Why doesn't the MSMS set mass in the header of the spectrum window match the peak mass? - WKB28313

This article is a portion of a Troubleshooting Path.  To begin troubleshooting this issue, please select the link below.

ENVIRONMENT

ANSWER

When acquiring data using MSMS, Tof-MRM MS methods, or 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 than 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 QTof

This seems to be linked with having a calibration loaded—if uncal.cal is loaded, the readback fault is not seen.

This is due to 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 was investigated by Waters software developers, but it was found impossible to fix without causing other issues.

It is important to remember that the set mass recorded in the MassLynx header is the value sent to the quadrupole electronics to allow them to exclude all but a specified mass from being passed to the collision cell and the time of flight detector for MSMS analysis. This is not the same as an accurate (to 4 decimal places) observed parent ion mass. In part this is because it does not have to be highly accurate in order for just the ion that triggered the switch to MSMS to be passed to the collision cell and the time of flight detector.

ADDITIONAL INFORMATION

This also adversely affects UNIFI 1.9.4 post-processing of data from the affected instruments. See article 28317.

When MassLynx DDA data is imported into waters_connect with UNIFI 1.9.13 the parent mass is calculated from the data rather than being read from the header file. UNIFI 1.9.13 is therefore not affected by this anomaly in MassLynx DDA data