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

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

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/trun/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
> 
> 
> 
> --------------------------------------------------------------------
> ----------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, 
> Nevada.The future of the web can't happen without you.  Join us at 
> MIX09 to help
> pave the way to the Next Web now. Learn more and register at
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>