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

2022-10-18 Thread 2kl...@gmail.com 


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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