[Psidev-pi-dev] Issue 42 in psi-pi: Issues with the CV

[<cod...@go...>]

Comment #48 on issue 42 by dcreasy: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

OK, I assume that we can now agree on adding:
   mgf title
   mgf scans
   mgf rawscans
(The rawscans will be in the next release of Mascot, so isn't documented  
yet)

Yes, I totally agree that the retention time (possibly multiple times as  
you say)
should be a generic term.
For better or worse, we decided after much discussion not to share CV with  
mzML, so
we'd need to have our own term for retention time. In fact, it looks as  
though we
already have PI:00114 (although this can't currently be used because it's  
not in the
mapping file). Even though we aren't sharing CV, we should at least use the  
same name
and description as in mzML:

[Term]
id: MS:1000016
name: scan time
def: "The time that an analyzer started a scan, relative to the start of  
the run."
[PSI:MS]
xref: value-type:xsd\:float "The allowed value-type for this CV term."
is_a: MS:1000503 ! scan attribute
relationship: has_units UO:0000003 ! time unit

Any objections?

We'd not considered the use case of of running a search straight from a  
native
format... However, are you doing some sort of peak detection? Are you  
merging
together any spectra - i.e. will there be multiple nativeIDs for each  
spectrum? Might
the same nativeID be used for multiple spectra. (I notice that nativeIDs  
don't have
to be unique in mzML.)

-David

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