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A MALDI with a TOF re ectron and Fourier transform ion cyclotron esonance mass analyzers are also beginning to be used21 A typical procedure for protein sequencing begins by digestion with a protease such as trypsin in order to obtain a collection of tryptic peptides Other enzymes and their cleavage sites are described elsewhere22 This peptide collection can be ionized using ESI, separated by the rst quadrupole according to m/z ratios, and then fragmented (CID), with the resulting fragments analyzed in the third quadrupole The mass spectrum can be analyzed to establish the peptide sequence, or compared directly with a peptide database Figure 1512 depicts this typical protocol The CID procedure causes more or less random peptide bond cleavage Therefore, a number of fragments are obtained that differ by a single amino acid residue.

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Several types of fragments are produced, and their nomenclature is shown in Figure 1513 Two main classes of ions are formed by CID, those that contain the C terminus plus one or more additional residues (ions of types xn , yn, and zn ) and those that contain the N-terminus and one or more additional residues (ions of types an , bn , and cn ) Ions of types yn and bn are formed by the rupture of amide bonds, and the mass differences between these fragments are limited to the masses of the naturally occurring 19 different amino acid residues (Table 159) Isoleucine and leucine,a One letter codes are customary in the MS area eprinted, with permission, from M Mann and M Wilm, Anal Chem 66 (No 24), 1994, 4390-4399 Error Tolerant Identi cation of Peptides in Sequence Databases by Peptide Sequence Tags .

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