Re: [Psidev-ms-dev] Retention time in PSI-MS ontology

[Lennart M. <len...@eb...>]

Hi Kent,


Thanks for pointing that out, but I had seen these myself and assumed 
that they were used to document the actual acquisition time during which 
the final spectrum was acquired (the final spectrum represented in the 
mzData binary arrays is thus a summation over all the individual 
detector recordings during that time slot).

As such, I would expect this value to be either constant (I guess most 
mass specs do not allow dynamic setting of this value, but I could be 
wrong) and certainly small (say from 0.5 to 8 seconds). Having '900' in 
the seconds field, say, would therefore probably lead to confusion?


Cheers,

lnnrt.

Kent Laursen wrote:
> Hi Lennart,
> 
> There is not currently a term labeled retention time in the MS CV.  The
> current terms for the purpose are:
> 
> [Term]
> id: PSI:1000038
> name: Time In Minutes
> def: "Acquisition time in minutes." [PSI:GPS]
> is_a: PSI:1000460 ! Unit
> relationship: part_of PSI:1000459 ! Spectrum Instrument Description
> 
> [Term]
> id: PSI:1000039
> name: Time In Seconds
> def: "Acquisition time in seconds." [PSI:GPS]
> is_a: PSI:1000460 ! Unit
> relationship: part_of PSI:1000459 ! Spectrum Instrument Description
> 
> Regards,
> 
> Kent
> 
>> -----Original Message-----
>> From: psi...@li... [mailto:psidev-ms-dev-
>> bo...@li...] On Behalf Of Lennart Martens
>> Sent: Thursday, November 09, 2006 9:27 AM
>> To: psi...@li...
>> Subject: [Psidev-ms-dev] Retention time in PSI-MS ontology
>>
>> Hi,
>>
>>
>>
>> I am processing some mzXML files into mzData for insertion into the
>> PRIDE database, and I can't seem to find an ontology term for 'retention
>> time' in the PSI-MS ontology.
>>
>> If there is one, and I just can't find it for some silly reason, please
>> let me know.
>>
>> If there isn't any, could this be added? It seems like a sensible thing
>> as it is a common enough piece of data.
>>
>>
>> Thanks in advance,
>>
>>
>> lnnrt.
>>
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> 
> 

-- 
Dr. Lennart Martens

Senior Software Developer
Proteomics Services
Sequence Database Group
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
United Kingdom

Tel.:  +44 (0)1223 492 610 (Direct Line)
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