[Psidev-ms-dev] Precursor ionSelection vs selectionWindow

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

Hi All,

I may be completely wrong here, but I think that the selectionWindowList 
/ selectionWindow elements are a bit misleading when looking at the 
usage in the example files. It seems like they are used to define scan 
ranges, so scanWindow might be a better name.
For me the selection window is the m/z-window that is let through the 
quadrupole, which means that is the same as the precursor ion selection 
window.
In some experiments you would let a large mass range  through the 
quadrupole instead of the typical few mass units, so there it would be 
nice to be able to define the ionSelection as a window (instead of 
single m/z value), as I think has been requested by Rune already. Isn't 
that what 'selectionWindow' should be used for?

Second question:
Are there any mzML precursor ion scan examples? I don't get how to 
define that the first quadrupole is scanning and the last one is set in 
a triple quadrupole instrument. Maybe if the spectrum type could be set 
to Parent scan spectrum / Precursor scan spectrum (is there a CV term, I 
cannot find one), and that the scanWindow / selectionWindow is used to 
define the scan range of Q1, but where to put the m/z in Q3?  Would that 
be a second selectionWindow/scanWindow that defines Q3?  In this case, 
how to know which selectionWindow  is Q1 scan range and Q3 respectively?
Or would the Q3 m/z be put under precursor ionSelection (even if it in 
this case is a product) just to distinguish the two?

Can anyone sort this out for me?

Fredrik