[Psidev-ms-dev] DTA to mzML conversion

[Fredrik L. <Fre...@im...>]

Hi All,

In the Proteios platform we're including converters from some peak list 
formats to mzData, and now also to mzML. It is clearly not optimal with 
such conversion since instrument settings etcetera are lost. However, I 
guess there will be need for such converters if someone wants to use 
their old instruments with manufacturer peak picking algorithms.

There are sample files generated from DTAs and ProteinLynx by the 
converters (0.99.1) at:
http://trac.thep.lu.se/trac/fp6-prodac/browser/trunk/mzML

The converters will be part of the new release of the Proteios Software 
Environment, but if anyone would like to try them with their files, 
there is a standalone package (mzMLconverters.zip) at the address above 
which should work under Windows/Linux/OSX with Java 1.5 or higher.

Please notice that the output files are not schematically valid since 
some terms are still missing in the CV.

For the conversion of multiple DTA files to one mzML file there is a 
small problem which is related to how lcq_dta generates dta files: If 
the charge state of the precursor can not be determined, a spectrum can 
result in two DTA files which are identical apart from the precursor. 
There are two solutions on how to handle this:
1) Two spectra, with the same scanNumber but different spectrum Ids (The 
solution used by the current converter)
2) One spectrum, two precursors. However, this will not work with the 
current schema since there can only be one sourceFileRef for a spectrum.
Do you all think solution 1 is fine, or is there a better solution? 
Solution 2 seems to need schema changes.
Other comments are also welcome

Thanks,

Fredrik