Re: [Psidev-ms-dev] Example files

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

Yes, looks like I forgot about neutral change spectra while getting so 
ambitious with the mapping file changes. Either we need some basic logic 
in the mapping file (if spectrum is this type, this use this rule, else 
another rule), or this is another one of those special rules. I'll fix 
this later today.

-Matt


Fredrik Levander wrote:
> Hi, I am afraid that it will not be possible to make the neutral loss 
> spectra valid with a required target mass for precursor and product, 
> since there are none those a spectra (just two moving isolation 
> windows). So I guess these new rules will have to be changed back to MAY 
> again, even if they should be required in most other types of spectra. 
> The other exception is precursor ion spectra, were the precursor 
> isolation window is also moving.
>
> Fredrik
>
> Marc Sturm wrote:
>   
>> Hi all,
>>
>> good news from the example files. I just validated all examples from the 
>> website. Only two files contain minor errors:
>>
>> -------
>>
>> file name: MzMLFile_PDA.mzML
>> file type: mzML
>>
>> Validating mzML file against XML schema version 1.10
>> Success: the file is valid!
>>
>> Semantically validating mzML file:
>> Error: CV term must have a unit: MS:1000515 - intensity array
>> Error: CV term must have a unit: MS:1000515 - intensity array
>> Failed: errors are listed above!
>>
>> -------
>>
>> file name: neutral_loss_example_1.1.0.mzML
>> file type: mzML
>>
>> Validating mzML file against XML schema version 1.10
>> Success: the file is valid!
>>
>> Semantically validating mzML file:
>> Error: Violated mapping rule 'precursor_isolationwindow_must' at element 
>> '/mzML/run/spectrumList/spectrum/precursorList/precursor/isolationWindow', 
>> 1 should be present, 0 found!
>> Error: Violated mapping rule 'product_isolationwindow_must' at element 
>> '/mzML/run/spectrumList/spectrum/productList/product/isolationWindow', 1 
>> should be present, 0 found!
>> Failed: errors are listed above!
>>
>> Best,
>>   Marc
>>