Cross-platform clinical proteomics using the Charité Open Standard for Plasma Proteomics (OSPP)

Introduction:
Human plasma is a preferred body fluid for clinical investigations due to its minimally invasive collection and rich physiological information. LC-MS-based plasma proteomics holds immense promise in characterising human disease, identifying biomarkers, and advancing diagnostic technologies. However, for widespread clinical adoption, there is an ongoing need to improve proteomic workflows in terms of accuracy, reproducibility, platform transferability, and cost-effectiveness.
Objective:
To develop a peptide panel based on a previously developed targeted panel for COVID-19. The new panel, Charité Open Peptide Standard for Plasma Proteomics (OSPP), consists of 211 stable-isotope labeled peptides from 131 consistently quantified plasma proteins, it is designed for high-throughput targeted and untargeted plasma and serum proteomics studies in large clinical cohorts.
Methods:
We utilised targeted plasma proteomics MRM (Agilent 6495C), MRM-HR (ZenoTOF 7600) and discovery proteomics techniques on various LC (Waters M Class, Agilent 1290, Thermo Vanquish Neo) and MS platforms (ZenoTOF, TimsTOF, and Exploris 480) to comprehensively test the peptide panel.
Results:
The targeted peptide panel that was previously established for COVID-19 demonstrated exceptional abilities in categorising the disease, predicting outcomes, and comparing across different platforms. It also has the potential to be applied to comparable types of diseases (Fig 1). By analysing more than 10,000 plasma samples from various disease categories, we have increased the number of peptides in OSPP to 211, derived from 131 plasma proteins that were consistently quantified. These peptides have shown consistent quantification properties in human studies, across different platforms and matrices, and are suitable for chemical synthesis (Fig 2). The OSPP measures proteins that are crucial for human disease, which are derived from proteins involved in many biological processes, including those commonly employed in clinical tests or targeted by FDA-approved medications .
In an acute COVID-19 patient cohort (Fig 3), we used the OSPP to i) achieve patient classification and biomarker identification, ii) generate comparable quantitative proteome data with both targeted and untargeted approaches, and iii) estimate absolute peptide quantities for cross-platform alignment across various MS methods. The OSPP is cost-effective, adding only less than 1€ per sample. OSPP also successful implementation in a real-world cohort comprising over 15,000 samples underscores the scalability and practical utility of our peptide panel in addressing critical translational medicine challenges.
Conclusion:
The OSPP offers high analytical consistency, cost-effectiveness, and versatility, facilitating adaptable and accessible high-throughput plasma proteomics in large clinical cohorts, addressing critical needs in translational medicine.