[Bioc-devel] Extracting mzR compatible acquisition number from mzIdentML files

Steffen Neumann sneumann at ipb-halle.de
Wed May 1 19:11:24 CEST 2013


On Wed, 2013-05-01 at 14:43 +0200, Thomas Dybdal Pedersen wrote:
> I'm in the final stage of preparing an mzIdentML parser for submission
> to Bioconductor (https://github.com/thomasp85/mzID) The parser is
> intended to be quite sparse and not interpret the content of the
> mzIdentML file that much.

That's great news to hear that PSI standards see more adoption in BioC.

> So the question is: How can I ensure that I extract the right value
> from the spectrumID for an mzR compatible acquisitionNum? I realize
> that the generation of the acquisitionNum in mzR is probably handled
> by the RAMP module, but I hope some of the mzR folks (or others) can
> help.

RAMP is indeed the "problem" here. mzR has been developed with 
the concepts of pluggable backends in mind, and netCDF and RAMP
are currently implemented. 

Please see https://github.com/sneumann/mzR/wiki/Extending-mzR
for our ideas to add a "proper" pwiz backend, which directly 
wraps the pwiz msdata C++ object instead of indirectly going
through RAMP. That new backend would solve your problems.

Note also that Laurent Gatto also envisioned that the same approach 
could add a backend to mzIdentML. 


IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
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