When Steve Carr, senior director of the Proteomics Platform at the Broad Institute of MIT and Harvard, began working in proteomics, the field was able to detect only the most abundant proteins in a given sample. In recent years, increasingly sensitive mass spectrometers have paved the way for enormous progress: scientists are now able to detect and analyze nearly all proteins expressed in a sample, including ones present only in miniscule amounts.

Recent improvements in sample handling and mass spectrometer sensitivity are now enabling further advances, in the form of single-cell and spatial proteomics technologies. These methods can identify proteins in individual cells, rather than bulk tissue, and map the location of specific proteins within a tissue, allowing scientists to learn more details about how cells function and communicate. This progress is in part driven by optimized methods and more powerful tools developed by researchers such as Claudia Ctortecka, a postdoctoral associate in the Proteomics Platform headed by Carr, and colleagues in the Platform.

Carr and Ctortecka are seeking collaborations to apply new single-cell and spatial proteomics technologies to ever more complex questions. They hope to push the technology further and use it in combination with tools from other fields to learn about the full range of cellular activity, from gene expression to post-translational modifications.

We spoke with Carr and Ctortecka about the potential of spatial and single-cell proteomics and their hopes for future collaborations.

What can single-cell and spatial proteomics now enable?

Carr: In the past, proteomics used bulk material — samples consisting of millions of cells — all lysed together and then profiled at the proteome and post-translational modification level. In doing that, we lost information about the uniqueness of each cell, and we had limited information about the spatial heterogeneity of tissues that plays a decisive role in disease.

Single-cell proteomics technologies with an analysis depth of thousands of proteins quantified per cell have only recently emerged. It’s also only recently become possible to develop spatial profiling methods capable of deep-scale, unbiased proteome analysis in defined regions of tissue.

Ctortecka: Earlier in the field’s history, we were mostly monitoring cell identity, looking for the most abundant proteins that describe what type of cell we're talking about. Now we're getting more and more sensitive. We can find subpopulations of a specific cell type that we're interested in. We can see transition states; we can see cells that are morphologically very different. And we can derive meaningful biological information by doing this.

We’re also now able to do better and more reproducible protein quantitation, which is key. The presence of one protein alone doesn't tell you much about a cell state. It's a matter of how much of that protein is present relative to its environment. The relative difference between cell A and cell B might give you an idea of why one cell reacts to a treatment and the other cell does not.