Closed GoogleCodeExporter closed 8 years ago
We can also move EnzymeRef to be attributes of PeptideEvidenceList for a
slightly cleaner representation IMO. And then I make the references specific to
each terminus to dirty it up again. ;)
One list of fully tryptic peptides:
<PeptideEvidenceList nTerminusEnzyme_ref="EZ_TRYP"
cTerminusEnzyme_ref="EZ_TRYP">
Two lists of semitryptic peptides:
<PeptideEvidenceList nTerminusEnzyme_ref="EZ_TRYP">
<PeptideEvidenceList cTerminusEnzyme_ref="EZ_TRYP">
One list of nontryptic peptides:
<PeptideEvidenceList>
For two non-independent enzymes there are two fully specific lists:
<PeptideEvidenceList nTerminusEnzyme_ref="EZ_LYSC"
cTerminusEnzyme_ref="EZ_ARGC">
<PeptideEvidenceList nTerminusEnzyme_ref="EZ_ARGC"
cTerminusEnzyme_ref="EZ_LYSC">
There are four semi-specific lists:
<PeptideEvidenceList nTerminusEnzyme_ref="EZ_LYSC">
<PeptideEvidenceList nTerminusEnzyme_ref="EZ_ARGC">
<PeptideEvidenceList cTerminusEnzyme_ref="EZ_LYSC">
<PeptideEvidenceList cTerminusEnzyme_ref="EZ_ARGC">
But again just a single non-specific list.
Adding a third enzyme makes it really bad but I hope the pattern is clear. This
certainly makes it unambiguous what each list represents!
Original comment by matt.cha...@gmail.com
on 7 Apr 2011 at 4:24
Heidelberg:
- seems to be not necessary to repeat the search or to report the results or
judge their quality
- Furthermore it seems to be a rather rare case and may be solved when it comes
up
Original comment by eisena...@googlemail.com
on 12 Apr 2011 at 12:22
OK so that seems to shoot down my suggestions without answering any of my
questions. If we're not going to be unambiguous with the enzyme information,
why include it at all? We could just go back to having 0 or more
PeptideEvidence elements instead of PeptideEvidenceLists. And of course remove
missedCleavages again.
Original comment by matt.cha...@gmail.com
on 12 Apr 2011 at 1:24
Agreement TeleCon 21.4.2011: It was of course not intended to shoot down your
suggestions without answering questions or giving arguments, sorry for that. It
was again discussed in the TeleCon, that grouping the <PeptideEvidence>
elements makes sense to give missedCleavages and the other attributes their
appropriate relation point. So the <EnzymeRef> will remain an element as it is.
A cvParam sub-Element will be added to <EnzymeRef> for the description of
terminal specificity.
action points: 1) I will change the schema accordingly; 2) I will send David
and Juan-Antonio two new CV terms: "Enzyme specificity N-term" and "Enzyme
specificity C-term".
Original comment by eisena...@googlemail.com
on 21 Apr 2011 at 4:50
If I understand correctly, the resulting syntax would look like this for a
semi-tryptic search:
<PeptideEvidenceList>
<PeptideEvidence ...>
...
<EnzymeRef ref="EZ_TRYP">
<cvParam name="N-terminal enzyme specificity"/>
<cvParam name="C-terminal enzyme specificity"/>
</EnzymeRef>
</PeptideEvidenceList>
<PeptideEvidenceList>
<PeptideEvidence ...>
...
<EnzymeRef ref="EZ_TRYP">
<cvParam name="N-terminal enzyme specificity"/>
</EnzymeRef>
</PeptideEvidenceList>
<PeptideEvidenceList>
<PeptideEvidence ...>
...
<EnzymeRef ref="EZ_TRYP">
<cvParam name="C-terminal enzyme specificity"/>
</EnzymeRef>
</PeptideEvidenceList>
What about the non-specific case? No EnzymeRef?
Original comment by matt.cha...@gmail.com
on 21 Apr 2011 at 5:00
Original issue reported on code.google.com by
matt.cha...@gmail.com
on 7 Apr 2011 at 4:12