[Psidev-ms-dev] Spectrum id's

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

Hi,

Looking at the latest mzData schema, if my understanding is correct,
each peak list is represented by a "spectrum" element.  I note that
these now require an "id" attribute.  It appears that this ID is then
referred to in the "precursorList" element by the attribute 
"spectrumRef", correct?

If you are processing scan data from an LC-MSMS run, normally
peak lists are only produced for MS2 scans (and potentially groups of
them).  Therefore, the MS1 scans aren't output and so have no assigned
ID.  But that means that the precursor reference in the schema is 
invalid.  Does this mean we are required to output bogus MS1 peak lists?

I'm also a little unclear on the official intended purpose of the 
"precursorList" element, is it for:

(a) Where you have say an MS3 scan and you want to list the MS2 and MS1
precursor m/z values; or

(b) Where you have merged two or more grouped MS2 scans to produce a 
single peak list and you need to list each of the original MS1 precursor 
m/z values; or

(c) All of the above.

Thanks,
Chris