An automated biological specimen preparation and mass spectrometry analysis system for analyzing a plurality of biological specimens, comprising: a sample preparation system comprising a sample preparation station and a sample preparation controller , the sample preparation system configured to prepare samples taken from the plurality of biological specimens; and a sample analysis system comprising a sample analysis station and a sample analysis controller , the sample analysis system including a mass spectrometer configured to quantify one or more analytes in one or more of the prepared samples, the sample analysis station including one or more liquid chromatography pumps and at least one liquid chromatography mobile phase container; characterized in that the automated biological specimen preparation and mass spectrometry analysis system for analyzing a plurality of biological specimens further comprises a transport assembly including a robot assembly operating on one or more tracks configured to move at least one liquid sample between the sample preparation station and the sample analysis station; the sample preparation station and the sample analysis station being contained within a compartmental unitary cover permitting isolation of each of the sample preparation station and sample analysis station, such that the sample preparation station is positioned substantially on a first side of the system, at a height that is greater than a height of a base of the mass spectrometer; the mass spectrometer being positioned substantially on a second side of the system that is opposite to the first side, at a height that is less than a height of a base of the sample preparation station; and the at least one liquid chromatography mobile phase container being positioned at a height that is greater than a height of the one or more liquid chromatography pumps. a sample preparation system comprising a sample preparation station and a sample preparation controller , the sample preparation system configured to prepare samples taken from the plurality of biological specimens; and a sample analysis system comprising a sample analysis station and a sample analysis controller , the sample analysis system including a mass spectrometer configured to quantify one or more analytes in one or more of the prepared samples, the sample analysis station including one or more liquid chromatography pumps and at least one liquid chromatography mobile phase container; characterized in that the automated biological specimen preparation and mass spectrometry analysis system for analyzing a plurality of biological specimens further comprises a transport assembly including a robot assembly operating on one or more tracks configured to move at least one liquid sample between the sample preparation station and the sample analysis station; the sample preparation station and the sample analysis station being contained within a compartmental unitary cover permitting isolation of each of the sample preparation station and sample analysis station, such that the sample preparation station is positioned substantially on a first side of the system, at a height that is greater than a height of a base of the mass spectrometer; the mass spectrometer being positioned substantially on a second side of the system that is opposite to the first side, at a height that is less than a height of a base of the sample preparation station; and the at least one liquid chromatography mobile phase container being positioned at a height that is greater than a height of the one or more liquid chromatography pumps. <EOS>