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Abstract Comparative functional genomics offers a powerful approach to study species evolution. To date, the majority of these studies have focused on the transcriptome in mammalian and yeast phylogenies. Here, we present a novel multi-species proteomic dataset and a computational pipeline to systematically compare the protein levels across multiple plant species. Globally we find that protein levels diverge according to phylogenetic distance but is more constrained than the mRNA level. Module-level comparative analysis of groups of proteins shows that proteins that are more highly expressed tend to be more conserved. To interpret the evolutionary patterns of conservation and divergence, we develop a novel network-based integrative analysis pipeline that combines publicly available transcriptomic datasets to define co-expression modules. Our analysis pipeline can be used to relate the changes in protein levels to different species-specific phenotypic traits. We present a case study with the rhizobia-legume symbiosis process that supports the role of autophagy in this symbiotic association. 

This Perspective covers discovery and mechanistic aspects as well as initial applications of novel ioni-zation processes for use in mass spectrometry that guided us in a series of subsequent discoveries, in-strument developments, and commercialization. With all likelihood, vacuum matrix-assisted ionization on an intermediate pressure matrix-assisted laser desorption/ionization source without the use of a laser, high voltages, or any other added energy was the defining turning point from which key developments grew that were at the time unimaginable, and continue to surprise us in its simplistic preeminence, and is therefore a special focus here. We, and others, have demonstrated exceptional analytical utility with-out a complete understanding of the underlying mechanism. Our current research is focused on how best to understand, improve, and use these novel ionization processes through dedicated platform and source developments which convert volatile and nonvolatile compounds from solid or liquid matrices into gas-phase ions for analysis by mass spectrometry using e.g., mass-selected fragmentation and ion mobility spectrometry to provide reproducible, accurate, and sometimes improved mass and drift time resolution. The combination of research and discoveries demonstrated multiple advantages of the new ionization processes and established the basis of the successes that lead to the Biemann Medal and this Perspective. How the new ionization processes relate to traditional ionization is also presented, as well as how these technologies can be utilized in tandem through instrument modification and implementa-tion to increase coverage of complex materials through complementary strengths.