Assembly of a freeze dryer and a separate transport vehicle that is mobile with respect to the freeze dryer, wherein the freeze dryer comprises a freeze dryer housing with an access opening towards an inner freeze drying chamber inside the freeze dryer housing, multiple shelves that are arranged spaced apart above each other inside the freeze dryer chamber and provided with a horizontally extending first flat supporting surface for supporting containers, or vials, and a side edge in front of the access opening, wherein the mobile transport vehicle comprises a mobile undercarriage supporting, a storage housing with an access opening towards an inner storage chamber, a carrier provided with a second flat supporting surface for supporting the containers inside the storage housing, and a container shifter for pushing out containers away from the second flat supporting surface in a pushing out direction parallel to the second flat supporting surface, wherein the carrier comprises a plate shaped abutment extension on which a part of the second flat supporting surface or its elongation extends, a front mounting part under the abutment extension, and a gripping extension that is connected to the front mounting part and that is at least partly directed towards the abutment extension, wherein the transport vehicle is configured for aligning the carrier with one of the shelves on a vertical height in which the abutment extension extends above the first flat supporting surface and the gripping extension at least partly extends under the side edge, and for moving the carrier towards that shelf in order to confine the side edge between the abutment extension and the gripping extension.