Advances in single-cell RNA-sequencing (transcriptomics) and genomics have been instrumental in our understanding of gene expression and human disease. While advancements have been made in single-cell protein analysis, state of the art technologies still have significant limitations. 
Most proteomic methods rely on antibodies to detect select protein epitopes and can analyze only a few dozen proteins per cell. Additionally, many antibodies have low specificity for their targets, which result in nonspecific protein detection. Although some highly specific and well-validated antibodies can be useful to analyze a few proteins across many cells, the low specificity and limited throughput of the current generation of single-cell protein analytical methods pose challenges for understanding the interactions and functions of proteins at single-cell resolution 
Another challenge involves the quantification and analysis of post-translational modifications, which regulate the abundance and activity of many proteins. Existing methods for the quantification of PTMs in complex samples requires enrichment to the sample for the PTMs of interest. These enrichment steps typically result in significant loss of material. 
Technology Overview
Dr. Slavov and his team have developed a method, which they have termed Single Cell ProtEomics by MS (SCoPE-MS), for quantifying proteins and post translational modifications by mass spectrometry in very limited samples of complex proteomes. Their method, which does not require the use of antibodies, allows for the quantification of thousands of proteins across hundreds of single-cell samples. A key driver of this progress is the development of multiplexed experimental designs in which proteins from single cells and from the total cell lysate of a small group of cells, called carrier proteins, are barcoded and then combined. Since this only involves enrichment of the carrier materials, and not the low-input samples, they are able to avoid any enrichment-associated losses from the low-input material. 
Procedurally, the first step involves PTM enrichment of a bulk sample with similar protein composition as the low-input samples to be quantified. The enriched material in each case is used as a carrier channel for selective identification of only modified peptides in the whole proteome mixtures. As a result of data independent MS/MS tandem mass tag-based quantitation analysis, they are able to quantify the levels of PTM labeled peptides from ultra-low amount samples, down to the proteomes of single mammalian cells with diameters of 11 microns. 
- The proposed method increases the sensitivity and throughput of PTM quantification by orders of magnitude over previous state of the art methods. 
- PTM-SCoPE allows quantifying PTMs in single human cancer and stem cells, and thus the inference of signaling activities in single human cells from heterogenous mixtures. 
- Avoids loss of sample through traditional enrichment processes. 
- Disease diagnostic 
- Drug development 
- Development of cells for regenerative therapies 
- License
- Research Collaboration
- Partnering
Patent Information:
Drug Discovery
For Information, Contact:
Vaibhav Saini
Senior Manager Commercialization
Northeastern University
Nikolai Slavov
Bogdan Budnik
Ezra Levy