proteowizard-developer

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

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...>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
>