Investigate parsing of mzIdentML `SubstituteModification` entries

[RalfG]

A concrete use case this happens is with Mascot search results. For example, this mzIdentML snippet is from exporting results of a search against SwissProt:

   <Peptide id="peptide_28284_10">
     <PeptideSequence>APLLVPGFCVAXNQPTMR</PeptideSequence>
     <Modification location="0" monoisotopicMassDelta="144.102063">
       <cvParam accession="UNIMOD:214" name="iTRAQ4plex" cvRef="UNIMOD" />
     </Modification>
     <Modification location="9" residues="C" monoisotopicMassDelta="45.987721">
       <cvParam accession="UNIMOD:39" name="Methylthio" cvRef="UNIMOD" />
     </Modification>
     <SubstitutionModification location="12" originalResidue="X" replacementResidue="A" />
   </Peptide>

Originally posted by @vrkosk in https://github.com/compomics/ms2rescore/issues/106#issuecomment-2014909164