Scan or SIM mode?

SIM mode

A quadrupole mass filter can be operated in two different modes. These modes are termed Scan and Selected Ion Monitoring (SIM). In SIM, the mass filter is set to pass one ion. This setting is maintained for a relatively long period of time. This mode is used when the analyst has prior knowledge of what ions to expect. By spending our time looking only at expected masses, we achieve better averaging, more data points, and a definite improvement in signal-to-noise. This mode provides the greatest sensitivity and is used for quantitative applications.

Scan mode

In Scan mode, the mass filter is set to sequentially operate through a range of masses. For general unknowns, the selected mass may initially be at 100, then 101, then 102, and so on. This mode is used when the analyst does not have prior knowledge of what ions to expect. This mode is used to generate spectra for interpretation or a library search. This mode produces fewer data points, worse signal-to-noise and less sensitivity than SIM. But because we are obtaining the entire spectra, we can then do spectral interpretation or library matching. With careful optimization, it can do an adequate job of quantitation.


Newer mass spectrometers have electronics that are fast enough to be able to perform both scan and SIM acquisition during the same run. First a scan will be performed followed by the SIM.This interleaving acquisition continues throughout the run. Two acquisition files are created: one for the SIM data and one for the scan data. The data analysis can use one or the other, or both.For a given hardware design, the operational parameters of the mass spectrometer are set by the user to provide for the sensitivity and accuracy demanded by the analysis method. Parametersare set in the following areas:

Tuning: set lens voltages, resolution, detector gain, ...Acquisition: set mass range, mass filter mode (scan or SIM), time range, ...

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