SPIDoc’s DN stems from the need to prepare for emerging viruses enabling a fast response, as became evident lately. Basically, better knowledge of the dynamic nature of viral structures is required and fundamental to combat with appropriate treatments. In this perspective, several technologies were developed for structural biology, including a cutting-edge approach combining mass spectrometry (MS) and X-rays for single particle imaging (SPI) in MS SPIDOC. Despite these advances, a major bottleneck that the scientific community will face in coming years will be the lack of expertise with a broad knowledge from theory, instrument development and application relevant to structural biology with MS. SPIDoc’s therefore aims to train the next generation of scientists with such expertise by a dedicated intersectoral training programme. SPIDoc’s projects are highly interlinked and the proposed training programme aims to provide the doctoral candidates with the basic and advanced knowledge to build a common interdisciplinary language, to work in teams and to acquire deep knowledge by a combination of lectures and practical sessions. An important aspect will be given to data management and the establishment of currently lacking standards for native MS metadata. The research training is complemented by transferrable skills courses, setting the basis for progressing through the doctoral studies as well as for future career progression. Within these modules, training on equal opportunities and unconscious bias are included, shaping the future generation towards creating fair workplaces. Special attention will be paid to green-practice measures from the everyday practice in laboratories and offices up to the institutional level. By including developments from computational theory to instrumentation, the SPIDoc’s beneficiaries and associated partners will closely work together to advance cutting-edge technologies and apply them towards fast response.