Spatial Proteomics Services

Proteins are functional molecules of all cells and are effectors of almost all biological processes. Their subcellular localization is tightly regulated and closely related to protein function in health and disease. Therefore, the vast majority of drug targets are proteins. This makes capturing the spatial proteome and resolving the localization of proteins and their dynamics at the subcellular level essential for a comprehensive understanding of cell biology, developing protein biomarkers, facilitating therapeutic and diagnostic tools, and more.

We offer spatial proteomics services

Spatial proteomics is the large-scale analysis of proteins and their localization and dynamics within tissues. CD Genomics offers imaging and mass spectrometry-based spatial proteomics methods that enable a quantitative and spatial analysis of multiple protein markers in whole tissue sections at single-cell resolution. Offering our customers the possibility to explore hundreds of protein targets at the subcellular level in a variety of cellular states and conditions. It is critical for understanding the role of microenvironmental heterogeneity in organ biological function and for discovering novel protein biomarkers for disease.

Imaging-based spatial proteomics

• Antibody-based visualization
• FP tagging-based visualization

Figure 1. Example images of 12 cellular organelles and structures obtained using antibody-based visualization and fluorescence microscopy. (Lundberg, E., et al., 2019)

Mass spectrometry-based spatial proteomics

• Combined with absolute protein quantification allows estimation of the copy number of proteins in each average cell in which a detected translocation occurs.
• Organelle proteins are localized by isotope tagging maps to track organelle rearrangements. Reveals individual protein translocations associated with organelle rearrangements.
• Generate protein correlation profiles to monitor subcellular translocations of proteins in tissues.

Types of samples we can analyze

Species: human, mouse, rat, etc.

Tissue types: heart, lung, eyes, liver, kidney, spleen, stomach, testis, ovary, breast, lymph node, brain, intestine, thyroid, skin, pancreas, bone tissue, etc.

Sample requirements

• Suitable for fresh-frozen (FF) and formalin-fixed-paraffin-embedded (FFPE) tissue sections.
• You need to prepare at least 3 tissue samples.

Practical applications

• Screen hundreds of proteins to identify potential drug targets.
• Explore the effects of small molecules/substances on specific organelles, protein families, or proteins within specific pathways.
• Validate knockout cell lines and antibodies by assessing fluorescence signal reduction and quantitative image analysis.
• Screen for proteins co-localized with specific markers in different cellular conditions.
• Confirm data from mass spectrometry experiments, such as protein translocations.
• Assessment of immune cell infiltration in pathological tissue biopsies.

Technical features and advantages

• Characterize cell type distribution and interactions in tissue samples.
• Enables high-throughput subcellular analysis of protein targets in single cells using immunofluorescence.
• Reveals complex structures, including single-cell variants, dynamic protein translocations, changing interaction networks, and proteins localized in multiple compartments.
• Targeted phenotypic screens are available to elucidate drug mechanisms of action.

We do it better

CD Genomics is committed to providing a spatial multi-omics platform that combines spatial proteomics data with spatial transcriptomics, spatial genomics, and spatial metabolomics data to provide more comprehensive insights into tissue biology and the discovery of new biomarkers. Addressing a wide range of client needs from discovering new cell types, determining the function of cell types, understanding how cells are affected by the microenvironment, to discovering how cells organize and interact to influence disease progression, finding patterns in the cellular landscape that correlate with the therapeutic response or patient outcomes, and determining the efficacy of prognostic or predictive biomarkers.

Reference

1. Lundberg, E., et al., (2019). "Spatial proteomics: a powerful discovery tool for cell biology." Nature Reviews Molecular Cell Biology, 20, 285-302.