Cross-species proteomics quantification pipeline distinguishes donor versus host extracellular matrix in explanted biomaterials

Abstract Xenogenic biomaterial durability, including bioprosthetic heart valves (BPVs), is compromised by pathological extracellular matrix (ECM) remodeling, resulting in progressive structural degeneration. Mass spectrometry-based proteomics can help reveal BPV degeneration mechanisms; however, peptide sequence similarity between donor and host species complicates protein-level analysis. We present a cross-species proteomic analytical strategy for xenogenic biomaterials and cross-species proteomic datasets. In silico tryptic digestion of human and bovine protein databases identified over 400 overlapping proteins with a high protein percent identity. Explanted human BPV tissue was divided into macroscopically distinct regions of degeneration and analyzed by mass spectrometry. A peptide-level strategy quantified protein abundances in a species-delineated analysis. We highlighted degeneration region-specific depositions of key human ECM proteins and bovine ECM proteins whose abundance is time dependent. We demonstrated that single-species analysis of a cross-species proteome results in inaccurate quantification. This study highlights the importance of distinguishing between donor and host species proteomes for accurate protein quantification. While focused on clinically explanted biomaterials, our approach is broadly applicable to all forms of xenotransplantation and the use of xenogenic matrices. Competing Interest Statement T.K. is an employee of Kowa Company, Ltd and was a visiting scientist at Brigham and Womens Hospital during this study. Kowa had no role in study design/data collection/analysis/manuscript preparation. M.C.B. is a consultant for BioMarin Pharmaceuticals, Inc. E.A. has a research grant from Pfizer and is a member of the scientific board of Elastrin Therapeutics, Inc. The other authors declare no competing interests. Abbreviations - BPV - Bioprosthetic Valve - ECM - Extracellular Matrix - MS - Mass Spectrometry