PROJECT SUMMARY Deep proteomic and metabolomic profiling of biological tissues is an overarching goal of modern biological and biomedical research. It remains a key – and conspicuous – missing component from the full spectrum of -omics that mainly capitalize on next-generation sequencing of DNA and RNA. Today's existing methodologies for proteomic and metabolomic analysis currently lag far behind the capabilities of tools for genomics and transcriptomics, both in terms of depth-of-coverage and throughput. The proposed effort will meet this challenge by advancing revolutionary new methods for label-free single-molecule proteomic and metabolomic profiling and combining them with novel methods for sub-cellular spatial analysis. Protein concentrations within a mammalian cell span ~8 orders of magnitude; in human blood serum this increases to ~11 orders. Yet, within these immensely complex milieus, even the most sparsely expressed proteins are important. Cellular signaling, gene regulation, early responses to exogenous biological stimuli, and disease onset all generally result in the expression of small copy numbers of proteins. It is thus essential both to discover rare cellular proteins and to attain holistic proteomic maps – but these goals remain far beyond present technological capabilities. Further, deciphering the instantaneous state of an organism's proteome – and, especially, observing its post-translational modifications (PTMs) as they dynamically evolve in response to cellular function, stress, and disease – will provide transformational knowledge for many fields. Deep proteome discovery will tackle the cellular proteome's complexity, allowing identification of proteins over its entire dynamic range of concentration – from the most prolifically expressed cellular proteins to those only sparsely expressed with a few copies per cell. This project's success will enable deep spatial profiling of the cellular proteome and metabolome with high throughput and, thereby, discovery of rare cellular proteins and metabolites. It will fundamentally change the resolution of protein analysis down to the level of individual molecules in subcellular compartments. Its achievement will complete the constellation of single-cell -omics, thereby broadly advancing research worldwide in fields that span from fundamental biology to the frontiers of clinical medicine. In the proposed effort, existing and well-validated techniques for spatially-resolved tissue sampling will be pushed downward into the sub-cellular realm. Scaling these methods downward is feasible now solely because of the single-molecule resolution of the proposed approach. This project builds upon a significant body of recent efforts focused upon creating instrumentation for deep profiling of the single-cell proteome. The effort proposed here will further advance these achievements – and will incorporate high-resolution tissue-sampling methods to deliver, with minimal loss, biological analytes to instrumentation enabling single-molecule analysis. Pursued together, these efforts will enable the first realization of spatial proteomics with sub-cellular resolution.

PROJECT NARRATIVE Deep proteomic and metabolomic profiling of biological tissues is an overarching goal of modern biological and biomedical research, but it remains a key – and conspicuous – missing component from the spectrum of -omics, specifically genomics and transcriptomics, which capitalize on next-generation sequencing of DNA and RNA. The proposed effort will meet this challenge by advancing revolutionary new methods for label-free single- molecule proteomic and metabolomic profiling, combining them with novel methods for sub-cellular spatial analysis. Its achievement will complete the constellation of single-cell -omics, thereby broadly advancing research worldwide in fields that span from fundamental biology to the frontiers of clinical medicine.