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. Author manuscript; available in PMC: 2013 May 15.
Published in final edited form as: Anal Chem. 2012 Apr 23;84(10):4513–4519. doi: 10.1021/ac300367p

Figure 4.

Figure 4

Average probability of error (A) and average quantitative error (B) binned by precursor m/z value for IRMPD experiments. For each experiment, the RF amplitude was held constant, resulting in a fixed low-mass cutoff (LMCO) and dynamic precursor q- value. IRMPD activation times were set in a data-dependent manner by multiplying the precursor m/z by a coefficient. Using this strategy, we are able to normalize IRMPD PSM production and quantitative accuracy across a wide range of precursor m/z values. Coefficients 1 – 5 correspond to increased IRMPD irradiation time. Increasing irradiation time increases secondary dissociation, resulting in better quantitative accuracy, but confounding spectral interpretation.