Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

2021-04-14 Thread Oded 
Hi David,
This time I used 
*xinteract -NinteractDecoyCount.pep.xml -p0.05 -l7 -PPM -OANEdp -dDECOY0 
Seq69478_QE2.pep.xml. *
With TPP 5.2 the count of DECOY1 ids at 1% error rate is 84   and the total 
count of DECOY ids is 151 (out of 7102 PSMs).
With  TPP 6.0 the count of DECOY1 ids at 1% error rate is 7 and the total 
count of DECOY ids is 9 (out of 5308 PSMs).
You can find the new interact files 
here:https://www.dropbox.com/t/s7ZqgkP1f0Yzl0Xn.
Many thanks,
Oded



On Wednesday, 14 April 2021 at 08:34:42 UTC+3 David Shteynberg wrote:

> Hi Oded,
>
> I think the old 5.2.0 might be under estimating the error rate as compared 
> to the new release candidate.   You cannot see the decoys here because of 
> the settings you used.  However your database has two independent sets of 
> decoys available DECOY0 and DECOY1.  Can you use one of the set for 
> PeptideProphet and use the other set to get a decoy count at a given 
> PeptideProphet probability cutoff.  I suspect the 5.2.0 TPP will show more 
> unknown decoys than the new release candidate.   Can you test if this is 
> the case here?  I can run a more in depth analysis when I am back from 
> vacation next week. 
>
> Cheers,
> David
>
> On Tue, Apr 13, 2021, 2:07 PM Oded  wrote:
>
>> Dear David,
>> This is PeptideProphet issue (we don't use iProphet for this analysis). 
>> With the search parameters that I sent you followed by running the 
>> PeptideProphet command of *xinteract -Ninteract.pep.xml -p0.05 -l7 -PPM 
>> -OANEp -dDECOY Seq69478_QE2.pep.xml,*
>> and lastly using a cutoff of 1% error rate we obtain with TPP 5.2 2836 
>> correct assignments and with TPP 6.0 only 2228 correct assignments. The 
>> probability for 1% error rate is 0.84 in TPP 5.2 and 0.9090 in TPP 6.0).
>> In the following link, you will find the interact files (new and old):
>> https://www.dropbox.com/t/mwtpCLeEJRLCwbi1 
>> 
>> Thanks,
>> Oded
>>
>>
>>
>> On Tuesday, 13 April 2021 at 03:38:33 UTC+3 David Shteynberg wrote:
>>
>>> Dear Oded,  
>>>
>>> Thanks for this.  I ran a quick test and I actually observed a few more 
>>> PSMs for PeptideProphet 6.0.0-rc14 for the same PeptideProphet probability 
>>> cutoff for this dataset.  Is the issue you see with PeptideProphet or 
>>> iProphet results?   Which spectra were getting excluded in the your testing 
>>> of 5.2.0 vs 6.0.0, can you give me some specific examples? Are you certain 
>>> you are using identical analysis parameters for PeptideProphet and what are 
>>> those parameters? 
>>>
>>> Cheers, 
>>>
>>> David
>>>
>>> On Mon, Apr 12, 2021, 2:15 PM Oded  wrote:
>>>
 And also the search results with the new vs the old version (although I 
 think they are more or less the same): 
 https://www.dropbox.com/t/8VyBVdeuoWdk982q


 On Tuesday, 13 April 2021 at 00:09:05 UTC+3 Oded wrote:

> Hi David,
> You can find the mzML, Comet parameters and FASTA file here:
> https://www.dropbox.com/t/Yld0ZBWhsuFajeLj
> The link is valid for 7 days.
> Many thanks,
> Oded
>
> On Monday, 12 April 2021 at 23:46:08 UTC+3 David Shteynberg wrote:
>
>> I don't mind taking a crack at it over vacation.   Please let me know 
>> where I can pull the data from. I might not have quick solution for you 
>> but 
>> I can get started looking for the problem.  Which search engine did you 
>> use 
>> here?   I would need mzML data search results and the fasta database to 
>> get 
>> started. 
>>
>> Thanks!
>>
>>
>>
>> Thanks!
>>
>> On Mon, Apr 12, 2021, 1:38 PM Oded  wrote:
>>
>>> Hi David,
>>> Thank you for the quick reply. We are using TPP v6.0.0-rc14 
>>> Noctilucent, Build 202103031119-8400 (Windows_NT-x86_64).
>>> As for the data let me know when you are back and I will transfer 
>>> you either the raw file or the search results.
>>> Enjoy your vacation.
>>> Thanks,
>>> Oded
>>> On Monday, 12 April 2021 at 22:17:53 UTC+3 David Shteynberg wrote:
>>>
 Hi Oded,  Which release candidate are you referring to?  The 
 earlier candidates may have a bug that is corrected in a later 
 version. If 
 you can share some data and specifics about the missing PSMs I can run 
 it 
 here and troubleshoot the problem.   

 Thanks!

 David 

 P.S. I am on vacation this week so will troubleshoot next week.

 On Mon, Apr 12, 2021, 11:49 AM Oded  wrote:

> Hi there,
> We recently

Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

2021-04-13 Thread 'David Shteynberg' via spctools-discuss 
Hi Oded,

I think the old 5.2.0 might be under estimating the error rate as compared
to the new release candidate.   You cannot see the decoys here because of
the settings you used.  However your database has two independent sets of
decoys available DECOY0 and DECOY1.  Can you use one of the set for
PeptideProphet and use the other set to get a decoy count at a given
PeptideProphet probability cutoff.  I suspect the 5.2.0 TPP will show more
unknown decoys than the new release candidate.   Can you test if this is
the case here?  I can run a more in depth analysis when I am back from
vacation next week.

Cheers,
David

On Tue, Apr 13, 2021, 2:07 PM Oded  wrote:

> Dear David,
> This is PeptideProphet issue (we don't use iProphet for this analysis).
> With the search parameters that I sent you followed by running the
> PeptideProphet command of *xinteract -Ninteract.pep.xml -p0.05 -l7 -PPM
> -OANEp -dDECOY Seq69478_QE2.pep.xml,*
> and lastly using a cutoff of 1% error rate we obtain with TPP 5.2 2836
> correct assignments and with TPP 6.0 only 2228 correct assignments. The
> probability for 1% error rate is 0.84 in TPP 5.2 and 0.9090 in TPP 6.0).
> In the following link, you will find the interact files (new and old):
> https://www.dropbox.com/t/mwtpCLeEJRLCwbi1
> 
> Thanks,
> Oded
>
>
>
> On Tuesday, 13 April 2021 at 03:38:33 UTC+3 David Shteynberg wrote:
>
>> Dear Oded,
>>
>> Thanks for this.  I ran a quick test and I actually observed a few more
>> PSMs for PeptideProphet 6.0.0-rc14 for the same PeptideProphet probability
>> cutoff for this dataset.  Is the issue you see with PeptideProphet or
>> iProphet results?   Which spectra were getting excluded in the your testing
>> of 5.2.0 vs 6.0.0, can you give me some specific examples? Are you certain
>> you are using identical analysis parameters for PeptideProphet and what are
>> those parameters?
>>
>> Cheers,
>>
>> David
>>
>> On Mon, Apr 12, 2021, 2:15 PM Oded  wrote:
>>
>>> And also the search results with the new vs the old version (although I
>>> think they are more or less the same):
>>> https://www.dropbox.com/t/8VyBVdeuoWdk982q
>>>
>>>
>>> On Tuesday, 13 April 2021 at 00:09:05 UTC+3 Oded wrote:
>>>
 Hi David,
 You can find the mzML, Comet parameters and FASTA file here:
 https://www.dropbox.com/t/Yld0ZBWhsuFajeLj
 The link is valid for 7 days.
 Many thanks,
 Oded

 On Monday, 12 April 2021 at 23:46:08 UTC+3 David Shteynberg wrote:

> I don't mind taking a crack at it over vacation.   Please let me know
> where I can pull the data from. I might not have quick solution for you 
> but
> I can get started looking for the problem.  Which search engine did you 
> use
> here?   I would need mzML data search results and the fasta database to 
> get
> started.
>
> Thanks!
>
>
>
> Thanks!
>
> On Mon, Apr 12, 2021, 1:38 PM Oded  wrote:
>
>> Hi David,
>> Thank you for the quick reply. We are using TPP v6.0.0-rc14
>> Noctilucent, Build 202103031119-8400 (Windows_NT-x86_64).
>> As for the data let me know when you are back and I will transfer you
>> either the raw file or the search results.
>> Enjoy your vacation.
>> Thanks,
>> Oded
>> On Monday, 12 April 2021 at 22:17:53 UTC+3 David Shteynberg wrote:
>>
>>> Hi Oded,  Which release candidate are you referring to?  The earlier
>>> candidates may have a bug that is corrected in a later version. If you 
>>> can
>>> share some data and specifics about the missing PSMs I can run it here 
>>> and
>>> troubleshoot the problem.
>>>
>>> Thanks!
>>>
>>> David
>>>
>>> P.S. I am on vacation this week so will troubleshoot next week.
>>>
>>> On Mon, Apr 12, 2021, 11:49 AM Oded  wrote:
>>>
 Hi there,
 We recently download the TPP 6.0 RC and while using it we noticed
 that we obtain fewer peptides IDs than what we got for the same 
 dataset and
 search output with version 5.2.
 Many of the missing peptides seem to have decent Expect value and
 MS/MS following a visual inspection.
 This seems that this is due to changes in PeptideProphet and are
 not related to the search itself that was done with Comet.
 Is there any additional parameter that should be included in the
 new version in order to restore the missing peptides?
 Many thanks,
 Oded

 --
 You received this message because you are subscribed to

Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

2021-04-13 Thread Oded 
Dear David,
This is PeptideProphet issue (we don't use iProphet for this analysis). 
With the search parameters that I sent you followed by running the 
PeptideProphet command of *xinteract -Ninteract.pep.xml -p0.05 -l7 -PPM 
-OANEp -dDECOY Seq69478_QE2.pep.xml,*
and lastly using a cutoff of 1% error rate we obtain with TPP 5.2 2836 
correct assignments and with TPP 6.0 only 2228 correct assignments. The 
probability for 1% error rate is 0.84 in TPP 5.2 and 0.9090 in TPP 6.0).
In the following link, you will find the interact files (new and old):
https://www.dropbox.com/t/mwtpCLeEJRLCwbi1 

Thanks,
Oded



On Tuesday, 13 April 2021 at 03:38:33 UTC+3 David Shteynberg wrote:

> Dear Oded,  
>
> Thanks for this.  I ran a quick test and I actually observed a few more 
> PSMs for PeptideProphet 6.0.0-rc14 for the same PeptideProphet probability 
> cutoff for this dataset.  Is the issue you see with PeptideProphet or 
> iProphet results?   Which spectra were getting excluded in the your testing 
> of 5.2.0 vs 6.0.0, can you give me some specific examples? Are you certain 
> you are using identical analysis parameters for PeptideProphet and what are 
> those parameters? 
>
> Cheers, 
>
> David
>
> On Mon, Apr 12, 2021, 2:15 PM Oded  wrote:
>
>> And also the search results with the new vs the old version (although I 
>> think they are more or less the same): 
>> https://www.dropbox.com/t/8VyBVdeuoWdk982q
>>
>>
>> On Tuesday, 13 April 2021 at 00:09:05 UTC+3 Oded wrote:
>>
>>> Hi David,
>>> You can find the mzML, Comet parameters and FASTA file here:
>>> https://www.dropbox.com/t/Yld0ZBWhsuFajeLj
>>> The link is valid for 7 days.
>>> Many thanks,
>>> Oded
>>>
>>> On Monday, 12 April 2021 at 23:46:08 UTC+3 David Shteynberg wrote:
>>>
 I don't mind taking a crack at it over vacation.   Please let me know 
 where I can pull the data from. I might not have quick solution for you 
 but 
 I can get started looking for the problem.  Which search engine did you 
 use 
 here?   I would need mzML data search results and the fasta database to 
 get 
 started. 

 Thanks!



 Thanks!

 On Mon, Apr 12, 2021, 1:38 PM Oded  wrote:

> Hi David,
> Thank you for the quick reply. We are using TPP v6.0.0-rc14 
> Noctilucent, Build 202103031119-8400 (Windows_NT-x86_64).
> As for the data let me know when you are back and I will transfer you 
> either the raw file or the search results.
> Enjoy your vacation.
> Thanks,
> Oded
> On Monday, 12 April 2021 at 22:17:53 UTC+3 David Shteynberg wrote:
>
>> Hi Oded,  Which release candidate are you referring to?  The earlier 
>> candidates may have a bug that is corrected in a later version. If you 
>> can 
>> share some data and specifics about the missing PSMs I can run it here 
>> and 
>> troubleshoot the problem.   
>>
>> Thanks!
>>
>> David 
>>
>> P.S. I am on vacation this week so will troubleshoot next week.
>>
>> On Mon, Apr 12, 2021, 11:49 AM Oded  wrote:
>>
>>> Hi there,
>>> We recently download the TPP 6.0 RC and while using it we noticed 
>>> that we obtain fewer peptides IDs than what we got for the same dataset 
>>> and 
>>> search output with version 5.2.
>>> Many of the missing peptides seem to have decent Expect value and 
>>> MS/MS following a visual inspection. 
>>> This seems that this is due to changes in PeptideProphet and are not 
>>> related to the search itself that was done with Comet.
>>> Is there any additional parameter that should be included in the new 
>>> version in order to restore the missing peptides?
>>> Many thanks,
>>> Oded
>>>
>>> -- 
>>> 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 view this discussion on the web visit 
>>> https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com
>>>  
>>> 
>>> .
>>>
>> -- 
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Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

2021-04-12 Thread 'David Shteynberg' via spctools-discuss 
Dear Oded,

Thanks for this.  I ran a quick test and I actually observed a few more
PSMs for PeptideProphet 6.0.0-rc14 for the same PeptideProphet probability
cutoff for this dataset.  Is the issue you see with PeptideProphet or
iProphet results?   Which spectra were getting excluded in the your testing
of 5.2.0 vs 6.0.0, can you give me some specific examples? Are you certain
you are using identical analysis parameters for PeptideProphet and what are
those parameters?

Cheers,

David

On Mon, Apr 12, 2021, 2:15 PM Oded  wrote:

> And also the search results with the new vs the old version (although I
> think they are more or less the same):
> https://www.dropbox.com/t/8VyBVdeuoWdk982q
>
>
> On Tuesday, 13 April 2021 at 00:09:05 UTC+3 Oded wrote:
>
>> Hi David,
>> You can find the mzML, Comet parameters and FASTA file here:
>> https://www.dropbox.com/t/Yld0ZBWhsuFajeLj
>> The link is valid for 7 days.
>> Many thanks,
>> Oded
>>
>> On Monday, 12 April 2021 at 23:46:08 UTC+3 David Shteynberg wrote:
>>
>>> I don't mind taking a crack at it over vacation.   Please let me know
>>> where I can pull the data from. I might not have quick solution for you but
>>> I can get started looking for the problem.  Which search engine did you use
>>> here?   I would need mzML data search results and the fasta database to get
>>> started.
>>>
>>> Thanks!
>>>
>>>
>>>
>>> Thanks!
>>>
>>> On Mon, Apr 12, 2021, 1:38 PM Oded  wrote:
>>>
 Hi David,
 Thank you for the quick reply. We are using TPP v6.0.0-rc14
 Noctilucent, Build 202103031119-8400 (Windows_NT-x86_64).
 As for the data let me know when you are back and I will transfer you
 either the raw file or the search results.
 Enjoy your vacation.
 Thanks,
 Oded
 On Monday, 12 April 2021 at 22:17:53 UTC+3 David Shteynberg wrote:

> Hi Oded,  Which release candidate are you referring to?  The earlier
> candidates may have a bug that is corrected in a later version. If you can
> share some data and specifics about the missing PSMs I can run it here and
> troubleshoot the problem.
>
> Thanks!
>
> David
>
> P.S. I am on vacation this week so will troubleshoot next week.
>
> On Mon, Apr 12, 2021, 11:49 AM Oded  wrote:
>
>> Hi there,
>> We recently download the TPP 6.0 RC and while using it we noticed
>> that we obtain fewer peptides IDs than what we got for the same dataset 
>> and
>> search output with version 5.2.
>> Many of the missing peptides seem to have decent Expect value and
>> MS/MS following a visual inspection.
>> This seems that this is due to changes in PeptideProphet and are not
>> related to the search itself that was done with Comet.
>> Is there any additional parameter that should be included in the new
>> version in order to restore the missing peptides?
>> Many thanks,
>> Oded
>>
>> --
>> 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 view this discussion on the web visit
>> https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com
>> 
>> .
>>
> --
 You received this message because you are subscribed to the Google
 Groups "spctools-discuss" group.
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>>> To view this discussion on the web visit
 https://groups.google.com/d/msgid/spctools-discuss/7f5e47e5-56df-4552-88ca-b6d4396f3d8en%40googlegroups.com
 
 .

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Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

2021-04-12 Thread Oded 
And also the search results with the new vs the old version (although I 
think they are more or less the same): 
https://www.dropbox.com/t/8VyBVdeuoWdk982q


On Tuesday, 13 April 2021 at 00:09:05 UTC+3 Oded wrote:

> Hi David,
> You can find the mzML, Comet parameters and FASTA file here:
> https://www.dropbox.com/t/Yld0ZBWhsuFajeLj
> The link is valid for 7 days.
> Many thanks,
> Oded
>
> On Monday, 12 April 2021 at 23:46:08 UTC+3 David Shteynberg wrote:
>
>> I don't mind taking a crack at it over vacation.   Please let me know 
>> where I can pull the data from. I might not have quick solution for you but 
>> I can get started looking for the problem.  Which search engine did you use 
>> here?   I would need mzML data search results and the fasta database to get 
>> started. 
>>
>> Thanks!
>>
>>
>>
>> Thanks!
>>
>> On Mon, Apr 12, 2021, 1:38 PM Oded  wrote:
>>
>>> Hi David,
>>> Thank you for the quick reply. We are using TPP v6.0.0-rc14 Noctilucent, 
>>> Build 202103031119-8400 (Windows_NT-x86_64).
>>> As for the data let me know when you are back and I will transfer you 
>>> either the raw file or the search results.
>>> Enjoy your vacation.
>>> Thanks,
>>> Oded
>>> On Monday, 12 April 2021 at 22:17:53 UTC+3 David Shteynberg wrote:
>>>
 Hi Oded,  Which release candidate are you referring to?  The earlier 
 candidates may have a bug that is corrected in a later version. If you can 
 share some data and specifics about the missing PSMs I can run it here and 
 troubleshoot the problem.   

 Thanks!

 David 

 P.S. I am on vacation this week so will troubleshoot next week.

 On Mon, Apr 12, 2021, 11:49 AM Oded  wrote:

> Hi there,
> We recently download the TPP 6.0 RC and while using it we noticed that 
> we obtain fewer peptides IDs than what we got for the same dataset and 
> search output with version 5.2.
> Many of the missing peptides seem to have decent Expect value and 
> MS/MS following a visual inspection. 
> This seems that this is due to changes in PeptideProphet and are not 
> related to the search itself that was done with Comet.
> Is there any additional parameter that should be included in the new 
> version in order to restore the missing peptides?
> Many thanks,
> Oded
>
> -- 
> 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 view this discussion on the web visit 
> https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com
>  
> 
> .
>
 -- 
>>> 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 view this discussion on the web visit 
>>> https://groups.google.com/d/msgid/spctools-discuss/7f5e47e5-56df-4552-88ca-b6d4396f3d8en%40googlegroups.com
>>>  
>>> 
>>> .
>>>
>>

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Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

2021-04-12 Thread Oded 
Hi David,
You can find the mzML, Comet parameters and FASTA file 
here:https://www.dropbox.com/t/Yld0ZBWhsuFajeLj
The link is valid for 7 days.
Many thanks,
Oded

On Monday, 12 April 2021 at 23:46:08 UTC+3 David Shteynberg wrote:

> I don't mind taking a crack at it over vacation.   Please let me know 
> where I can pull the data from. I might not have quick solution for you but 
> I can get started looking for the problem.  Which search engine did you use 
> here?   I would need mzML data search results and the fasta database to get 
> started. 
>
> Thanks!
>
>
>
> Thanks!
>
> On Mon, Apr 12, 2021, 1:38 PM Oded  wrote:
>
>> Hi David,
>> Thank you for the quick reply. We are using TPP v6.0.0-rc14 Noctilucent, 
>> Build 202103031119-8400 (Windows_NT-x86_64).
>> As for the data let me know when you are back and I will transfer you 
>> either the raw file or the search results.
>> Enjoy your vacation.
>> Thanks,
>> Oded
>> On Monday, 12 April 2021 at 22:17:53 UTC+3 David Shteynberg wrote:
>>
>>> Hi Oded,  Which release candidate are you referring to?  The earlier 
>>> candidates may have a bug that is corrected in a later version. If you can 
>>> share some data and specifics about the missing PSMs I can run it here and 
>>> troubleshoot the problem.   
>>>
>>> Thanks!
>>>
>>> David 
>>>
>>> P.S. I am on vacation this week so will troubleshoot next week.
>>>
>>> On Mon, Apr 12, 2021, 11:49 AM Oded  wrote:
>>>
 Hi there,
 We recently download the TPP 6.0 RC and while using it we noticed that 
 we obtain fewer peptides IDs than what we got for the same dataset and 
 search output with version 5.2.
 Many of the missing peptides seem to have decent Expect value and MS/MS 
 following a visual inspection. 
 This seems that this is due to changes in PeptideProphet and are not 
 related to the search itself that was done with Comet.
 Is there any additional parameter that should be included in the new 
 version in order to restore the missing peptides?
 Many thanks,
 Oded

 -- 
 You received this message because you are subscribed to the Google 
 Groups "spctools-discuss" group.
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 an email to spctools-discu...@googlegroups.com.
 To view this discussion on the web visit 
 https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com
  
 
 .

>>> -- 
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>>
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>> https://groups.google.com/d/msgid/spctools-discuss/7f5e47e5-56df-4552-88ca-b6d4396f3d8en%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

2021-04-12 Thread 'David Shteynberg' via spctools-discuss 
I don't mind taking a crack at it over vacation.   Please let me know where
I can pull the data from. I might not have quick solution for you but I can
get started looking for the problem.  Which search engine did you use
here?   I would need mzML data search results and the fasta database to get
started.

Thanks!



Thanks!

On Mon, Apr 12, 2021, 1:38 PM Oded  wrote:

> Hi David,
> Thank you for the quick reply. We are using TPP v6.0.0-rc14 Noctilucent,
> Build 202103031119-8400 (Windows_NT-x86_64).
> As for the data let me know when you are back and I will transfer you
> either the raw file or the search results.
> Enjoy your vacation.
> Thanks,
> Oded
> On Monday, 12 April 2021 at 22:17:53 UTC+3 David Shteynberg wrote:
>
>> Hi Oded,  Which release candidate are you referring to?  The earlier
>> candidates may have a bug that is corrected in a later version. If you can
>> share some data and specifics about the missing PSMs I can run it here and
>> troubleshoot the problem.
>>
>> Thanks!
>>
>> David
>>
>> P.S. I am on vacation this week so will troubleshoot next week.
>>
>> On Mon, Apr 12, 2021, 11:49 AM Oded  wrote:
>>
>>> Hi there,
>>> We recently download the TPP 6.0 RC and while using it we noticed that
>>> we obtain fewer peptides IDs than what we got for the same dataset and
>>> search output with version 5.2.
>>> Many of the missing peptides seem to have decent Expect value and MS/MS
>>> following a visual inspection.
>>> This seems that this is due to changes in PeptideProphet and are not
>>> related to the search itself that was done with Comet.
>>> Is there any additional parameter that should be included in the new
>>> version in order to restore the missing peptides?
>>> Many thanks,
>>> Oded
>>>
>>> --
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>>> 
>>> .
>>>
>> --
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> .
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Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

2021-04-12 Thread Oded 
Hi David,
Thank you for the quick reply. We are using TPP v6.0.0-rc14 Noctilucent, 
Build 202103031119-8400 (Windows_NT-x86_64).
As for the data let me know when you are back and I will transfer you 
either the raw file or the search results.
Enjoy your vacation.
Thanks,
Oded
On Monday, 12 April 2021 at 22:17:53 UTC+3 David Shteynberg wrote:

> Hi Oded,  Which release candidate are you referring to?  The earlier 
> candidates may have a bug that is corrected in a later version. If you can 
> share some data and specifics about the missing PSMs I can run it here and 
> troubleshoot the problem.   
>
> Thanks!
>
> David 
>
> P.S. I am on vacation this week so will troubleshoot next week.
>
> On Mon, Apr 12, 2021, 11:49 AM Oded  wrote:
>
>> Hi there,
>> We recently download the TPP 6.0 RC and while using it we noticed that we 
>> obtain fewer peptides IDs than what we got for the same dataset and search 
>> output with version 5.2.
>> Many of the missing peptides seem to have decent Expect value and MS/MS 
>> following a visual inspection. 
>> This seems that this is due to changes in PeptideProphet and are not 
>> related to the search itself that was done with Comet.
>> Is there any additional parameter that should be included in the new 
>> version in order to restore the missing peptides?
>> Many thanks,
>> Oded
>>
>> -- 
>> 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 view this discussion on the web visit 
>> https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

2021-04-12 Thread 'David Shteynberg' via spctools-discuss 
Hi Oded,  Which release candidate are you referring to?  The earlier
candidates may have a bug that is corrected in a later version. If you can
share some data and specifics about the missing PSMs I can run it here and
troubleshoot the problem.

Thanks!

David

P.S. I am on vacation this week so will troubleshoot next week.

On Mon, Apr 12, 2021, 11:49 AM Oded  wrote:

> Hi there,
> We recently download the TPP 6.0 RC and while using it we noticed that we
> obtain fewer peptides IDs than what we got for the same dataset and search
> output with version 5.2.
> Many of the missing peptides seem to have decent Expect value and MS/MS
> following a visual inspection.
> This seems that this is due to changes in PeptideProphet and are not
> related to the search itself that was done with Comet.
> Is there any additional parameter that should be included in the new
> version in order to restore the missing peptides?
> Many thanks,
> Oded
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
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> email to spctools-discuss+unsubscr...@googlegroups.com.
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> https://groups.google.com/d/msgid/spctools-discuss/b7c2e3b7-3061-4ec7-94d8-f70e43538f2an%40googlegroups.com
> 
> .
>

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