Baking will be indicated by non-quantitative carryover from one injection to another, which may arise from either from syringe contamination or inlet contamination. If the source of the contamination is suspected to be the inlet, change the septum and inlet liner and check for improvement. If there is still contamination, try baking the inlet at a temperature considerably hotter than that used for the analytical method, but below your column maximum temperature. You may also wish to set the column temperature to an elevated value (slightly higher than the final temperature of the analytical method, but below the column maximum temperature). The instrument should be baked for several hours.
The MS should NOT be acquiring data during the bake-out, unless there is some compelling reason to do so.