fixing precursors property

[liquidcarbon]

otherwise error:

site-packages/pymzml/spec.py in precursors(self)
    169             precursor(list): list of precursor ids for this spectrum.
    170         """
--> 171         if self._precursors is None:
    172             precursors = self.element.findall(
    173                 "./{ns}precursorList/{ns}precursor".format(ns=self.ns)

AttributeError: 'Spectrum' object has no attribute '_precursors'

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[MKoesters]

Hi @liquidcarbon ,

Thanks for your contribution! I'll have a look at the PR, I might change your fix a little bit.

Please also notice that precursors is deprecated, I suggest you switch to using selected_precursors

Best, Manuel

[liquidcarbon]

Please also notice that precursors is deprecated, I suggest you switch to using selected_precursors

Thanks for looking into it! My impression was precursors gives you MS1 scan ID whereas selected_precursors return mz and intensity (and sometimes charge, if provided in MZML). MS1 scan ID is helpful, would be nice to keep it.

Speaking of charge, do you happen to know why in MZML files sometimes you have charge information, and sometimes don't?

                <selectedIon>
                  <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="388.712829589844" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
                  <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2"/>  # sometimes this line is absent
                  <cvParam cvRef="MS" accession="MS:1000042" name="peak intensity" value="4.435413823438e07" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of detector counts"/>
                </selectedIon>

[MKoesters]

Ups, the spectrum ID was supposed to be already part of selected_precursors, precursors will definitely stay until it moved to selected_precursors

Speaking of charge, do you happen to know why in MZML files sometimes you have charge information, and sometimes don't?

I actually don't know, but I could imagine that the mass spec was simply not able to determine the charge state (maybe due to low resolution for older instruments or missing isotope peaks? @fu @StSchulze Do you have any idea why that happens?