more robust scan number retrieval from mzIdentML

[vladpetyuk]

Not every SpectrumIdentificationResult containst "scan=" substring in the spectrumID attribute. See specifications of spectrumIDFormat on page 10 of mzIdentML specification. Consider switching to extracting through MS:1001115 element of PSI-MS controlled vocabulary.

[lgatto]

Is this something that is available in MSnbase or mzR, or something we could add?

[vladpetyuk]

Actually, it looks like openIDfile() does not return what is stored in cvParam elements. mzID does. More importantly at this point is to understand if this is the right place to extract scan numbers. It looks like MS:1001115 listed as obsolete (whatever that implies) in the vocabulary. Do you have any input on that?