This invention relates to mass spectrometers comprising a reaction cell and where mass spectra are collected both from unreacted ions and also from reaction product ions. In particular, although not exclusively, this invention finds use in tandem mass spectrometry where mass spectra are collected from precursor and fragment ions. The present invention provides an arrangement where ions may be sent to a reaction cell for fragmentation or other processing before onward transport to a mass analyser. Alternatively, ions may be passed directly to a mass analyser along a bypass path.