New era in proteomics research European experts in the field of proteomics collaborated to advance existing technology and provide novel tools to the scientific community. The outcome of the PROSPECTS project is believed to revolutionise proteomics research, offering quantitative protein analysis in space and time. Industrial Technologies © Thinkstock Proteins are the functional units of cells and are therefore key to understanding cellular processes in health and disease. The comprehensive study and characterisation of a large group of proteins is called proteomics. First-generation proteomics approaches, however, only provided limited quantitative annotation with no information on protein localisation. The EU-funded project 'Proteomics specification in time and space' (PROSPECTS) brought together leading research groups and small and medium-sized enterprises (SMEs) to pursue a common goal. The main goal of the PROSPECTS consortium was to improve existing technology in order to enable protein analyses in time and space. The project partners developed powerful instrumentation and utilised complementary technologies such as mass spectrometry, cryo-electron microscopy and cell imaging to incorporate temporal and spatial dimensions into their analyses. Combining mass spectrometry with ultra-high pressure liquid chromatography considerably improved protein sample detection by increasing sensitivity and speed for single-shot analysis. Furthermore, the incorporation of optical and ion-beam methods enabled researchers to slice frozen cells grown on microscopy slides and study/investigate their proteome. The snap-freezing of biological samples preserved protein integrity and facilitated the analysis of macromolecular protein complexes such as the proteasome. An important part of the PROSPECTS work was devoted to the development of mathematical computational models capable of predicting cell function and protein interaction. These could elucidate the proteins’ perturbation in disease processes. During proteome analysis, it is equally important that information on the subcellular localisation of proteins can also be extracted. To this end, PROSPECTS used the mass spectrometry-based technique of stable isotope-labelled amino acids. The scientists were thus able to determine the distribution of proteins in the cell membrane, cytosol and nucleus. Analysis of the half-lives and the turnover rates of over 5 000 proteins added the temporal dimension to their method. PROSPECTS’ complementary methodologies can be applied to elucidate the impact on the proteome of aberrantly misfolded proteins such as those involved in neurodegenerative diseases. The established experimental workflows and the unique instrumentation were quickly released commercially, offering the biological and biomedical communities the opportunity to perform an unprecedented in-depth proteomic analyses.
