Functional Enrichment Across Organism Massomes

In this work, we present an alternative idea of studying protein function directly: based on the accessible property of protein mass. After analyzing proteins with similar mass (isomass) ranges across organisms massomes (2), we found that certain biological functions are not uniformly distributed among masses, but rather tend to be grouped around specific mass ranges. We showed that biological functional classes found in this manner could be seen across the three examined organisms: human, worm and fly. This study leads to useful property that the mass-based biological functional classes are preserved across the organisms. Thus, this work outlines a potentially useful constraint, based on mass, for evolution of similar functions. In addition, the results of this work can constrain the search for protein candidates based on mass ranges with high functional information. Thus, this approach yields a roadmap that can be used in experimental design for functional exploration of proteomes in mass-based technologies such as gel electrophoresis and mass spectrometry. 2 Methods and Results We analyzed the relationship between protein mass and function in three different species of varying levels of complexity: Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens. For each organism, proteins were grouped by mass and partitioned into 1 kDa sized mass bins (e.g. 0-1kDa, 1-2kDa, etc). Within these bins, we analyzed all potential protein functions according to the Gene Ontology (GO) (3) to find if certain functions are enriched; that is, if a function appears at a specific mass range more likely than would be expected by chance. After assembling the whole genome protein identifiers (via GI) to GO terms annotations for H.sapiens, D.melanogaster, C.elegans, using the OBOES tool (4), we computed GO mass enrichments of biological processes categories for these organisms. These individual enrichments were then combined into a commonality enrichment matrix. This allowed us to identify GO categories commonly enriched in all three organisms and their corresponding enriching mass ranges. From the list of ten GO categories found to be commonly enriched in all three organisms,