Mass spectrometry (MS) instrumentation has undergone several improvements over the years, including increased sensitivity, ease-of-use, and possibilities for more sophisticated and time-efficient experiments. These developments have led to an increase in the number of biological applications. In the 1990s and until recently, new instrumental innovations in organic MS had focused mainly upon front-end techniques — ionization interfaces specifically. In particular, electrospray ionization (ESI), atmospheric-pressure chemical ionization (APCI), and matrix-assisted laser desorption–ionization (MALDI) have evolved from these developments and have seen significant performance improvements over the years. Along the way, a few other interesting liquid chromatography–mass spectrometry (LC–MS) interfaces (for example, thermospray, particle-beam) have paved the way for modern LC–MS, but have then disappeared quickly from research laboratories. Also, a promising new ionization source, atmospheric-pressure photoionization (APPI) was introduced just a few years ago. As a result of all these innovations, rather good and stable MS sample introduction devices are available for a wide range of compound classes and most researchers seem quite satisfied with what they presently have available at their disposal. Continuing research on these ionization sources currently is aimed at enhancing the performance of such devices, through miniaturization, automation, and parallel-analyses. Lately, however, MS instrumentation research is dominated by improvements in the performance of the actual mass analyzers. Moreover, there is a growing trend toward combining different analyzer designs in order to increase the versatility and allow multiple experiments to be performed simultaneously using a single instrument. One of the most recent examples of such a novel hybrid instrument is the linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer (LIT-FT-ICR), which will be discussed subsequently in more detail. This instrument allows fast, multistage tandem MS (MS-MS) experiments as well as ultra-high resolution and accurate mass determinations. The driving force behind this recent trend of improving analyzer designs mainly has been scientists from biotechnology and pharmaceutical research laboratories. Their time is costly and their analytical protocols now routinely include the use of multiple MS instruments.

This article illustrates the technical principles and typical applications of the most common mass analyzers used in bioanalytical laboratories today. The classical mass spectrometer — the magnetic sector instrument — is not covered by this tutorial. Although these instruments allow very selective scan modes, their implementation is much less routine and is beyond the scope of this article. Moreover, magnetic sector instruments seem to have reached the apex of their technological development, while improvements in instrument technologies based upon other mass analyzers continue to evolve and develop in new directions. Magnetic sector instruments still are employed for specialized analyses, for example, in the petroleum industry or for the analysis of dioxins by gas chromatography–mass spectrometry (GC–MS).

There are four basic types of mass analyzers found in modern MS: time-of-flight (TOF), quadrupole and a recent derivative, quadrupole linear ion trap (LIT), quadrupole ion trap (QIT), and FT-ICR. The first part of this article will cover TOF and quadrupole analyzers; Part II will address QIT and FT-ICR. More interestingly, however, there are several very advanced permutations of these analyzers, which through the combination of different analyzers create enhanced MS-MS capabilities, novel scan modes, or superior mass resolution and accuracy. For example, the quadrupole-time-of-flight (QqTOF) instrument has developed into one of the most successful hybrid MS designs, allowing the generation of triple quadrupole–like MS–MS spectra, combined with high resolution and accurate mass capability in the TOF analyzer. This combined potential, together with flexible data-dependent acquisition routines, has been proven to be of significant importance for proteomics MS. Rather than just explaining the underlying physical principles, we will concentrate on their characteristic features, their limitations, and their applications (more details, in particular on the fundamental operating principles, can be found in textbooks on mass spectrometry; for example [1]). In addition, several unique techniques and unusual or exotic mass analyzer designs are highlighted throughout the text. We have chosen all of the examples from our own research; as a result, this overview is biased toward applications to small molecules. Therefore, some interesting recent hybrid designs with mostly proteomics applications, such as ion trap-TOF, only are described briefly.