Cristina Gil Gonzalez (Copenhagen / DK), Paola Pisano (Copenhagen / DK), Michael Wierer (Copenhagen / DK)
The discovery of biomarkers is essential for combating diseases and maintaining public health. Biomarkers enable prevention, early diagnosis, and personalized treatment of diseases. Plasma serves as a primary source for biomarker discovery due to its ease of accessibility, and reliability in assessing overall health status. Despite a significant increase in biomarker studies in recent years, only a small number of biomarkers have been approved and translated into clinical practice. This is mainly due to the numerous challenges that persist in identifying reliable biomarkers, most predominantly the ability to run large sample cohorts, and the proteomic depth that can be achieved.
The aim of this study is to enhance the efficiency and throughput in plasma proteomics by implementing and systematically comparing different sample preparation workflows. This includes (i) various lysis conditions with optional clean-up steps for non-enzyme-compatible buffers, (ii) different enzyme combinations for protein digestion, and (iii) different peptide purification strategies. All samples will be loaded onto Evotips and analyzed on a Evosep- Astral LC-MS setup.
The ultimate goal is to find the optimal method for large-scale analysis of neat plasma, surpassing the current widely-used protocol consisting of heat denaturing, trypsin-lys-c digestion and Evosep desalting. Coupled with the exceptional sequencing speed of the Thermo Astral instrument, this will pave the way for accurate and precise high-throughput analysis of large plasma cohorts, facilitating the identification of new, relevant biomarkers.