[Psidev-ms-dev] Standardize representation for MS^e and AIF

[Chambers, M. <mat...@gm...>]

Hi all,

Over the last few months there have been quite a few users asking me about how to distinguish the low and high energy levels in MS^e [1]. It 
seems most users expect them to correspond to MS1 and MS2 (most of the users were actually reporting all MS^e scans being the same MS level 
as a bug). As far as I know, reporting both low and high energy MS^e spectra as MS1 is the current standard approach. But it seems obvious 
that users need a way to distinguish between the low and high energy spectra, so something needs to change with mzML. I see a few options 
and there may be others.

1. Keep the existing schema: continue treating low energy spectra as MS1, but treat high energy spectra as MSn (ms2) with an isolationWindow 
the same width as the scanWindow, and add a bogus selectedIon in the middle of the window.

2. Change the schema: make isolationWindow and selectedIonList optional so collision energy can be stored in the activation element without 
specifying bogus window/ion information.

3. Change the schema: allow the activation element in either the <scan> element or the <precursor> element? This would avoid the need to 
have a "precursor" for a spectrum which really doesn't have one.

With either option 2 or 3, there are a few aspects to decide:
   a. Should low energy MS^e spectra be considered MS1 or MSn (ms2)? If MS1, should they still have an activation element in order to 
preserve collision energy info?
   b. If low energy spectra are treated as MS1, should high energy spectra be considered MS1 or MSn (ms2)? High energy spectra certainly 
need the activation element.
   c. Should MS^e spectra get their own spectrum type instead of trying to shoehorn them into MS1/MSn? Perhaps a general term like 
"broadband fragmentation spectrum"?

It's not clear to me which option is the best, but if I had to choose I'd probably pick 1. Because it won't force schema-validating parsers 
to update, and old software will still be able to read the new files (but that would only be a good thing in SOME cases; in other cases the 
software should probably give an error that it can't handle that kind of data).

This has been an outstanding issue for mzML for a while. I hope we can finally get it resolved.

Thanks,
-Matt


[1] Briefly, MS^e is a data-independent-acquisition method where all ions are fragmented simultaneously rather than isolating any specific 
precursors. It's up to the analyzing software to make sense of the resulting complex spectra by looking at how the peaks change over time. 
The technique may or may not be combined with ion mobility separation (HDMS^e ). The spectra are acquired in an every-other-scan scheme, 
i.e. low-high-low-high-low-high. Low energy spectra have very little collision energy, but it's not exactly zero.
^