Noise analysis for 2D tandem Fourier transform ion cyclotron resonance mass spectrometry

In principle, two-dimensional (2D) Fourier transform ion cyclotron resonanc e (FTICR) mass spectrometry offers identification of all precursor-product ion pairs (equivalent to all precursor ion scans, all product ion scans, an d all neutral loss scans), as well as relative rate constants for all precu rsor gas-phase ion-molecule reactions and distinction between fragmentation and adduction processes, in a single, automatically acquired data set. How ever, although the principles of 2D FTICR techniques were demonstrated more than ten years ago, very few analytical applications have yet been demonst rated. Here, we apply 2D FT/FTICR tandem mass spectrometry, by stored wavef orm inverse Fourier transform modulation of ion cyclotron radius (and thus ion kinetic energy), to an experimental mixture of proton-bound (and sodium -bound) amino acid dimer ions. Although several ion fragmentation pathways may be identified, interpretation is hindered by significant noise along ea ch slice passing through a precursor ion peak on the diagonal of the 2D mas s spectrum. By analogy to "t(1)" noise in 2D nuclear magnetic resonance spe ctroscopy, we are able to simulate such noise by varying the absolute and r elative numbers of trapped precursor ions in data acquisitions correspondin g to different horizontal slices of the final 2D spectrum. Signals at harmo nic multiples of the ion cyclotron frequencies are well modeled by simulati ons allowing for nonlinear dependence of product ion abundance on precursor ion cyclotron radius modulation magnitude. The present results show that s uccessful future implementation of 2D FT/FTICR tandem mass spectrometry exp eriments will require careful control of the number of trapped precursor io ns, to avoid loss in dynamic range by "contamination" of the rest of the ma ss spectrum by signals from the most abundant ions. (C) 2001 Elsevier Scien ce B.V.