mzML reader enforces order of MS1 and MS/MS spectra in the file

[andzajan]

Hi,

Curent implementation of the mzML parser is assuming that MS/MS spectrum in the file is preceeded by MS1 spectrum, but this is not required by mzML specification, see
https://github.com/smith-chem-wisc/mzLib/blob/master/mzLib/Readers/MzML/Mzml.cs#L1092-L1100

For example if have a file where MS/MS spectra are listed at the beginning with MS1 data being refrenced and listed after all MS/MS scans.

For example, if MS/MS spectrum has index of 0 method GetOneBasedPrecursorScanNumber will return hard to interpret error message.

MS/MS spectrum meta data:

<spectrum index="0" id="controllerType=0 controllerNumber=1 scan=1" defaultArrayLength="23" dataProcessingRef="SpectrumSelector">`

<precursorList count="1">
     <precursor spectrumRef="controllerType=0 controllerNumber=1 scan=2880">

And corresponding MS1 specttrum in the file has index 2879:

<spectrum index="2879" id="controllerType=0 controllerNumber=1 scan=2880" defaultArrayLength="29086" dataProcessingRef="SpectrumSelector">`

Would it be possible to change this function not to enforce order of the MS1 MS/MS spectra or at least report descriptive error?