Sources of negative peaks in hadamard transform/fourier transform mass spectrometry/mass spectrometry

Multidimensional approaches to tandem Fourier transform ion cyclotron resonance (FTICR) mass spectrometry/mass spectrometry (MS/MS) have been developed in recent years for structural characterization of species in mixtures. One approach, using Hadamard S-matrix encoding of precursor ions followed by dissociation, often produces data containing anomalous peaks with 'negative' intensity. Variations in product-ion abundance between experiments have been cited as the factor leading to the appearance of such negative peaks. Here, the effects of amplitude and frequency differences on the relative amplitudes of peaks for simple magnitude-mode difference spectra of two Lorentzians are simulated and discussed within the context of the negative peaks observed in Hadamard transform FTICRMS/MS. The simulations show that both amplitude and frequency variations in the product-ion peak shapes will lead the appearance of negative peaks. Means of eliminating negative peaks from the Hadamard FTICRMS/MS experiments are discussed and evaluated.