The main objective of the proposed collaborative project Prot-HiSPRA is to remove time-consuming bottlenecks of existing proteomics technologies (sample preparation, fractionation, proteolysis, separation, data collection, and data mining) and bring the proteome driven analysis into time sensitive clinical practice. Prot-HiSPRA is an objective-driven research project and it aims at generating new knowledge and new technologies which will improve the European competitiveness in the field of applied proteomics. Prot-HiSPRA is planned for the duration of 36 months which is necessary in order to ensure a high-quality validation of the developed high-throughput methodologies. A strong participation of SMEs (partner 2 – MAYLAB, partner 3 – CELS - left the onsortium, partner 6 – RTDs, partner 7 - BIA) will ensure strong innovation and exploitation during HiSPRA. Research activities in the Prot-HiSPRA program can be divided into a technological core project that is tailored to significantly improve on technologies in the fields of proteomics, bioinformatics, and integrated biology. Analytical methods developed with the Prot-HiSPRA project will be exemplified by applying for analysis of clinical samples originating from in vitro fertilization (IVF) procedures. During the IVF process, especially at the moment when decisions are made which embryo can be implanted, decisions must be made so that the process has the greatest chance for success. To further elevate pregnancy rates for IVF a non-invasive, rapid, and robust methods for judging the embryos status is urgently needed to examine the embryos´ proteome. These methods could not only be applied in the described field of reproductive medicine but also in any the other fields of clinical analysis where fast and reliable diagnosis on a proteomic basis could be made available.