UNIFI finds no components in SYNAPT G2-Si MSMS data - WKB28317

SYMPTOMS

• UNIFI fails to find components in MSMS data, although the parent mass peaks are clearly present in the Investigate tab

ENVIRONMENT

• UNIFI 1.8.2
• UNIFI 1.9.4
• SYNAPT G2-Si
• SYNAPT G2
• Synapt
• Q-Tof Premier
• MassLynx 4.1
• MassLynx 4.2

CAUSE

This is a problem with MassLynx MSMS data generated on Q-Tof instruments (see article 28313). Rather than recording the peak mass of the integrated spectrum peak when MassLynx stores a scan of data, the requested set mass is initially defined to the electronics to record the data. When MassLynx reads that scan of data back in, it incorrectly applies the TOF calibration to the given set mass before writing it to disk within the scan stats, which are then stored within the raw file. When the data is imported into UNIFI, it takes the incorrect peak mass in the MassLynx data as the observed m/z of the parent ion. This is often so different than the expected mass in the UNIFI processing method that it falls outside the mass tolerance specified in the Target by Mass section of the UNIFI method. Hence, UNIFI cannot match the observed mass to the expected mass.

FIX or WORKAROUND

UNIFI 1.9.4 and earlier : The only known workaround is to increase the mass tolerances in the UNIFI processing method. You might need to go to 40 ppm. However be aware that this will likely result in false positive identifications.

This problem does not occur in waters_connect with UNIFI 1.9.13 (and later versions). When MassLynx MSMS data is imported into waters_connect with UNIFI 1.9.13 the software does not read the set mass from the MassLynx spectrum header file. Instead it calculates the set mass from the spectrum data, which gives the correct set mass value.and allows more rigorous mass tolerances to be used in the processing method.

ADDITIONAL INFORMATION

This same problem is likely to affect DDA data imported to UNIFI from an affected instrument / MassLynx version, including MassLynx MSMS or DDA data acquired on Xevo G2-XS.