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

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Comment #49 on issue 42 by matthew....@vanderbilt.edu: Issues with the CV
http://code.google.com/p/psi-pi/issues/detail?id=42

Can you point me to the discussion about (not) sharing CV? That seems a bit  
crazy to
me (and contrary to the PSI CV guidelines?). I'm sure there are reasons  
though, I
just want to see them. :)

All of these terms are also things that would potentially be in an mzML  
file created
from MGF (just like the Thermo filter line may be included from Thermo  
files), so
that's why I suggested they all go in the MS CV. MGF is after all a generic  
MS
format, not necessarily specific to proteomics even. :)

NativeIDs in mzML must be unique. You just had to bring up merged spectra  
didn't you?
;) It gets pretty painful and hazy when the original acquisitions and their  
merged
forms are kept in the same file. There's 2 issues there:
1) support representing both the merged spectra and the separate  
acquisitions as
independent spectra? or only support one or the other
2) if yes to 1, and nativeID must be unique, there are several possible  
solutions:
   a) just taking the first acquisition's nativeID won't be unique, so we  
extend the
nativeID syntax to support either ranges (Thermo: "controller=0  
scan=[2,10]") or
lists of nativeIDs ("controller=0 scan=2,controller=0 scan=15,controller=0  
scan=50")
or perhaps a combination of both
   b) use a special convention for nativeIDs of merged spectra that  
indicates to a
semantic validator that the nativeID is irrelevant and only the  
acquisitionList is
important; e.g. nativeID="merged" (since nativeID is string and not xsd:ID,  
it won't
be invalid syntax)

Really there's no nativeID for a merged spectrum, so anything we come up  
with is a
workaround.

Finally, several vendor formats allow peak picking straight out of their  
API, namely
Thermo, ABI, and Bruker. So for these formats MyriMatch works straight off  
by just
asking for the centroids. For other formats, we don't have an external peak  
picker
yet (in ProteoWizard) but we will "Real Soon Now." And no, when reading  
straight from
the vendor file we don't merge, so nativeIDs are direct.

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