nano/µ-HPLC-MS system for discovery and high-throughput proteome analysis

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Key technology for proteomics is the combination of liquid chromatography (LC) and mass spectrometry (MS), which can identify several thousand proteins in a complex sample. The goal of the MPC and the other users/collaboration partners is to systematically investigate health and disease conditions for a general understanding of underlying mechanisms at the protein level and to identify potential protein biomarkers for prognostic and therapeutic purposes. In this context, discovery studies focus on various questions. a) Protein identification: Which proteins are formed under the given conditions in a certain cell type, tissue or body fluid? b) Protein quantification: Which proteins are differentially expressed? c) Protein localisation: Where is a protein formed and/or accumulates? d) Functional proteomics: How does the function of a protein change depending on its amount, modification, localisation or network? e) Protein-protein interactions: Which proteins interact with each other (e.g. when and where)? In the field of clinical proteomics, a large number of patient samples are often available, but their analysis is often not feasible using a standard discovery platform due to the long analysis time. A prerequisite for a clinical application with a large number of samples is a high-throughput platform. For this, a mass spectrometer with high sensitivity, mass accuracy, data acquisition speed, robustness and reproducibility is essential. The biggest challenge in identifying and quantifying proteins from biological samples is the enormous complexity of the peptide mixtures. Therefore, another important requirement for both discovery and high-throughput studies is to resolve the complexity of the samples optimally to achieve high proteome coverage. To reach the highest possible robustness and reproducibility for large-scale studies, the use of an LC system combining low-pressure sample loading and off-line gradient formation is crucial. This system can provide optimal separation performance, allows the required short gradients without loss of sample loading time, and thus increases the capacity for MS analyses. The device applied for here is intended to extend the discovery proteomics platform within the MPC and also establish a high-throughput proteomics platform. The current lack of such a combined platform precludes the processing of central projects, as the volume of samples exceeds the capacity of the MPC. The acquisition of a state-of-the-art system designed for discovery as well as high-throughput studies will create the infrastructure to handle these projects and improve the quality and efficiency of MS experiments.