non integer m/z values on 5977

MSD Chemstation Data Analysis F.01.03.2357 is the currently sold version.  Agilent supports the current version and one revision back of software so if you can't quickly find an answer in help call your country's toll free number and ask....or post here, but it might be a bit longer to get an answer here.

Select "Options" and the "Show Command Line"

Click in the command line and type       mzdecimal 0      <enter>

and at the bottom it will show:

and then spectra will look like this:

You can zoom once and they're still whole numbers:

but zoom twice and it give tenths:

Does that give you what you want?

69,000 runs is quite a lot of runs, depending on the samples, sample prep, concentrations, number of peaks, amount injected, inlet mode, etc....but still quite a few for a not incredibly old GCMS.   Next PM, ask your local Field Service Engineer about what more can be easily cleaned while the system is vented and the source is removed.

That's what I was looking for but when I print a report with our macro I still get the decimal values.  It sounds like values may be off from the integers because of a dirty system but our tune looks OK.  Is this a problem with the tuning or just the way the system is?  The values can change over a sequence too.

If you're running a custom macro you'll need to talk to whoever wrote it.   Those abundances are incredibly tiny. Allowable electronic signal is somewhere around 50 counts, so unless that is background subtracted the only really useful ions there are 269.2, 327.2, and 369.2.

The ion values are not off if they show some tenths of an amu. The system scans in 0.1 amu steps and the perfectly chemistry/physics formed ions may be at any of the 0.1 amu steps.  If your hardware tune is good, the tune ion peak shapes are symmetrical, at the proper locations, and the relative ion ratios are in the allowable ranges, there's more than likely nothing wrong with the MS.