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

[Kent L. <knl...@in...>]

Hi Lennart,

Retention time is a chromatography term.  If you are referring to the time
between mass spectrum acquisitions, this can be computed by subtracting
consecutive absolute acquisition times.  However, these time intervals are
not necessarily identical/constant, so it is more precise to do the math on
acquisition times.

As far as I know, there is not a term for what you are describing.  Since it
would be useful to add this term to MS CV (time in between mass spec scans,
so to speak) you can email this request to Trish.  Perhaps something like
duty cycle would fit nicely with instrument description.

FYI, the upcoming merger will address separation as pragmatically necessary.

Regards,

Kent

> -----Original Message-----
> From: Lennart Martens [mailto:len...@eb...]
> Sent: Thursday, November 09, 2006 10:37 AM
> To: Kent Laursen; psi...@li...
> Subject: Re: [Psidev-ms-dev] Retention time in PSI-MS ontology
> 
> 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)
> Fax:  +44 (0)1223 494 484
> Skype: lennart_martens