Re: [Psidev-pi-dev] OMSSA example doc - a few questions

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

Hi!

> > I am in the process of trying to put
together an example instance
> > document for OMSSA and have a few
questions.  To make things more
> > complicated I have gone for an
example where I run the search on a
> > concatenated forward/reverse
database.
Great! We need real use cases / example
docs, otherwise our discussions
are quite academic.

> > At the moment I have all the
> > results in the analysisXML file i.e.
in the ConceptualMoleculeCollection
> > I am listing all proteins and
peptides identified including the
reverse
> > sequences.  I am unsure if (a) I am
supposed to be listing all results
> > and (b) if all results are supposed
to be listed how I mark the reverse
> > ones as decoy or does it not matter?
> In some ways it doesn't matter,
because they are just lists of
> proteins/peptides.
I agree, what you list is your decision,
but it would be helpful to
report this decision. So e.g. a CVparam,
that it was a reverse search;
and a FDR threshold, if you list only
the forward proteins below this
threshold.


> However, you might like to look at
Martin's example which contains
Originally I shouted out for an own
Analysis type "Quality Assurance"
but I was convinced that it is not
necessary.
In our (MPC) use case I decided to list
ALL identified proteins,
the forward and decoy; to mark the
decoy, I reported a "decoy pattern"
CVParam.
I have no FDR threshold, or I could have
set it to "1.0".

The decoy pattern belongs to the
ProteinDetermination, because in 
doing a SpectrumIdentification, it has
no meaning.

> > I am also listing all results
(forward and reverse) in DataCollection.
> I'd recommend two sets of results:
> <SpectrumIdentificationList
id="OMSSA_forward"> ...
> <SpectrumIdentificationList
id="OMSSA_reverse">
But you cannot specify two result sets
of ONE SpectrumIdentification.
So with this suggestion you would have
to have one SpectrumIdentification 
for the forward and one for reverse.
I used one and reported a decoy pattern.


> AnalysisXML is (currently) expected to
> report for just one 'cutoff' -
> i.e. a consumer of the analysisXML
> document couldn't recalculate the
> value. 
Yes, we agreed to have another
AnalysisXML for another cut-off.
I should put that into the wiki page ;-)

> > N-terminal peptide what would pre
be? pre="" or  pre="-"? 
> We just need to decide and document -
> maybe at the conference call later
> today.
New issue 34; in SEQUEST it is "-";
Oh, I see, that David finished this
issue just-in-time because we decided on
that in TeleCon 26th June.  ;-)
It is in the wiki now...


> > Finally the database searched was a
> custom database, is there anywhere
> > to report how a database was
> generated?
> Possibly outside the scope of
> AnalysisXML.
In Inputs we have SearchDatabase. 
Then follows DatabaseName.
We could add DatabaseProperties...
That would be quite useful to describe
the type of decoy DB.

 Bye
   Martin