Top-Down Proteomics

Top-Down approach refers to the ionization of intact proteins and MS or MS/MS analysis of intact species or fragment ions generated in mass spectrometer by induced dissociation. This tehnique can eliminate most of the problems associated with the Bottom-Up approach and allow for high specificity protein identification and characterization of different proteoforms: information that would otherwise be lost with protein digestion and unattainable with other large scale, whole proteome approaches. Major obstacle problem in Top-Down proteomics represent sample complexity - biological samples are inherently complex with a multitude of different proteins and their proteoforms; thus, effective implementation of the Top-Down approach requires extensive separation and/or enrichment step preceding mass analysis. In this chapter, we will first describe methods of used for fractionation of intact proteins. Following that, we will discuss ionization techniques and instrumentation used in Top-Down proteomics.