Ion mobility data cannot be imported into Progenesis QI - WKB58911

SYMPTOMS

• Ion mobility data cannot be imported into Progenesis QI
• MS data from the same instrument can be imported into Progenesis QI

ENVIRONMENT

• SYNAPT G2-Si
• MassLynx 4.2 SCN 983
• Progenesis QI

CAUSE

The problem is caused by the options selected in the IMS acquisition method.
If you select the "Add Drift Time Function" option on the Mobility tab of the MassLynx method editor, it saves the mobility data as collapsed retention time data to a separate function in the Raw file. In other words it creates a function_1.cdt file containing the IMS data but also saves the same data as a RT/mz file called function_2.dat. This option is intended only for infusion data, not for data created using LCMS, or UPC2MS.

If you look at both Driftscope and MassLynx simultaneously, the problem is clearer. In the Drifscope window, only function 1 is open, which shows both the .dat (MS chromatogram) and .cdt (IMS) data for function 1. In the MassLynx window, the function 1 .dat file and the function 2 .dat files are open. This shows that the function 2 .dat chromatogram (bottom trace) in MassLynx is identical to the function 1 .cdt (mobility) function (bottom trace) in Driftscope, except that MassLynx is treating the drift bins as retention time

FIX or WORKAROUND

1. Modifiy the IMS method by clearing the selection of "Add Drift Time Function".
2. Save the modified method.
3. Reacquire the data using the modified method.
4. Import the new data into Progenesis QI.

ADDITIONAL INFORMATION