Re: [spctools-discuss] Xpress ratio in pepXML do not match those in XPressPeptideUpdateParser.cgi

2022-11-16 Thread 2kl...@gmail.com 
Dear Luis,
Apologies for the delay. How can I send you the file/s?
Thanks
On Wednesday, November 2, 2022 at 10:15:37 PM UTC+2 2kl...@gmail.com wrote:

> Hi Luis,
> Sure. I don't have internet access all the time in the coming week but 
> will send you a download link when possible.
> I should also mention that I should update that we upgrade to version TPP 
> v6.2.0 Nacreous-dev, Build 202209191518-8727 and things a somewhat better.  
> Thanks a lot.
>
> On Sunday, October 30, 2022 at 1:41:41 AM UTC+3 Luis wrote:
>
>> Hello,
>> That is quite odd; Are you able to share a pepXML file so we can 
>> troubleshoot?  You can contact me directly to arrange a file transfer.
>> Thanks,
>> --Luis
>>
>>
>> On Tue, Oct 18, 2022 at 12:21 PM 2kl...@gmail.com <2kl...@gmail.com> 
>> wrote:
>>
>>> Hi all,
>>>
>>> I am using the TPP v6.1.0 Parhelion, Build 202108271510 for analyzing 
>>> dimethylation following Comet (or MSFragger) search with the light label 
>>> set as fixed and the heavy mass difference as variable. Xpress settings 
>>> include mass tolerance of 20 ppmת a Minimum number of chromatogram points 
>>> needed for quantitation:3 and Number of isotopic peaks to sum is set to 0.
>>>
>>> When I open the interact.pep.xml file with the viewer and filter the 
>>> results based on probability, for some of the peptides there is a 
>>> discrepancy between the ratio shown in the pepXML and the one in the 
>>> XPressPeptideUpdateParser. The differences can be relatively large (for 
>>> example, 0.1 versus 1.5)
>>>
>>> Similar results are obtained if the Number of isotopic peaks to sum is 
>>> set to 1, 2 or 3.
>>>
>>> Can you please advise?
>>> Many thanks,
>>> OK
>>>
>>> -- 
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>>> Groups "spctools-discuss" group.
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>>>  
>>> 
>>> .
>>>
>>

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Re: [spctools-discuss] Xpress ratio in pepXML do not match those in XPressPeptideUpdateParser.cgi

2022-11-02 Thread 2kl...@gmail.com 
Hi Luis,
Sure. I don't have internet access all the time in the coming week but will 
send you a download link when possible.
I should also mention that I should update that we upgrade to version TPP 
v6.2.0 Nacreous-dev, Build 202209191518-8727 and things a somewhat better.  
Thanks a lot.

On Sunday, October 30, 2022 at 1:41:41 AM UTC+3 Luis wrote:

> Hello,
> That is quite odd; Are you able to share a pepXML file so we can 
> troubleshoot?  You can contact me directly to arrange a file transfer.
> Thanks,
> --Luis
>
>
> On Tue, Oct 18, 2022 at 12:21 PM 2kl...@gmail.com <2kl...@gmail.com> 
> wrote:
>
>> Hi all,
>>
>> I am using the TPP v6.1.0 Parhelion, Build 202108271510 for analyzing 
>> dimethylation following Comet (or MSFragger) search with the light label 
>> set as fixed and the heavy mass difference as variable. Xpress settings 
>> include mass tolerance of 20 ppmת a Minimum number of chromatogram points 
>> needed for quantitation:3 and Number of isotopic peaks to sum is set to 0.
>>
>> When I open the interact.pep.xml file with the viewer and filter the 
>> results based on probability, for some of the peptides there is a 
>> discrepancy between the ratio shown in the pepXML and the one in the 
>> XPressPeptideUpdateParser. The differences can be relatively large (for 
>> example, 0.1 versus 1.5)
>>
>> Similar results are obtained if the Number of isotopic peaks to sum is 
>> set to 1, 2 or 3.
>>
>> Can you please advise?
>> Many thanks,
>> OK
>>
>> -- 
>> 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/8bd33f85-6997-4380-9cbf-d64dc518ad76n%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [spctools-discuss] Xpress ratio in pepXML do not match those in XPressPeptideUpdateParser.cgi

2022-10-29 Thread 'Luis Mendoza' via spctools-discuss 
Hello,
That is quite odd; Are you able to share a pepXML file so we can
troubleshoot?  You can contact me directly to arrange a file transfer.
Thanks,
--Luis


On Tue, Oct 18, 2022 at 12:21 PM 2kl...@gmail.com <2kl...@gmail.com> wrote:

> Hi all,
>
> I am using the TPP v6.1.0 Parhelion, Build 202108271510 for analyzing
> dimethylation following Comet (or MSFragger) search with the light label
> set as fixed and the heavy mass difference as variable. Xpress settings
> include mass tolerance of 20 ppmת a Minimum number of chromatogram points
> needed for quantitation:3 and Number of isotopic peaks to sum is set to 0.
>
> When I open the interact.pep.xml file with the viewer and filter the
> results based on probability, for some of the peptides there is a
> discrepancy between the ratio shown in the pepXML and the one in the
> XPressPeptideUpdateParser. The differences can be relatively large (for
> example, 0.1 versus 1.5)
>
> Similar results are obtained if the Number of isotopic peaks to sum is
> set to 1, 2 or 3.
>
> Can you please advise?
> Many thanks,
> OK
>
> --
> You received this message because you are subscribed to the Google Groups
> "spctools-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to spctools-discuss+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/8bd33f85-6997-4380-9cbf-d64dc518ad76n%40googlegroups.com
> 
> .
>

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