Re: [Psidev-ms-dev] MS3+ spectra

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

Hi Matt,

Are there any other examples of spectra which have more than one 
precursor than the MS3(or higher) spectra? I think the general MS2 case 
would be one precursor but possibly several selected ions. The only 
situation I can  think of where there might be several possible 
precursors selected would be some kind of merged spectrum, but that 
could probably also in most cases be written as having one precursor 
with several selected ions (if not the activation conditions were 
different from each other for the original MS2 precursors).
A CV term that clarifies the order of a certain precursor in the 
fragmentation hierarchy seems like a reasonable solution to clarify this 
if needed, anyway. I guess it is not really correct in xml to just use 
the order of apperance.

-Fredrik

Matthew Chambers skrev:
> Hi all,
>
> As far as I can tell, we don't have documentation or an official example 
> of how to handle this case. Fredrik made an example for this and sent 
> this example to the list on 12/28/2008:
> http://dev.thep.lu.se/fp6-prodac/svn/trunk/mzML/scans/5.ms3_scan.txt
>
> I'm concerned about the use of multiple precursors to represent the 
> precursor "history." This seems quite confusing. Most of the time I 
> would expect to see one precursor for the MS3 and if I wanted to know 
> what the original MS precursor was, I'd look at the MS2's precursor. 
> However, I can see that a method with a targeted MS3 (i.e. precursor and 
> 1st generation product masses already known) might not even record the 
> intermediate MS2 spectrum. So specifying the precursor hierarchy is 
> sensible, but IMO we need to do it in a distinct way from the way we 
> list multiple precursors that actually were fragmented to create the 
> current scan. A clear solution to me seems to be to allow precursor to 
> have a precursorList child element to explicitly indicate that the 
> nested precursorList represents a previous generation of fragmentation. 
> This is quite messy implementation-wise though, so another option is to 
> use a cvParam in the precursorList to explicitly indicate what it means 
> to have multiple precursors. This would mean that you couldn't mix 
> multiple isolation windows with MS3+ though.
>
> Thoughts?
> -Matt
>
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