In Systems Medicine, in addition to high-throughput molecular data (*omics), the wealth of clinical characterization plays a significant role in the overall understanding of a disease. Unique problems and challenges arise from the heterogeneity of data and require new solutions to software and analysis methods. The SMART and EurValve studies establish a Systems Medicine approach to heart valve diseases - the primary cause of subsequent heart failure. With the aim to ascertain a holistic understanding, different *omics and the clinical picture of patients with aortic stenosis (AS) and mitral regurgitation (MR) are collected. Our task within the SMART consortium was to develop an IT platform for Systems Medicine as a basis for data storage, processing, and analysis as a prerequisite for collaborative research. Based on this platform, this thesis deals on the one hand with the transfer of the used Systems Biology methods to their use in the Systems Medicine context and on the other hand with the clinical and biomolecular differences of the two heart valve diseases. To advance differential expression/abundance (DE/DA) analysis software for use in Systems Medicine, we state 21 general software requirements and features of automated DE/DA software, including a novel concept for the simple formulation of experimental designs that can represent complex hypotheses, such as comparison of multiple experimental groups, and demonstrate our handling of the wealth of clinical data in two research applications - DEAME and Eatomics. In user interviews, we show that novice users are empowered to formulate and test their multiple DE hypotheses based on clinical phenotype. Furthermore, we describe insights into users' general impression and expectation of the software's performance and show their intention to continue using the software for their work in the future. Both research applications cover most of the features of existing tools or even extend them, especially with respect to complex experimental designs. Eatomics is freely available to the research community as a user-friendly R Shiny application. Eatomics continued to help drive the collaborative analysis and interpretation of the proteomic profile of 75 human left myocardial tissue samples from the SMART and EurValve studies. Here, we investigate molecular changes within the two most common types of valvular heart disease: aortic valve stenosis (AS) and mitral valve regurgitation (MR). Through DE/DA analyses, we explore shared and disease-specific protein alterations, particularly signatures that could only be found in the sex-stratified analysis. In addition, we relate changes in the myocardial proteome to parameters from clinical imaging. We find comparable cardiac hypertrophy but differences in ventricular size, the extent of fibrosis, and cardiac function. We find that AS and MR show many shared remodelling effects, the most prominent of which is an increase in the extracellular matrix and a decrease in metabolism. Both effects are moresubstantial in AS. In muscle and cytoskeletal adaptations, we see a greater increase in mechanotransduction in AS and an increase in cortical cytoskeleton in MR. Tue decrease in proteostasis proteins is mainly attributable to the signature of female patients with AS. We also find relevant therapeutic targets. In addition to the new findings, our work confirms several concepts from animal studies and heart failure studies by contributing the most extensive collection of human tissue from in vivo collected biopsies to date. Our dataset provides a resource for isoformspecific protein expression in two of the most common valvular heart diseases. Apart from the general proteomic landscape, we demonstrate the added value of the dataset by showing proteomic and transcriptomic evidence for increased expression of the SARS-Co V -2- receptor at pressure load but not at volume load in the left ventricle and also provide the basis of a newly developed metabolic model of the heart.