Supplemental Figure S1
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Fig. S1. Peptide fragmentation for one of the factor XIII A1 peptides that was identified in barnacle cement. The corresponding tandem mass spectra, and the b and y ions that were identified, are shown in Fig. 5B. The precursor ion is denoted by an arrow in Fig..5B (inset). Since the charge of the detected precursor ion (1164.67 m/z) is +2, the atomic mass of the ion is 2329.34 a.m.u. Collision-induced dissociation of the precursor ion produces fragments of the ion with a combined mass of 2329.34 a.m.u. Although fragmentation of the precursor ion is a random process, the collision energy is tuned to favor fragmentation at the (rigid) peptide bond, producing b and y ions across the sequence. Detection of these b and y ions is used for the database search, since the mass of these fragments is unique to the corresponding peptide sequence. For example, detection of the b10 ion fragment represents the sequence EEFYVLNDIGV and detection of the y11 ion fragment represents the sequence VIFYGEVNDIK of the identified peptide. These two ion fragments alone confirm the sequence of the identified peptide. Additional b and y ions provide further sequence confirmation of the identified peptide. Tandem mass spectrometry cannot be confused with peptide sequencing methods. In tandem mass spectrometry not all b and y ions are expected to be detected because of the nature of the technique.