Single-Cell Proteomics: A Key Technology for Revealing Cellular Heterogeneity
In multicellular organisms, although cells share nearly identical genomes, they differ markedly in morphology, function, and fate. This phenomenon, referred to as cellular heterogeneity, lies at the core of complex biological processes such as development, disease progression, and drug response. To gain a deeper understanding of this heterogeneity, researchers have progressively transitioned from population-averaged measurements to multi-omics analyses at single-cell resolution. Among these advances, single-cell proteomics (SCP) has emerged as a frontier breakthrough following single-cell RNA sequencing, reshaping our understanding of the dynamics of biological systems.
Why Must Single-Cell Research Focus on the Protein Level?
1. Proteins Directly Define the Functional State of Cells
Proteins act as the direct executors of cellular activities, performing essential roles in signal transduction, metabolic regulation, structural support, and immune recognition. Compared with RNA, proteins more accurately reflect the functional phenotype of cells. For instance, whether a T cell is activated is often determined not by its mRNA expression but by the expression and modification states of key proteins on its surface or within the cell.
2. Regulation of Transcription and Translation Is Not Synchronized
Although RNA sequencing reveals heterogeneity at the transcriptional level, transcription and translation do not correspond in a one-to-one manner. Factors such as translation efficiency, protein stability, and post-translational modifications can substantially influence cell fate before such changes are detectable at the RNA level. Single-cell measurements at the protein level enable comprehensive capture of these functional differences.
3. A Critical Tool for Identifying Rare Cell Subpopulations
In cancer, stem cell, and immunological studies, rare cell subpopulations frequently execute pivotal biological functions, such as tumor stem cells, drug-resistant cells, and regulatory T cells. Single-cell proteomics can elucidate the protein-level characteristics and dynamic trajectories of these rare populations, providing crucial insights into the regulatory dynamics of biological systems.
Mainstream Technical Approaches of Single-Cell Proteomics
1. Mass Spectrometry-Driven Quantification of Single-Cell Proteins
Mass spectrometry-based single-cell proteomics (SCP) methods leverage high-sensitivity and high-resolution instrument platforms to achieve high-throughput, wide-coverage proteome analysis at the single-cell scale. The SCoPE-MS series, exemplified by the Tandem Mass Tag (TMT) multiplex labeling strategy, utilizes carrier channels in TMT labeling to enhance signals, thereby improving quantitative depth and data consistency. Building on these approaches, SCP platforms continue to increase analytical throughput and quantitative precision by integrating ultra-sensitive mass spectrometry systems such as Orbitrap and time-of-flight (TOF). These advancements enable single-cell-level profiling of thousands of proteins, supporting large-scale cell atlas construction and mechanistic investigations.
2. Antibody-Based Protein Expression Detection Methods
Antibody-labeling approaches, including mass cytometry (CyTOF) and CITE-seq, represent another critical category of single-cell protein detection technologies. CyTOF employs metal-labeled antibodies to simultaneously detect over 40 proteins, making it widely applicable in immune atlas generation. CITE-seq combines antibody-derived protein information with single-cell RNA sequencing, enabling integrated analyses of both protein and transcriptomic dimensions. These techniques offer advantages such as high throughput, direct detection, and well-established sample processing workflows, making them particularly suitable for investigating the distribution and dynamic changes of known biomarkers within cell populations.
3. Multi-Omics Integration Driving Mechanistic Insights
The convergence of sequencing and mass spectrometry technologies is driving the emergence of single-cell multi-omics analyses as a major research trend. Integrating single-cell proteomic data with transcriptomic, epigenomic, or metabolomic datasets enables researchers to characterize cell states from multiple perspectives. For instance, in studies of the tumor immune microenvironment, combining protein and transcriptomic data can simultaneously resolve cell types and functional states, thereby enhancing the precision and scope of mechanistic investigations.
Single-cell proteomics provides a novel perspective for elucidating the molecular landscape of cellular heterogeneity. By achieving single-cell resolution at the protein level, researchers can more accurately identify functional cell states, uncover regulatory mechanisms, and track disease progression. This technology is profoundly shaping multiple fields in life sciences, serving as a critical driver of future omics advancements. As a specialized platform dedicated to proteomics and mass spectrometry services, MtoZ Biolabs remains committed to monitoring the latest developments in single-cell proteomics, offering comprehensive analysis services to support researchers in uncovering the molecular basis of cellular heterogeneity.
MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider.
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