In one embodiment a method of controlling an engine system includes providing a first cylinder with a first inlet valve, a first outlet valve, and a first throttle, controlling the first inlet and the first outlet valve in accordance with an SI valve lift profile, activating a first spark in the first cylinder while controlling the first inlet and the first outlet valve in accordance with the SI valve lift profile, controlling the first inlet and the first outlet valve in accordance with an HCCI valve lift profile, activating a second spark in the first cylinder while controlling the first inlet and the first outlet valve in accordance with the HCCI valve lift profile, and controlling the SOI timing of the first throttle in an HCCI SOI mode while controlling the first inlet valve and the first outlet valve in the HCCI valve lift profile after activating the second spark.