MS TIP No. 16 - INCOS Procedure for Calibrating on the Finnigan 4500


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by John Delaney

Affiliation: Betz Laboratories

I subscribe to the Mass Spec Source and have found it to contain lots of useful information and timely tips. This tip describes an Incos procedure to use while calibrating that your readers should find valuable.

While tuning and calibrating on a Finnigan 4500 (operating under SuperIncos) it is desirable to maximize the intensity of the FC43 ions, or any other cal gas for that matter, without saturating any of the dominant ions (eg. 69 m/z for FC43). Instead of acquiring a few scans at one EM voltage, checking the ion abundances in LIST, adjusting the EM voltage and re-acquiring, one can obtain a mass spectrum at the correct multiplier setting in this way:

Tune the MS

Set the electron multiplier (EM) to a moderately low value, eg. -1200V

go into ACQuire and type G25;e;KAL

KAL is a macro written in executive:

KAL = map/c (v1000000;d1,25;e)

= chro (i;69;d1,25)


While monitoring the MS signal in MAP, increase the EM voltage ca. 100 V every 5 scans until 25 scans are acquired. At the end of the acquisition, the macro automatically displays the data with a mass chromatogram. The point where the 69 m/z peak saturates is easily seen (ticks), and the scan with which to calibrate can be taken from the previous plateau.

Figure 1.