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

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

[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 
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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

[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

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 .

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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

['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
>>>
>>> --
>>> 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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> 
> .
>

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

[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

['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.
> To unsubscribe from this group and stop receiving emails from it, send an
> 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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[spctools-discuss] Changes in number of peptides identifications in TPP 6.0 RC

[Oded]

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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