MS instruments are continuously evolving. Although MS instruments are already very sensitive and fast and have a high mass accuracy, there is still the potential to further improve these technical aspects in the near future. The high mass accuracy of FTICR instruments makes the relatively new field of top-down proteomics very attractive. Compared to bottom-up proteomics, top-down proteomics has the advantage to access complete protein sequences, to assign PTMs, and to prevent the protein inference problem, which results from the loss of connectivity between peptide and protein. However, this field still has some limitations that require further improvement—for example, interpretation of complex spectra.
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