Re: [Psidev-ms-dev] scanList example

[Matthew C. <mat...@va...>]

Sorry David, I misspoke. Right now the schema does guarantee that 
spectrum::id is unique. I believe this won't be a problem in the future 
because we will always add a unique axis to the nativeID (like Waters 
RAW has function=x instead of "process=x scan=x" and pointing to the 
sourceFile). And since we currently don't have any cases where there are 
different nativeID formats for MS spectra (BAF/U2 is the only case and 
that's MS/UV), I think mzIdentML is fine to say it supports mzML. Thanks 
for forwarding the issues to the list, I don't know how many here are 
also subscribed to PI.

-Matt


David Creasy wrote:
> 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
>>>>
>>>>   
>>>>         
>>> ------------------------------------------------------------------------------
>>> _______________________________________________
>>> Psidev-ms-dev mailing list
>>> Psi...@li...
>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>>       
>
>