mzML is a hot topic, and some changes are ahead. There is a preliminary package mzR which you can find at https://github.com/sneumann/mzR
This package grew out of the mzML code in XCMS, and (c|sh)ould become the affyIO for MS in Bioconductor.
Before mzR is accepted into BioC, you will have to use the patched XCMS version at https://github.com/sneumann/xcms (which is highly experimental !!!!)
Please do report all your findings, we already have a collection of files where e.g. MS2 data information is absent, but depending on your use case it might be sufficient.