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

[David C. <dc...@ma...>]

Hi Lennart,
The intention was certainly that these are for the retention time, but I 
can't see any documentation that confirms this.  Certainly Mascot 
Distiller, Mascot, Bruker CompassXport, the Sciex wiff converter, 
Bioworks and the Insilicos viewer all assume that this is the case.

Best regards,
David



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.
>>>
>>> -------------------------------------------------------------------------
>>> Using Tomcat but need to do more? Need to support web services, security?
>>> Get stuff done quickly with pre-integrated technology to make your job
>>> easier
>>> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>>> _______________________________________________
>>> Psidev-ms-dev mailing list
>>> Psi...@li...
>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>
> 

-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

dc...@ma...
http://www.matrixscience.com

*** please note change of address ***