non integer m/z values on 5977

Most really need that level of reporting. Many ions are not exactly on the integer and knowing how close they are to what is expected helps with identification, seeing problems, and troubleshooting.

To set whole mass units - 

There is allowable mass axis drift at the 0.1 amu level. Tuning or just doing a mass axis calibration resets it. Typically the mass axis does not move much at all over a few days.

The ions created in the ion source and filtered by the instrument are always perfect.  For example, 69, 219, and 502 in your autotune are really 68.9946, 218.9852, and 501.9709.  The tune ion peak shape in a single quad GCMS is due to the filter limitations of an eight inch quadrupole with the ions travelling Mach 6-10 down the length.

Thanks for the explanation Paul. We tune everyday though so I'm surprised we are getting the mass drift.  Also, we aren't on mass hunter yet, just the regular chemstation software.  Can the same settings be changed without mass hunter? 

Our SOP has us tune every day but we can reconsider that.  We are running acquisition version B.07.06.2704 I see it also says Mass Hunter but we use the old "Enhanced Data Analysis" for all reports etc.  We probably have over 50,000 injections on each of our instruments with PMs done annually by Agilent. 

What version of "Enhanced Data Analysis" ?  Go to Help, About...

On the GC you can see how many run starts have been done:

• 8890 and Intuvo: Service Mode, Instrument, Usage
• 7890: Service Mode , Diagnostics, Instrument Status
• 6890: Options, Diagnostics, Instrument Status

The preventive maintenance service delivery does not include remedial cleaning.  One symptom is that the time between necessary source cleaning is getting shorter.  A clean source into a dirty system gets dirty sooner.

69,000 runs under service mode.  Version F.01.03.2357 for chemstation data analysis

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.

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.