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702 Jensen and Wilm<br />

Fig. 4. Parent ion scan for the leucine/isoleucine immonium ion (m/z 86) detects peptide<br />

ions below the chemical noise level. (A) The nanoelectrospray quadrupole mass spectrum (Q 1<br />

scan) of a tryptic peptide mixture displays only polymer ion signals and chemical background<br />

which suppress peptide ions. (B) The nanoelectrospray triple-quadrupole MS/MS precursor ion<br />

(m/z 86) analysis of the same sample reveals several peptide ion signals that subsequently can<br />

be selected for sequencing by product ion analysis by tandem mass spectrometry.<br />

Fig. 5. Peptide tandem mass spectrum acquired in separate segments in a triple-quadrupole<br />

instrument. The m/z range above the precursor ion, [M+2H] 2+ , is acquired at low collision<br />

energy and at relatively low mass resolution to efficiently generate and detect large peptide<br />

fragment ions. The m/z range below the precursor ion is acquired at higher resolution and with<br />

stepped collision energies, that is, intermediate collision energy to generate low m/z sequence<br />

ions and high collision energy to generate immonium ions and the a 2 and b 2 fragments.

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