MS is a powerful tool in life sciences and thus also in plant biology. Proteome analysis by MS is a robust and fast technology giving information about protein composition, PTMs, localization, and quantity. Today a variety of mass spectrometers exists and it is not possible to judge which design is best. All of them have advantages and disadvantages. The choice of instrument is very much dependent on the type of experiment. All types of machines are continuously further developed to increase their performance and to circumvent disadvantages. The high mass accuracy and resolution makes FTICR-MS a very promising technology. However, its maintenance is very expensive and it also requires a lot of space. Therefore the latest ion traps, such as linear ion trap and the orbitrap, might be a cheaper and less space-using alternative. However, to study PTMs, not only high mass accuracy is important, but also good resolution in the LMW range is necessary, to detect diagnostic marker ions. In this range, Q and TOF analyzers are still important mass analyzers. Quadrupole is also still very advantageous for neutral loss scans to analyze, for example, phosphorylation. MS is becoming more and more automated, and the high throughput of samples yields huge amounts of data. Although several search algorithms exist and the output of good results is high, manual data interpretation is still required, especially to identify PTMs.

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