Comparative proteomics of serum from 31 mammalian species

[This talk was prepared for the 2020 US HUPO Conference in Seattle, WA, but was cancelled because of COVID Pandemic]

Systematically characterizing the diversity of mammalian proteomes will improve our understanding of biologically interesting phenotypes and recent adaptation. Our first step to build the molecular cartography of mammalian blood proteomes and provide a foundational understanding for future biomimicry studies has focused on 31 species with annotated genomes spanning three placental superordinal clades: Afrotheria, Laurasiatheria, and Euarchontoglires. Undepleted sera from up to four individuals from each species were digested with trypsin and analyzed by data-dependent acquisition. The NIST SRM 909c human serum was used throughout the experiment to confirm digestion consistency and provide a human reference. Data were analyzed in both an ID-free and ID-based manner. For the former, the compareMS2 molecular phylogenetic approach was employed that used the fraction of shared spectra to calculate pairwise distances between all samples. The calculated relationships are based not only on the sequence-dependent fragmentation spectra, which includes some of the genetic variation, but also the relative abundance and post-translational modifications of the proteins. The resulting phylogenetic tree correctly recapitulated mammalia, with the major exception that cetacean blood proteomes were more similar to carnivora than even-toed ungulates. The data was also searched using standard database approaches and the resulting identified proteins were matched to human ortholog sequences using BLAST. On average, 342 proteins were identified (240 to 502) with 57 being shared across all species, though within each clade there were more shared proteins (i.e., pinnipeds shared 205 proteins). Combining an ID-free method with ID-based methods is particularly useful when covering a large number of species whose genomes are not necessarily assembled and annotated to the same standard, as it provides an independent overview of the quality of and similarity between all datasets in a study. Ongoing analysis will identify differences in the blood proteome that may be linked to phenotypes within or between clades.