Methods and systems for transmitting ions in an ion guide are provided herein. In accordance with various aspects of the applicant's teachings, the methods and systems can cause at least a portion of ions entrained in a gas flow entering an ion guide to be extracted from the gas jet and be guided downstream along one or more path of gas flow, where the gas lacking the ions can be removed from the ion guide. In some embodiments, the ions extracted from the gas stream can be guided into a focusing region in which the ions can be focused, e.g., via RF focusing, to enter into subsequence processing stages, such as a mass analyzer.