Re: [Psidev-ms-dev] Unique scan numbers

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

How do you feel about generating arbitrary unique scan numbers and then 
using the id attribute to preserve the original filename and scan number:
<spectrum id="function1.1" scanNumber="1" ...>
<spectrum id="function1.2" scanNumber="2" ...>
...
<spectrum id="function2.1" scanNumber="100" ...>
<spectrum id="function2.2" scanNumber="101" ...>
...

Or probably more intuitive would be to store the parallel spectra 
sequentially (assuming that the same scan number from each function is 
correlated):
<spectrum id="function1.1" scanNumber="1" ...>
<spectrum id="function2.1" scanNumber="2" ...>
...
<spectrum id="function1.2" scanNumber="100" ...>
<spectrum id="function2.2" scanNumber="101" ...>
...

It's either that or store each function in a separate mzML file, because 
mzML doesn't support multiple runs in the same file.

-Matt


Fredrik Levander wrote:
> Hi All,
>
> In QTOF files from Waters with mixed MS1 and MS2 data we have several 
> parallel 'functions' with data being recorded into separate files. The 
> scan numbers are only unique within each function. In the raw data 
> folder we thus have several different spectra with the same scan number 
> (but different source files). When converting this into an mzML file it 
> would be good to keep the original scan numbers which are useful for 
> traceability, but to generate unique spectrum ids. I thus propose that 
> the requirement for unique scanNumbers within an mzML file is removed. 
> However, spectra should not be repeated within the file, so this would 
> NOT be applicable to the dta to mzML conversion use case.
> Would such a change generate problems for the readers?
> How is this solved in MassWolf?
>
>
> Regards
>
> Fredrik
>
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