Re: [Psidev-ms-dev] DTA to mzML conversion

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

Hi Matt and Rune,

Thanks for the comments. I agree that the important information is the 
scan number, since this is what you would like to look up in the raw 
data file. And it doesn't make much sense to have the scan repeated 
twice in the file, so I think we'll go for solution 2 and just keep the 
sourceFileRef to one of the files.
However, since we do have unique spectrum ids there should not be any 
real need to stick to the unique scan number requirement from what I got 
from the indexing discussion, even if it is still in the specs (?). 
Couldn't there be cases when data is collected in different channels 
where the scan numbers are the same in different channels?

Regards

Fredrik

Matthew Chambers skrev:
> Hi Fredrik,
>
> Our group has a converter that does this conversion (to mzXML or mzData 
> currently, not yet mzML, but they all have the same uniqueness 
> constraints on scan numbers and they all support multiple precursors at 
> least in theory); we went with solution 2 because solution 1 is invalid 
> for all the XML formats (i.e. it would need a schema change and that 
> change isn't likely to happen, whereas multiple sourceFileRefs would be 
> understandable). As I understand it, sourceFileRef is optional 
> ("<xs:attribute name="sourceFileRef" type="xs:anyURI" use="optional">"), 
> so if you can't or don't want to encode it correctly, just don't include 
> it. Our converter doesn't even bother to include the sourceFileRefs to 
> the DTAs, it's not helpful information IMO. As long as the conversion is 
> done without data loss, get it over with and then have mercy on your 
> filesystem by deleting the DTAs. ;)
>
> -Matt
>
>
> Fredrik Levander wrote:
>   
>> 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
>>
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