Data processing and automation in Fourier transform mass spectrometry

Ultra-high resolution mass spectrometers produce large amount of MS and MS/MS spectra, whose interpretations may not be easy even for experts in this field. Noise among other interfering problems (such as chemical background, side lobes, side bands, multiple harmonics) gather in those spectra and make them complex. Moreover, all physical characteristics (resolution, peak shape, signal to noise ratio and signal intensity) of mass spectra originate and are actually derived from their corresponding frequency spectra, which are generally obtained by applying Fourier transform to time domain detected transients. In this chapter, several data processing techniques will be discussed for obtaining magnitude and absorption modes frequency spectra and a review of most important mass calibration equations will be discussed in great detail. De-noising, peak alignment, sum formula calculations and batch processing of FTMS spectra will also be discussed in this chapter. Moreover, automation of FT-ICR mass spectrometers is reviewed here and the author illustrates in this chapter a hand-on technical experience for achieving a successful full automation of the 12. T FT-ICR mass spectrometer in Helmholtz Zentrum München metabolomics research laboratory, which could greatly enhance the productivity, by efficiently running in unattended mode on 24. h basis. We selected over 135 related references in signal processing and automation in an attempt to provide a comprehensive guidance to mass spectrometry scientists.