Re: [Psidev-ms-dev] scanList example

[David C. <dc...@ma...>]

Hi,
(Also from the pi list - just in case it gets lost here)

The documentation should probably also say:

"It is not valid for a user to combine multiple runs together into a 
single mzML file"
(Looking through the mailing list, there was some discussion about this 
a year or so ago at which time it looks as though it was supported).

and the statement referenced below that says:
   External  documents may use this identifier together with the mzML
   filename or accession to reference a particular spectrum.

needs changing to say:

"You can't simply point to the mzML with an id because that id is only 
unique in the mzML when combined with the sourceFileRef."


Thanks,
David

David Creasy wrote:
> Hi,
> 
> It came up on the 'pi' list that the mzML documentation doesn't include 
> anything about the 'merged=<index>' format.
> 
> I may be missing something, but the only reference I can see to 'merged' 
> is for <spectrum id= where it says:
> 
> The native identifier for a spectrum. For unmerged native spectra or 
> spectra from older open file formats, the format of the identifier is 
> defined in the PSI-MS CV and referred to in the mzML header. External 
> documents may use this identifier together with the mzML filename or 
> accession to reference a particular spectrum.
> 
> However, the plgs_example_1.1.0.mzML seems to make sense, so it's not a 
> high priority.
> 
>  From discussion on the pi list, I guess the documentation should also say:
> "merged=<index>" is a valid id for ANY nativeID format.
> 
> Thanks,
> David
> 
> Matt Chambers wrote:
>> It looks good. I think we should stick with "merged=<index>" for the id 
>> format, just because it's simpler to ignore the method of combination at 
>> that level. Presumably the other scan elements will have their own scan 
>> times in the final file? Can't think of anything else, good job! The 
>> file makes perfect sense to me, this approach is leaps and bounds better 
>> than previous attempts at showing merged scans.
>>
>> -Matt
>>
>>
>> Fredrik Levander wrote:
>>> Hi All,
>>>
>>> I uploaded a preliminary 1.1.0 mzML file which contains summed scans, 
>>> generated by conversion of a ProteinLynx Global Server file.
>>>
>>> http://dev.thep.lu.se/fp6-prodac/browser/trunk/mzML/scans/plgs_example_1.1.0.mzML
>>>
>>> The file still has to go through semantic validation, but I was mainly 
>>> wondering if anyone has opinions about how the spectrum/scan ids are 
>>> written, (and if the file makes sense at all)?
>>>
>>> Regards
>>>
>>> Fredrik
>>>
>>>   
>>
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