Re: [proteowizard-developer] updating to latest MS obo

[Brian P. <bri...@in...>]

OK - if I get it wrong I hope some unit tests will bark at me?

So many annoying trivial name changes, but this one (retention time) seems
like the tricky part.  It seems to me that retention time is certainly a
peptide thing, but doesn't it need to travel with the spectrum in order to
become a peptide thing?  Making it a spectrum thing as well?


On Wed, Sep 4, 2013 at 10:17 AM, Matt Chambers <mat...@gm...>wrote:

> I started working on this upgrade and got side-tracked. It was pretty
> thorny. Retention time is a
> peptide property, not a spectrum property. It was obsoleted because there
> are other retention time
> terms that are peptide-centric. The scan start time is a spectrum
> property. We should still read the
> obsolete term from old files, but we shouldn't write it anymore (to the
> IdentData data model).
>
> Hope this helps,
> -Matt
>
>
> On 9/3/2013 5:21 PM, Brian Pratt wrote:
> > Hmm, looking at the changes to the OBO for the "retention time s" item
> I'm not sure I like what I see:
> >
> > def: "OBSOLETE Retention time of the spectrum from the source file."
> [PSI:PI]
> > comment: This term was made obsolete because scan start time
> (MS:1000016) should be used instead.
> >
> > It seems like an error to insist that chromatography and mass spec
> analysis always take place in the
> > same time frame.  Or am I misunderstanding something?
> >
> >
> > On Tue, Sep 3, 2013 at 2:21 PM, Brian Pratt <bri...@in...
> > <mailto:bri...@in...>> wrote:
> >
> >     So I went to update cv.hpp/cpp for use with some new data
> compression patches that were
> >     submitted.  Wow, lots of action there, kind of a can of worms.  Much
> of it is just small name
> >     changes:
> >         MS_search_engine_specific_score_for_peptides = 1001143
> >     changes to
> >         MS_search_engine_specific_score_for_PSMs = 1001143
> >     and
> >        MS_modification_specificity_N_term
> >     changes to
> >        MS_modification_specificity_peptide_N_term
> >     etc.  So just a lot of editing the pwiz code to match the new names.
>  Kind of annoying, no worse.
> >
> >     In particular, though:
> >         MS_retention_time_s_ = 1001114,
> >     changes to
> >         MS_retention_time_s__OBSOLETE = 1001114
> >     makes me a bit queasy - just tossing the word OBSOLETE into
> >     pwiz\data\identdata\Serializer_pepXML.cpp creeps me out.  Or does
> this actually reflect the
> >     state of pepXML, that is, obsolete?
> >
> >     Brian
> >
> >
> >
> >
> >
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