The disclosure features mass spectrometry systems that include: an ion source; a module featuring an ion trap, an ion detector, and a module housing that at least partially surrounds the ion trap and the ion detector; and a vacuum pump featuring a housing having a recess dimensioned to receive the module, so that when the module is positioned within the recess of the vacuum pump housing, a portion of the module is surrounded by the vacuum pump housing, and during operation of the system, the ion source, ion trap, ion detector, and vacuum pump are connected along a common gas flow path and heat is transferred from the vacuum pump to the module.