Hi Sara,
That's some very neat work you've done. I can see why you'd propose it for quantitation, but it seems like a good general purpose format for any profile-centric
analysis. It seems especially suited for creating pseudo 2d gel images to summarize an MS experiment. I'm interested in seeing it read and written with
ProteoWizard (native C++). The main advantage of being able to build these from pwiz would be to convert directly from any of our supported open or RAW formats,
but you might also see considerable speed boost from using native C++. I'll follow up off-list.
-Matt
On 8/18/2010 3:55 AM, Sara Nasso wrote:
> Hi,
>
> since the mzQuant meeting is fast approaching I would like to let you know something about a work we did, in our Department, to solve some computational
> issues related to LC-MS (or mass spectrometry) data storage and access arised during my work on a quantification software I am developing. I think it could be
> worth to make use of such a data structure for data handling (i.e. handling of the data currently stored as Base64 encoded data in the mzML standard),
> especially when an analysis pipeline needs to be developed.
> It is just an idea and we actually did so, but I think it would be good to have an XML standard for all metadata and an efficient data structure, coupled to
> the XML, only for data handling. We customized a well known data structure suitable for the handling of huge sparse data to implement mzRTree, a data
> structure optimized for proteomics data (DOI:10.1016/j.jprot.2010.02.006 <http://dx.doi.org/10.1016/j.jprot.2010.02.006>), all information can be found here:
> http://www.dei.unipd.it/wdyn/?sez_alias=mzrtree
> We also developed a toolbox, to be released, which, using the JRAP library to gather the needed information, builds an mzRTree with all right parameters
> settings.
> Have a look and if you also think it would be worth to work on it, please write to us at /mzrtree AT dei.unipd.it/
> /I hope it could help,/
> /
> /
> cheers,
> Sara
>
> //
>
> //
>
> /
> ----------------------------------------------------------------------------------------------------------------------------------------------------------------
> //Sara Nasso, Ph.D. student
> Department of Information Engineering (DEI)
> University of Padova
> Via Ognissanti 72 35129 PADOVA, ITALY
> Voice: +39-049-8277834
> Fax: +39-049-8277826/
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