[Psidev-ms-dev] MS3+ spectra

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

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