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

[Fredrik L. <Fre...@el...>]

Hi,

A related issue is for the case of peak lists which have been generated 
from the combination of several scans. The 'TimeInMinutes' for these is 
obviously also a range of time. I've solved this by just putting the 
start acquisition time of the first spectrum in the range, but one could 
of course as well put the average time.  The same question appears as 
Lennart writes for individual scans if one want to be exact: is it the 
start time, or average, or end time of the scan which should be in the 
field? Is there any consensus opinion on which should be written, and is 
it documented somewhere?
I don't think this is very important for peak lists since there are 
references to all the scans in the raw file that were combined in the 
form of a list of acquisition-acqNumbers, but if mzData is to represent 
raw data it could become important for LC-MS alignment etc.

Regards

Fredrik Levander


Lennart Martens wrote:
> 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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>>     
>
>