Ghost peaks and sudden baseline shifts

No, I didn't realize that. The lightest component I would be interested in is around 44 MW. Do I do that via the Tune and Vaccum menu?

No it's in the method. Go to edit entire method and go through the screens. I forget exactly where it is in the MS area of the method, just look around or look in the manual if you have one or the help in the software.

You can change your scan range under MS Parameters.  Go to Method and Run Control view, I think it is Instrument menu, Edit MS Parameters.

Some gas filters cartridges are filled with N2 during manufacturing for shipping, so it takes some time after installation to purge it all out.  The low O2 shows that it's not a leak.  (Air leak would have N2/O2 ratio approx. 4.)  Agilent's Gas Clean filters are like this.  When I install one on a new system, I'll set the split flow to 250-300 mL/min overnight to purge the N2 from the filter.  Argon (40) sometimes shows up as an impurity in helium, and a gas filter won't remove it.

You can change your scan range under MS Parameters.  Go to Method and Run Control view, I think it is Instrument menu, Edit MS Parameters.

Some gas filters cartridges are filled with N2 during manufacturing for shipping, so it takes some time after installation to purge it all out.  The low O2 shows that it's not a leak.  (Air leak would have N2/O2 ratio approx. 4.)  Agilent's Gas Clean filters are like this.  When I install one on a new system, I'll set the split flow to 250-300 mL/min overnight to purge the N2 from the filter.  Argon (40) sometimes shows up as an impurity in helium, and a gas filter won't remove it.

Yes, I've seen this a few times (Ar contamination in the helium giving a strong 40 m/z). Only solution is to change the cylinder. I have also seen high N2 so much that it affected the ability to tune. This was due to having the wrong cylinder attached to the helium line.