A sample plate handling system for a time-of-flight mass spectrometer includes a transport chamber and a mass spectrometer chamber that is mechanically coupled to transport chamber. A two-dimensional translation stage is positioned in the mass spectrometer chamber. A sample plate transporter is mounted on the two-dimensional translation stage. A first portion of the sample plate transporter is mechanically attached to the two-dimensional translation stage. A second portion of the sample plate transporter defines a sample plate receiver that is positioned in the transport chamber. A sealing surface located between the first and the second portions connects the transport chamber and the mass spectrometer chamber. A motion of the two-dimensional translation stage in one direction aligns the sample plate transporter with the sealing orifice and a motion of the two-dimensional translation stage in the other direction moves the sealing surface of the sample plate transporter to engage the sealing orifice, thereby preventing gas flow between the mass spectrometer chamber and the transport chamber.