non integer m/z values on 5977

On a 5977 MS the reported m/z values are usually integer values but some are non-integer values.  What causes this?  Can this be prevented?   For example, in my alprazolam spectrum I see 204.1, 162.9, 115.3, 119.1.  Why aren't these whole mass units?  Sometimes it presents a problem because our standard might have mass value 115.1 and 115.6 but our sample has 115.3.

  • 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? 

  • 0.1 amu on a unit mass instrument like the MSD is not much drift at all.  See this blog: Don't Tune So Often! (+) Agilent Community .   How many runs on your system? It could be that after years of use it needs remedial cleaning including the quadrupole.  Everything that comes out of the column goes into the mass spec and that stuff accumulates and continuously redistributes on all the surfaces inside.

    What versions of Acquisition and Data Analysis software are you using?  That detail is necessary for a good answer as it changed at E.02.02.

  • 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

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