thread David Shteynberg
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  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=> decoy prefix>  DECOYPROBS NONPARAM" in additions to the options you already
>> have enabled.
>>
>> -David
>>
>> On Mon, Oct 3, 2016 at 10:39 AM, Ali  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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>>> Groups "spctools-discuss" group.
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>>> an email to spctools-discu...@googlegroups.com.
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>>> Visit this group at https://groups.google.com/group/spctools-discuss.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
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Re: [spctools-discuss] PeptideProphet returns zero probability for all of the X!Tandem search results

2016-10-03 Thread David Shteynberg
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=  DECOYPROBS NONPARAM" in additions to the options you already
have enabled.

-David

On Mon, Oct 3, 2016 at 10:39 AM, Ali  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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> For more options, visit https://groups.google.com/d/optout.
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