Advanced fundamentals in Fourier transform mass spectrometry

Fourier transform mass spectrometry (FTMS) is an enabling technique to many challenging applications in molecular sciences. In this chapter we revisit FTMS fundamentals to further rationalize the selection of data acquisition and data processing approaches for the everyday FTMS practice. Whereas the FT-ICR MS fundamentals have been investigated and extensively reported for more than 40 years, the same level of understanding and description is not available for the teenager and rapidly evolving Orbitrap FTMS. Despite the widespread presence of the Orbitrap technology and its exponential development over the past decade, the associated data processing procedures are not always comprehensively described in the scientific literature. With this Chapter, we thus attempt to better inform the general user about the basics in mass spectra summation (averaging) and noise characteristics, as well as the benefits and consequences of using the data reduction approaches. For the latter, we describe the principles and compare the outcome of the full profile and the reduced profile mass spectra representation. To further bridge the knowledge gap, we compared ICR and Orbitrap FTMS techniques in regard to their resolution performance reflected through the theoretical didactic examples.