New Views of Old Proteins: Clarifying the Enigmatic Proteome

Abstract

All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide a >10 years of projection for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we describe a next generation of approaches to define, quantify, and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.

Keywords: biotechnology; proteins; proteomics; single-cell biology; single-molecule sequencing.

Graphical abstract

Fig. 1

From human genes (far left), diverse forms of mature endogenous protein molecules are expressed (far right). Technologies are needed to fully measure the dynamic set of ∼1 million distinct proteoforms expressed in each cell (see the study by Aebersold et al. (4)).

Fig. 2

Proteoform measurement fills knowledge gaps. This figure details specific advantages of top–down measurements of intact proteins. Measuring proteoforms will improve molecular precision in asserting protein sequence and composition (i.e., primary structure). Such measurements should improve the efficiency of detection and assignment of function to all protein variants and their modifications in the coming decade.

Fig. 3

Multiple approaches for assessment of proteins in single cells. Antibody specificity dictates the protein detection specificity for technologies depicted in orange. bottom–up Mass Spectrometry, measures peptides; CODEX, codetection by antibody indexing; CyTOF, mass cytometry; nanoDESI, spatially resolved desorption by electrospray; PEA, proximity extension assay; PLAYR, proximity ligation assay for RNA; REAP, a rapid, efficient, and practical cell processing method; sc, single cell; top–down mass spectrometry, measures proteoforms.

Fig. 4

Multiplexed spatial assays. Source: Ref. (8).

Fig. 5

Capturing the multidimensional biology of our proteome.A, from a parts lists to interaction mapping and proteoform networks underlying cell-based biology. B, capturing time-resolved human biology at the protein level. Top, depiction of multiple spatiomolecular proteoform images collected over time. Bottom, temporal dynamics vary widely across disease progression (years) across cell differentiation (days) in human bone marrow and blood or through embryogenesis (months).

Fig. 6

Collaborative and big science models for approaching the human proteome in the decade ahead. Scope of the solution needs to match scope of the challenge, if we are to make interactions with the human proteome more deterministic for the goals of biomedical research, including regenerative medicine, more efficient drug development, and early detection of all types of human disease.