Cross-species proteomics in analysis of mammalian sperm proteins C4PR_LIV

Many proteomics studies are conducted in ‘model’ organisms for which a fully annotated and detailed, high quality proteome is available. By contrast, many studies in ecology and evolution lack a high quality proteome data set that can be used for protein discovery and quantification. This is particularly true of proteins in the reproductive system that have an immune function or drive sexual conflict, sperm competition and secondary sexual characteristics, as these are anticipated to have a high rate of evolution. This can compromise the potential for cross-species proteomics to yield confident identification. Here, we analysed the sperm proteome from a range of ungulates and rodents and explored the potential of proteomics, using routine data workflows, to be able to yield characterisation and quantification. We report that database searching is robust to cross-species matching for a core proteome, but that classes of proteins, notably those involved in sperm-egg interaction, are not readily analysed by this approach. Using iBAQ label free quantitative proteomics, we were also able to define a ‘core sperm proteome’ that was consistent across the ungulate and rodent groups, and which could be used as a reference for quantitative analysis of species-specific protein characterisation.