A Comment on "Deep Proteogenomics of a Photosynthetic Cyanobacterium"

Proteomic researchers strive to achieve complete annotation of protein-coding DNA sequences to provide a foundational context for their relevant biological data. A recent deep proteogenomic study using a photosynthetic cyanobacterium Synechocystis sp. PCC 6803 by Spät et al. proposed 64 refined open reading frames (ORFs). By searching LC-MS/MS data from affinity chromatography-isolated protein complexes, our laboratory identified that six of these high-abundance ORFs possess N-terminal initiation start sites that differ than those proposed in the alternative models. Our findings are supported by highly confident MS2 data, phylogenetic analysis, chemical labeling, and established data from two independent research groups. Based on these high-quality experimental identifications, we subsequently propose a standardized strategy and set of criteria for future deep proteogenomic efforts to ensure accurate and stringent proteogenomic annotation.