A method of operating a transport system, in particular a multi-carrier system, which comprises a plurality of linear motors, which are arranged in a row and have a guide track, and a plurality of transport elements that are movable along the guide track by means of the linear motors, has the following steps:



generating a travel job for a first one of the transport elements for travelling along at least a part section of the guide track,
generating a first movement profile of the first transport element for the travel job based on predetermined movement characteristic values,
matching the first movement profile with a second movement profile of a second transport element directly in front of the first transport element and determining whether a predetermined minimum distance between the first transport element and the second transport element is fallen below during the execution of the travel job,
updating the first movement profile to maintain the minimum distance if it has been determined that the minimum distance is fallen below, and
controlling the linear motors to move the first transport element in accordance with the first movement profile.