Mass spectrometers have been used for a long time in a variety of biological applications. Recent years, however, have witnessed a significant increase in the employment of mass spectrometers such as of time-of-flight, Fourier transform ion cyclotron resonance (FTICR) 1 , and Orbitrap, which provide accurate mass of analytes over wide mass range. The FTICR and Orbitrap analyzers outperform any other commonly used mass spectrometer with respect to the maximum mass resolution and accuracy routinely achievable even for small numbers of ions. Both these mass spectrometers share certain features, such as an image current detection system and the application of Fourier transform mathematical operations for generating mass spectra from time domain transients produced by the image current. Consequently, they are often referred to as Fourier transform-based mass spectrometers (FTMS).The combination of FTMS with ion preselection and fragmentation devices and their coupling to reversed-phase liquid chromatography (LC) represents a ubiquitous approach to both small molecule and proteomic analyses. Multidimensional LC separations have an important role to play in proteomics applications for reducing sample complexity, and complement well the high dynamic range of detection in an acquisition offered by FTMS instruments.The current article does not intend to be an exhaustive review paper on FTMS techniques; it is intended as teaching material for scientists without a physics background to assist them with understanding the mass spectrometry tools they are called to use in their everyday laboratory work. Thus, only the fundamental aspects of FTMS which are useful to a nonphysicist are introduced. The discussion then focuses on examples of where this technology can be applied and what are the benefits as well as limitations of this technology for practical proteomic applications.Need for High Resolution and Mass Accuracy-The mass accuracy is the ratio of the m/z measurement error to the true m/z, usually quoted in parts per million (ppm). The mass resolving power (resolution) is the measure of the ability to distinguish two peaks of slightly different m/z, herein understood as full width at half maximum (FWHM). Linearity of detection and very high fidelity in the determination of frequency are inherent to FTMS and allow very high resolving power, mass accuracy, and dynamic range to be achieved. But why would one need high mass accuracy and high resolution?The benefit of measuring a compound's mass with adequately high accuracy can directly determine its elemental composition. Accurate mass thus acts as a powerful "filter" useful for confirming the identity of a compound or even identification of an unknown. This is illustrated in Fig. 1 showing the fragmentation (tandem mass spectrometry (MS/MS)) spectrum of flavonoid quercetin (m/z 303). Mass deviation of less than 3 ppm for any detected fragment together with the richness of the fragmentation spectra itself enable confirming the elemental composition of the starting compound a...