This machine is a Clarus 680GC attached to an Axion iQT mass spectrometer. This mass spectrometer is a new design which harnesses the best parts of a triple quad and a TOF spectrometer.
MS/MS analysis allows for the selected fragmentation of specific ions to aid in identification of organic and bio-molecules. Output from the initial fragmentation process (MS1) is fed into a collision cell where selected ion ranges are fragmented again (MS2). The output from MS2 provides structural information about the parent ions, aiding in their identification.
MS/MS is a leading technique in sequence determination of peptides and other bio-molecules.