If you have a few more details that would be great. I will make an assumption that you have a 5977 MSD . The extractor tune is built from the autotune so the autotune has to be run first creating a valid Atune file. If the Autotune has been reset to default or is not valid for some reason, then autotune first, followed by the extractor tune. Also if you have just installed the extractor source, please make sure the wiring is correct. If none of the above solves your issue, please feel to contact Agilent service for live help or post a reply.
Did James suggestion help you? If it did please mark it as correct answer. If none of the above solves your issue, please feel to contact Agilent service for live help or post a reply.
Thank you for the response.
The problem is resolved now. I had tried to reconfigure the instrument followed by auto tune and etune but etune didnt worked. I was looking at the auto tune parameters and the Entrance voltage offset was on the higher side that suggested some leak or vaccum pressure not optimal (although, the abundance for m/z 28 and 18 were very low and the instrument passed the tune evaluation). I vented the instrument and cleaned the source and after installing it again, things worked fine. I have to admit that the source was dirty though and it may affect the ion body voltages and thereby extraction source tune.