[Bioc-devel] Extracting mzR compatible acquisition number from mzIdentML files
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
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
06120 Halle Tel. +49 (0) 345 5582 - 1470
+49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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