The characterization of historical artefacts at a molecular level is becoming an increasingly important aspect for cultural heritage. All the developments in extraction, separation and analytical methodologies can be helpful for challenging tasks, such as the identification of chemical compounds (proteinaceous binders, oils, varnishes) used by artists. Any information thus obtained, is fundamental to investigate the executive techniques and the constitutive materials, at the same time they can also be used to develop protocols for conservation treatment. In this paper, we present the molecular characterization of the organic components extracted from the preparation layers and the pictorial surface of an Egyptian wooden coffin. The artefact is part of the Egyptian Collection held at the Archeological National Museum of Naples (IT) and belongs to a specific type known with the name of "yellow coffin", dated at the beginning of the XXII Dynasty. Following the identification of the wood used to build the coffin, we performed on each of them an extraction of the organic components, which, according to differences in chemical-physical properties, were subsequently divided into three categories (monosaccharides, lipids and proteins) and separately analyzed. Pigments are not the subject of the current study. The ingenuity of our methodology relies on the use of powerful analytical methodologies (i.e. high-resolution MS) which led to the unambiguous identification of heterogeneous molecules.