Re: [Psidev-ms-dev] mzML comments

[Chris A. <ch...@ma...>]

Fredrik Levander wrote:
> Wilfred H Tang wrote:
>> For method 1 to 
>> work well, there must be a way to specify a m/z point spacing. Is 
>> there a way to do this currently? Furthermore, the program reading in 
>> the mzML must understand that the m/z point spacing implicitly 
>> requires reconstruction of all the zero-intensity data pairs; 
>> otherwise, for example, a mass spectrum plot would look funny.

Not only that, with profile data points missing it makes it very 
difficult (if not impossible) to fit the mass scale.  Then you have to 
look at alternatives like regridding the data.

>> A further complication for method 1 is that the m/z point spacing may 
>> not necessarily be a constant. For example, for the AB/Sciex QSTAR 
>> instrument, the m/z spacing is proportional to the square root of m/z, 
>> and this is a natural consequence of this being a TOF instrument.
> There is a method 3 which efficiently reduces space for profile spectra 
> which contain a lot of zeros.  All data points with zero intensity that 
> are surrounded by data points of zero intensity can be left out. If you 
> have the following arrays:
> int: 1 5 1 0 0 0 0 0 1 6
> m/z: 1 2 3 4 5 6 7 8 9 10
> These can be reduced to:
> int: 1 5 1 0 0 1 6
> m/z: 1 2 3 4 8 9 10
> This is ok to do in mzML.

If that's OK in mzML, there really should be a CV term to say "profile 
with points missing" otherwise you have to look through the data to try 
and figure out if the spectrum is complete or not.

> On the other hand, it would be very useful with a way to specify the m/z 
> spacing, since it can be quite tricky to get this for TOF data, 
> especially when a calibration function have been applied over the square 
> root spaced m/z values, so that they are no longer spaced exactly 
> proportional to the square root of m/z. Probably the initial spacing and 
> polynomial calibration functions could be specified using CV terms, just 
> that such terms are not in the CV (yet). Suggestions for this would be 
> welcome.

Agreed, but I suspect many instrument vendors will be unwilling to 
divulge their calibration functions/constants.

Regards,
Chris