Re: [Psidev-pi-dev] molecule table thoughts

[Martin E. <mar...@ru...>]

Meanwhile I think it saves us a lot, if
a peptide (with modifications) is found
in
more than one spectrum. In the
SpectrumSearchResultItem there is the
link between
spectrum and peptide (with mods)
TOGETHER with a score. Additionally we
have to
report the peptide sequence (with mods)
only once, although it may be found with
more
than one charge states.
 
  Bye
    Martin
 
 
Von:
psi...@li...urceforge.
net
[mailto:psi...@li...ur
ceforge.net] Im Auftrag von Angel
Pizarro
Gesendet: Sunday, April 27, 2008 4:46 PM
An: psi...@li...
Betreff: [Psidev-pi-dev] molecule table
thoughts
 
More and more I don't think our molecule
lookup table is gaining us anything.
Specifically, last time at the EBI,
Martin and I were discussing
modifications and how best and proper to
represent them and we came to the
conclusion that the modification
information should live directly next to
the scoring information. Also taking
into account that a protein
determination step is an analysis, we
can see that representing the protein
groups can also be defined within the
result set containing the scoring
information.

So the only thing that the molecule
table buys us is an easy look-up for
information without context and possibly
(although not proven) file size savings.
The cost is that the format MUST
reference the lookup table, adding
complexity to encoding and reading the
actual results. 

I don't think the convenience is worth
the cost. Can we move the identified
compound information to be collocated
with the results information?

-angel