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Added @XmlRootElement annotation to MzIdentMlType JAXB class to enable proper marshalling.
Changed how precursor ions are reported. PrecursorInfo now provides mzTarget as the actual targeted m/z, and also mzTargetMono, which is the assumed monoisotopic m/z of that ion.
Fixed regression bug in mzXML header parsing. Original files without parent location were causing NPEs.
PepXML parser updated to pepxml schema v120. Includes PTM Prophet and related changes.