fixing pepxml scores and spectrumID

[julianu]

Changed

• io.pepxml: Refactor spectrum naming logic to prefer 'spectrumNativeID' when available

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A fix to fetch all scores from a pepXML and use the "spectrumNativeID" for preferred spectrum naming.

[RalfG]

Thanks, @julianu! Would you say that most of these metadata values could serve as rescoring features? If so, we could put them in that PSM dictionary instead. What do you think?

[julianu]

Hej Ralf,
Yes, I think they can also be used for the rescoring (I am actually using them in my branch).
But if I remember correctly, these scores were also just not imported before this fix (sorry, don't remember 100% as it is already some time ago now).

[RalfG]

Ah, sorry. I misread the diff and thought that they were newly parsed from the file. Thanks for catching the bug!