When acquiring data using MSMS, tof-MRM MS methods, or using DDA methods that contain an include list, it is possible that when viewing the data back in the MassLynx spectrum window the quad set mass may be slightly different to that specified in the method
Similarly with DDA analysis, where the instrument is told to run a specific Quad set mass as directed from the MS survey acquisition, the mass in the survey scan and the mass in the result MSMS spectrum header may differ
When doing an MSMS/DDA switching experiment the recorded Set Mass as reported in the Spectrum header or in Spectrum -> SpectrumQTOF -> SetMass in the resulting raw file differs from the value set in the MS method, and from the mass shown in the peak annotation.
Example of MSMS data from a Synapt G2-Si
Example of DDA data from a Xevo G2-XS Q-tof
This seems to be linked with having a calibration loaded - if uncal.cal is loaded the read back fault is not seen
This is caused by a bug in the way MassLynx reports the set mass in the spectrum header. The set mass applied by the quad during acquisition is correct, but the mass reported in the spectrum header has a calibration incorrectly applied. This bug has been investigated by waters software developers but it found not to be possible to fix without causing other issues.
This also adversely affects Unifi post processing of data from the affected instruments. See article 28317