Re: [Psidev-ms-dev] mzML comments

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

Chris Allen wrote:
> 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.
>   
It's not clear to me what you mean here. If you're referring to the scan 
range, that is specified in <scanWindow>.


>>> 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.
>   
If profile data is not contiguous, it must have gone through some data 
processing to do the zero thresholding (typically resulting in output 
like method 3 which preserves the integrity of each profile). That 
processing would be represented in dataProcessing:

[Term]
id: MS:1000594
name: low intensity data point removal
def: "The removal of very low intensity data points that are likely to be spurious noise rather than real signal." [PSI:MS]

[Term]
id: MS:1000629
name: low intensity threshold
def: "Threshold below which some action is taken." [PSI:MS]

If users desire the unprocessed data, that is the job of the converter, or a "data unprocessor" :)