A mass spectrometer comprising: an atmospheric pressure ion source for generating analyte ions; a first vacuum chamber having a first axis; a nozzle-skimmer interface separating said first vacuum chamber from said ion source wherein at least some analyte ions generated by said ion source are transmitted, in use, through said nozzle-skimmer interface into said first vacuum chamber, wherein the direction along which the at least some analyte ions are transmitted through said nozzle-skimmer into said first vacuum chamber defines said first axis; a glow discharge device for generating Electron Transfer Dissociation reagent ions, said glow discharge device being maintained, in use, at a pressure in the range 0.01-100 mbar; a device (16, 19) for supplying reagent vapour to said glow discharge device so that Electron Transfer Dissociation reagent ions are formed in use by said glow discharge device; a second vacuum chamber comprising an ion guide, said second vacuum chamber having a second axis being defined by a transmission direction of said ion guide, wherein said second vacuum chamber is located downstream of said first vacuum chamber; and an Electron Transfer Dissociation fragmentation cell arranged in a vacuum chamber downstream of said first vacuum chamber, wherein, in use, at least some of said Electron Transfer Dissociation reagent ions are caused to interact with at least some analyte ions within said Electron Transfer Dissociation fragmentation cell so as to cause at least some of said analyte ions to fragment by Electron Transfer Dissociation; characterised in that: said second axis is orthogonal to said first axis; said mass spectrometer further comprises an isolation valve arranged in said first vacuum chamber and arranged downstream of said nozzle-skimmer interface, wherein said isolation valve comprises a first rotatable port wherein when said isolation valve is rotated to a first position then said first vacuum chamber downstream of said isolation valve is in fluid communication with said nozzle-skimmer interface and when said isolation valve is rotated to a second position then said first vacuum chamber downstream of said isolation valve is no longer in fluid communication with said nozzle-skimmer interface (8;17); and wherein said glow discharge device is located within said isolation valve. an atmospheric pressure ion source for generating analyte ions; a first vacuum chamber having a first axis; a nozzle-skimmer interface separating said first vacuum chamber from said ion source wherein at least some analyte ions generated by said ion source are transmitted, in use, through said nozzle-skimmer interface into said first vacuum chamber, wherein the direction along which the at least some analyte ions are transmitted through said nozzle-skimmer into said first vacuum chamber defines said first axis; a glow discharge device for generating Electron Transfer Dissociation reagent ions, said glow discharge device being maintained, in use, at a pressure in the range 0.01-100 mbar; a device (16, 19) for supplying reagent vapour to said glow discharge device so that Electron Transfer Dissociation reagent ions are formed in use by said glow discharge device; a second vacuum chamber comprising an ion guide, said second vacuum chamber having a second axis being defined by a transmission direction of said ion guide, wherein said second vacuum chamber is located downstream of said first vacuum chamber; and an Electron Transfer Dissociation fragmentation cell arranged in a vacuum chamber downstream of said first vacuum chamber, wherein, in use, at least some of said Electron Transfer Dissociation reagent ions are caused to interact with at least some analyte ions within said Electron Transfer Dissociation fragmentation cell so as to cause at least some of said analyte ions to fragment by Electron Transfer Dissociation; characterised in that: said second axis is orthogonal to said first axis; said mass spectrometer further comprises an isolation valve arranged in said first vacuum chamber and arranged downstream of said nozzle-skimmer interface, wherein said isolation valve comprises a first rotatable port wherein when said isolation valve is rotated to a first position then said first vacuum chamber downstream of said isolation valve is in fluid communication with said nozzle-skimmer interface and when said isolation valve is rotated to a second position then said first vacuum chamber downstream of said isolation valve is no longer in fluid communication with said nozzle-skimmer interface (8;17); and wherein said glow discharge device is located within said isolation valve. said second axis is orthogonal to said first axis; said mass spectrometer further comprises an isolation valve arranged in said first vacuum chamber and arranged downstream of said nozzle-skimmer interface, wherein said isolation valve comprises a first rotatable port wherein when said isolation valve is rotated to a first position then said first vacuum chamber downstream of said isolation valve is in fluid communication with said nozzle-skimmer interface and when said isolation valve is rotated to a second position then said first vacuum chamber downstream of said isolation valve is no longer in fluid communication with said nozzle-skimmer interface (8;17); and wherein said glow discharge device is located within said isolation valve.