Hot atmospheres of massive galaxies are enriched with metals. Elemental abundances measured in the X-ray band have been used to study the chemical enrichment of supernova remnants, elliptical galaxies, groups and clusters of galaxies. Here we measure the elemental abundances of the hot atmosphere of luminous infrared galaxy Arp 299 observed with XMM-Newton. To measure the abundances in the hot atmosphere, we use a multi-temperature thermal plasma model, which provides a better fit to the Reflection Grating Spectrometer data. The observed Fe/O abundance ratio is subsolar, while those of Ne/O and Mg/O are slightly above solar. Core-collapse supernovae (SNcc) are the dominant metal factory of elements like O, Ne, and Mg. We find some deviations between the observed abundance patterns and theoretical ones from a simple chemical enrichment model. One possible explanation is that massive stars with $M_{star}gtrsim23-27~M_{odot}$ might not explode as SNcc and enrich the hot atmosphere. This is in accordance with the missing massive SNcc progenitors problem, where very massive progenitors $M_{star}gtrsim18~M_{odot}$ of SNcc have not been clearly detected. It is also possible that theoretical SNcc nucleosynthesis yields of Mg/O yields are underestimated.