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

Abstract

The role of plasma and serum proteomics in characterizing human disease, identifying biomarkers, and advancing diagnostic technologies is rapidly increasing. However, there is an ongoing need to improve proteomic workflows in terms of accuracy, reproducibility, platform transferability, and cost-effectiveness. Here, we present the Charité Open Peptide Standard for Plasma Proteomics (OSPP), a panel of 211 extensively pre-selected, stable-isotope labeled peptides combined in an open, versatile, and cost-effective internal standard for targeted and untargeted plasma and serum proteomics studies. The selected peptides show consistent quantification properties in human studies, across platforms and matrices, are well suited for chemical synthesis, and distribute homogeneously over proteomics-typical chromatographic gradients. Being derived from proteins that function in a wide range of biological processes, including several that are routinely used in clinical tests or are targets of FDA-approved drugs, the OSPP quantifies proteins that are important for human disease. On an acute COVID-19 in-patient cohort, we demonstrate the application of the OSPP to i) achieve patient classification and biomarker identification, ii) generate comparable quantitative proteome data with both targeted and untargeted proteomic approaches, and iii) estimate absolute peptide quantities to achieve cross-platform alignment across targeted, data-dependent and data-independent acquisition (DIA) proteomic methods on different instrument platforms. The OSPP adds only cents of cost per proteome sample, thus making the use of an internal standard cost-effective and accessible. In addition to the standards, corresponding spectral libraries and optimized acquisition methods for several platforms are made openly available.