Proteins are the ultimate functional product of most gene expression so optimally one would prefer to look at proteins when trying to understand the mechanisms an organism uses to respond to a given condition. As with any other biomolecule, tools for identifying and quantifying proteins are a prerequisite to their successful study. Single proteins are typically detected using antibodies but very few antibodies have been generated against bee proteins and none have been commercialized. Of all the analytical methods available for studying proteins, mass spectrometry is the most sensitive, most accurate and least biased. Proteins can be identified by mass spectrometry by first hydrolyzing them with a specific protease such as trypsin. The masses and fragmentation patterns of the resulting peptides can then be determined and used to identify the peptides individually and the protein(s) they came from (i.e. proteomics). This process works best when all possible proteins that might be present are known and is only really successful when an organism’s genome has been sequenced. To this end, in recent years proteomics has begun to be applied in bees towards understanding a range of paradigms.
Where is the future of proteomics research in bees heading? Mapping protein expression across all tissues and castes in adult bees is the logical next step after sequencing the bee genome. The genome helps to determine which proteins may be present but where are those proteins expressed? The protein expression atlas in bees will tell that and will mark a significant step forward for bees as a model system as this would be the first such comprehensive atlas in any multicellular organism. Additional protein-based methods (protein extraction and immunochemical assays for protein abundance) are covered in further detail in the BEEBOOK paper on physiology and biochemistry (Hartfelder et al., 2013).