We present experimental and theoretical results for the fluctuation properties in the incomplete spectra of quantum systems with symplectic symmetry and a chaotic dynamics in the classical limit. To obtain theoretical predictions, we extend the random-matrix theory (RMT) approach introduced in [O. Bohigas and M. P. Pato, Phys. Rev. E 74, 036212 (2006)] for incomplete spectra of quantum systems with orthogonal symmetry. We validate these RMT predictions by randomly extracting a fraction of levels from complete sequences obtained numerically for quantum graphs and experimentally for microwave networks with symplectic symmetry and then apply them to incomplete experimental spectra to demonstrate their applicability. Independently of their symmetry class quantum graphs exhibit nongeneric features which originate from nonuniversal contributions. Part of the associated eigenfrequencies can be identified in the level dynamics of parameter-dependent quantum graphs and extracted, thereby yielding spectra with systematically missing eigenfrequencies. We demonstrate that, even though the RMT approach relies on the assumption that levels are missing at random, it is possible to determine the fraction of missing levels and assign the appropriate symmetry class by comparison of their fluctuation properties with the RMT predictions.
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