Effects on atmospheric prompt neutrino fluxes of present uncertainties affecting the nucleon composition are studied by using the PROSA fit to parton distribution functions (PDFs). The PROSA fit extends the precision of the PDFs to low x, which is the kinematic region of relevance for high-energy neutrino production, by taking into account LHCb data on charm and bottom hadroproduction. In the range of neutrino energies explored by present Very Large Volume Neutrino Telescopes, it is found that PDF uncertainties are far smaller with respect to those due to renormalization and factorization scale variation and to assumptions on the cosmic ray composition, which at present dominate and limit our knowledge of prompt neutrino fluxes. A discussion is presented on how these uncertainties affect the expected number of atmospheric prompt neutrino events in the analysis of high-energy events characterized by interaction vertices fully contained within the instrumented volume of the detector, performed by the IceCube collaboration.
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