Closed GoogleCodeExporter closed 9 years ago
From Martin:
> I think the current schema is not okay, because it allows "average" in one
SpecIdent and "mono" in another,
> so it is not well-defined for the masses in elements or attributes.
> We need a global attribute :-) or element. Or it can be done later in semantic
validation :-( .
Original comment by dcre...@gmail.com
on 7 Aug 2008 at 1:55
I think it's actually _required_ to be like this. For example, at least one
search
engine allows you to specify mono for masses below x and average for masses
above x.
So, in this case, the output should be similar to the N15 example that I've
supplied,
with two separate mass tables. Maybe you could look at the
Mascot_N15_example.xml and
see if you think that this is OK.
Original comment by dcre...@gmail.com
on 7 Aug 2008 at 1:56
Um... what about average peptide masses and monoisotopic fragment masses - or
vice versa.
Original comment by dcre...@gmail.com
on 7 Aug 2008 at 1:59
regarding comment3: that could be another type of search, e.g. "mass type
setting
PepAvg FragMono" as child CV term of "mass type settings" next to "mass type
setting
average isotopic" and "mass type setting monoisotopic".
Oh, I get the point. There is no mechanism to reference two mass tables in one
search...!?
But is that type of search common? We should close this issue for milestone 1...
Original comment by eisena...@googlemail.com
on 7 Aug 2008 at 2:17
Summary:
Different SpectrumIdentification runs may have different (e.g. average and
mono) mass
tables.
Remaining problems:
1) giving the mass of a peptide may then duplicate the sequence information
(when a
peptide is identified in the avg AND in the mono run)
possible solution: drop any mass information and give it only in relation to a
run
(i.e. in the PeptideEvidence or SpectrumIdentificationItem elements)
2) if parent masses are avg and fragment masses are mono (and fragments are
reported); at the moment we have only one mass table!
3) if masses below X Da are avg and above X Da are mono
Original comment by eisena...@googlemail.com
on 1 Sep 2008 at 12:57
The mono / average problem is solved meanwhile:
because we have a MassTable_ref from the <Peptide> elements and the
possibility to have more than one mass table per
<SpectrumIdentificationProtocol>.
A peptide with the same sequence, but another mass table has to
be reported twice (or more often), but that is a bitter pill we have
to swallow
Original comment by eisena...@googlemail.com
on 9 Oct 2008 at 11:44
Original issue reported on code.google.com by
eisena...@googlemail.com
on 30 Jul 2008 at 12:13