Re: [Psidev-ms-dev] PSI-MSS WG Tuesday call reminder

[Mike C. <tu...@gm...>]

On Thu, Jun 11, 2009 at 2:41 PM, Matthew
Chambers<mat...@va...> wrote:
> The many internal references in mzML to me means that it shouldn't be
> considered a light-weight format that simple scripts could parse:
> reading mzML with software takes a substantial API.

I hope this is not true--I would be quite disappointed if mzML could
not be easily parsed by simple scripts.

> Thus the only
> remaining benefit for ASCII peak representation (AFAIK) is human
> readability of peak lists [...]

If one starts with the assumption that mzML is in its best form and
should not be changed, this conclusion follows directly.  But if we're
trying to decide whether mzML should be changed, this seems a bit like
begging the question.

> However, NIST library folks have a quite straight-forward way to meet
> the "human readability" requirement: XML comments. There's no reason you
> can't put what looks like an MGF peak list in an XML comment with every
> mzML spectrum (although presumably not profile-mode ones!).

I think this would be worse than the status quo.  If this change is to
be made, though, may I suggest that the ASCII peaks be used in the
"real" XML and that the binary peaks go in the comments?  :-)

Mike