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Please note that the content of this book primarily consists of articles available from Wikipedia or other free sources online. Top-down proteomics is a method of protein identification that uses an ion trapping mass spectrometer to store an isolated protein ion for mass measurement and tandem mass spectrometry analysis. The name is derived from the similar approach to DNA seqencing. Proteins are typically ionized by electrospray ionization and trapped in a Fourier transform ion cyclotron resonance (Penning trap) or quadrupole ion trap (Paul trap) mass spectrometer. Fragmentation for tandem mass spectrometry is accomplished by electron capture dissociation or electron transfer dissociation.