I have a 6495C. I performed a check tune and noticed that the abundances were low so I performed an autotune. The autotune abundances were still low so the capillary was changed. After changing the capillary, the autotune would not pass. I autotuned the polarities separately and was able to get positive mode to pass (beautifully), but negative would not. Doing a negative Q1/Q2 scan in manual tune I found that Q2 was looked great, but Q1 the masses were severely shifted from the assigned masses. I thought maybe a corrupt tune file, but loading older tune files and tuning from default did not resolve the issue. In addition, higher masses not seen in the scan and the middle masses are only seen in the widest resolution -- unit resolution is almost a flat line. I have attached photos of the negative Q1 scan for each mass width. The weird thing is that it is only Q1 and only in negative. I thought maybe the ion funnel or Q1 was contaminated in some way, but if that was the case then positive would not look great. I'm racking my brain trying to figure out the issue.
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