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.
