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calculatedMassToCharge and sequenceMass have the same information #48

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
Reported by Eugene Kapp

<SpectrumIdentificationItem calculatedMassToCharge="670.86261"
chargeState="2" Peptide_ref="peptide_1_1"

and

<Peptide id="peptide_1_1" sequenceMass="1341.72522"

These both have the same information. Do we really need both?

Original issue reported on code.google.com by dcre...@gmail.com on 5 May 2009 at 10:43

GoogleCodeExporter commented 8 years ago 
Pierre-Alain - email:

This is only true if chargeState is specified and has only one value 
that is not 0 or unknown. Is chargeState mandatory and only unique?

David: chargeState is not a required attribute. But neither is
calculatedMassToCharge.  There must have been a reason for having the calculated
value in both places, but we can't remember. However, it is useful to have the
calculatedMassToCharge here - less calculations for an importer to make.

Original comment by dcre...@gmail.com on 5 May 2009 at 3:10

GoogleCodeExporter commented 8 years ago 
As far as I remember the reason why both were kept is because they fulfil 
slightly
different roles. 

The Peptide element could be re-used by different SpectrumIdentificationItems 
(i.e.
different charge states would give different values). I think this is quite a 
weak
difference though and I wonder if we should get rid of some of the optional 
elements
on Peptide: sequenceMass and sequenceLength, the latter seems particularly 
pointless.
I notice that peptideSequence is optional, probably this should be mandatory? 
Are
there any use cases where a peptideSequence could not be provided?

It also appears that the sequenceMass and calculatedMassToCharge values don't 
tally
in the Sequest example! Another good reason to get rid of one or the other...

Original comment by andrewro...@googlemail.com on 7 May 2009 at 2:14

GoogleCodeExporter commented 8 years ago 
At the telecon on 2009-05-07 16:00 (http://psidev.info/index.php?q=node/412) we
agreed to try removing sequenceLength, sequenceMass and MassTable_ref from the
<Peptide> element. Added MassTable_ref to <SpectrumIdentificationItem>

The updated Mascot N15 example shows an example of using MassTable_ref

http://code.google.com/p/psi-pi/source/browse/trunk/examples/Mascot_N15_example.
mzid

Original comment by dcre...@gmail.com on 14 May 2009 at 12:22

GoogleCodeExporter commented 8 years ago

Original comment by andrewro...@googlemail.com on 14 May 2009 at 3:25