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How to calibrate MS over an extended high mass range using sodium iodide (NaI) or similar salts in MassLynx for SYNAPT G2 and Xevo G2 and later - WKB18128

Article number: 18128


Improve speed and reliability when calibrating QTof systems over an extended mass range 100 m/z to 4000-5000 m/z using the Assisted IntelliStart Calibration procedure.


  • Xevo QTof
  • Xevo G2 QTof
  • Xevo G2-S
  • Xevo G2-XS
  • SYNAPT G2-Si


  1. Tune for specific resolution for the mode of interest. Peaks that are deemed to be of subpar resolution are not picked and may have a "!" flag. The setting in the instrument setup panel (Settings > Instrument setup) dictates the expected resolution.
  2. Change the MS profile to a fixed 2000 m/z.
  3. Create a suitable Assisted Calibration profile using NaI reference file - MS mode - with 22 Volts Collision energy.
  4. Run the calibration routine as normal, and note that the ion profile has a more uniform distribution.
  5. Ensure that the DRE setting IntelliStart chooses for intensity dilution is at least 5%, preferably above 10%.
  6. When the acquisition finishes, use the peak picking window view to ensure that all reference peaks are automatically picked and that none is flagged with "!".
  7. If RMS error is 1 ppm or less, accept the calibration. 


To accurately calibrate the system, the IntelliStart procedure requires a statistically relevant signal for each peak over the entire mass range requested.

NaI in ESI produces a bell curve distribution, with lower intensity the higher in mass.

If peak intensities are saturated, too small, or of incorrect resolution, they cannot be used for calibration.

The software makes measurements of the intensity and adjusts the signal by using the DRE lens.

This reduces the entire signal height so that, at maximum, it is 0.5 IPP (TDC mode).

Because sodium iodide has a predominance at low mass, detuning leaves the high >4 kDa peaks extremely small.

To obtain good peak centering statistics, the system may need to acquire for a considerable time.

Suggested here is way around the issue by using the MS profile to effectively filter out the low mass but high intensity signals and then, with judicious application of collision energy, recreating some of the low mass population reference ions.


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