Re: [Psidev-ms-dev] precursor/product/neutral loss/SRM/MSE/MS3 scans

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

I think holidays and snow are hampering feedback, so far, but I could 
summarize the proposed schema changes to make it easier to follow.
Note that it will not change anything for product scans or normal MS 
scans (apart from the xmlns and version), the tiny example validates 
without problem.

Summary of changes:

 - Target namespace changed to allow schema to reside there. Version 
updated to 1.1.0
 - scanList minOccurs="0"
 - in spectrum, allow either precursors, product or neutraLoss element:
          <xs:choice minOccurs="0" maxOccurs="1">
              <xs:element name="precursorList" 
type="dx:PrecursorListType" />
              <xs:element name="product" type="dx:ProductType" />
              <xs:element name="neutralLoss" type="dx:NeutralLossType" />
          </xs:choice>
 - IsolationWindowType description generalized to accomodate all types 
of isolated ions. 
 - SelectedIonList description generalized to accomodate all types of 
isolated ions
 - Addition of ProductType and NeutralLossType (containing activation 
and isolationWindow, no selectIonList ).
 - Removed some keyrefs

If this is OK the schema is found at:

http://dev.thep.lu.se/fp6-prodac/browser/trunk/mzML/scans/mzML_dev_scans.xsd

and sample spectrum examples:
http://dev.thep.lu.se/fp6-prodac/browser/trunk/mzML/scans
(The link was not correct in the previous post)

Thanks,

Fredrik

Fredrik Levander wrote:
> Since it is quite unlikely with a sequence of isolation events within one scan, I revised the scan examples, xsd and examples to only allow either a precursorList, product or neutralLoss. This way there would not be any changes to normal MS2 files.
> The updated files are found at the same URL.
> http://dev.thep.lu.se/fp6-prodac/browser/trunk/mzML/scans
>
> These examples are really minimalistic, and probably they are not semantically complete, but at least they validate with the xsd.
>
> thoughts?
>
> Fredrik 
>
> ----- Original Message -----
> From: Fredrik Levander <Fre...@im...>
> Date: Thursday, December 18, 2008 5:02 pm
> Subject: [Psidev-ms-dev] precursor/product/neutral loss/SRM/MSE/MS3 scans
>
>   
>> Hi All,
>>
>> To find out whether mzML is OK for various scan types, I've tried 
>> to 
>> write down some example scans of different types in mzML format. As 
>> discussed previously, precursor and neutral loss scans didn't fit 
>> well 
>> into the schema. I've tried to make a minimal set of changes to the 
>> schema to support different scan types.
>> I've uploaded scan examples (product / precursor / neutral loss / 
>> MRM / 
>> MSe / MS3) and an updated schema and sample file for discussion at:
>> http://dev.thep.lu.se/fp6-prodac/browser/trunk/mzML/scans
>>
>> In schema terms my proposal would be to generalise precursorList by 
>> renaming it to isolationList and then allow elements of types 
>> 'precursor', 'product' and 'neutralLoss', that are all of the 
>> 'IsolationType', which is about the same as the previous 
>> 'PrecursorType'. This would make it possible to accomodate quite 
>> complex 
>> combinations of scans.
>>
>> Other  observations:
>> - The isolation window width might not be known, should the center 
>> mass 
>> be given instead then? See the neutral loss example.
>> - scanList should probably be optional (as was acquisitionList and 
>> scan 
>> preciously)
>> - keyrefs are only necessary for spectrumId, other keys are checked 
>> automatically since they are ID-IDREF.
>>
>> If anyone would like to download the files using subversion:
>> svn checkout  http://dev.thep.lu.se/fp6-prodac/svn/trunk/mzML/scans 
>> scans
>> Thanks,
>>
>> Fredrik
>>
>>
>>
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