Post-interface signal suppression, a phenomenon observed in a single-stage Orbitrap mass spectrometer coupled to an electrospray interfaced liquid chromatograph

Signal suppression is a common issue when analyzing compounds by liquid chromatography coupled to mass spectrometry (LC/MS/MS). Suppression of signals is caused by co-eluting matrix compounds and is thought to take place in the interface. This paper reports strong signal suppression effects which were observed when using a single-stage Orbitrap instrument which was coupled by an electrospray interface to a liquid chromatograph. This type of signal suppression (often the complete loss of certain analyte signal) is observed in addition to signal suppression originating in the electrospray interface. The location of where this phenomenon occurs was shown to be clearly beyond the interface region. It was suspected that not the Orbitrap cell itself, but the C-trap, which is an integral part within the Orbitrap instrument, was the probable location. Such post-interface signal suppression was observed and could be experimentally induced when multiply charged ions (e.g. electrospray protonated proteins) were co-eluting with the analytes. High concentrations of proteins, yet not exceeding the maximum ion capacity of the trap, can cause a complete loss of all low m/z masses. This paper describes the practical implication when analyzing heavy matrix samples and discusses strategies to reduce such detrimental effects. Copyright (C) 2010 John Wiley & Sons, Ltd.