Spatial Proteomics

Spatial proteomics is a discipline that studies the three-dimensional spatial distribution of proteins within cells and their interactions with other molecules. Different from traditional proteomics which mainly focuses on protein sequences, expression levels, and interactions, spatial proteomics pays more attention to the spatial location and dynamic changes of proteins within cells. This three-dimensional information is of great significance for our understanding of protein function and regulation mechanisms.

 

The general process of spatial proteomics technology is to obtain interested tissue regions or cells in the sample through high-precision laser capture microdissection (LCM) technology, and analyze the expression characteristics of proteins at different spatial positions through optimized ultra-micro proteomics technology, thereby obtaining target samples. The protein expression spectrum of different functional areas and different cell types. Its research methods are roughly divided into two types: spatial proteomics based on mass spectrometry and spatial proteomics based on fluorescence imaging.

 

1. Mass Spectrometry-Based Spatial Proteomics

Mass spectrometry-based spatial proteomics includes MSI and MIBI:

 

(1) Mass Spectrometry Imaging (MSI) is a high-precision technology that combines mass spectrometry with spatial positioning, which can accurately capture molecular mass and location information at the tissue and cell level. In proteomics research, MSI is widely used to analyze the spatial distribution of proteins in tissue sections, providing important clues for disease mechanism research and biomarker discovery. This technology does not require specific labeling, the sample pretreatment steps are simple, the spatial resolution is high, and it can exert the power of mass spectrometry. It can perform in situ imaging analysis of thousands of biomolecules at the same time.

 

(2) Multiplexed Ion Beam Imaging (MIBI) is a kind of Secondary Ion Mass Spectroscopy (SIMS). The principle is to combine spatial imaging methods with mass spectrometry, use metal isotope element-labeled antibodies, and simultaneously detect targets on sample sections for imaging, and then analyze multiple proteins in the same tissue. Compared with MSI, MIBI has higher sensitivity and resolution, can accurately quantify immune cell subsets and their spatial distribution in tumors, but this technology strictly limits the detection target to 100, and the cost is high, and the choice of isotopes is limited.

 

2. Fluorescence Imaging-Based Spatial Proteomics

The most widely used fluorescence imaging-based spatial proteomics is CODEX (CO-Detection by IndEXing). CODEX is a technology that uses a unique protein fluorescence labeling method to analyze the spatial distribution and interaction of proteins in tissues or cells. The core principle is to couple antibodies to specific oligonucleotide "barcode labels" (Barcode), not directly labeled with fluorescent dyes, and perform fluorescence imaging by specifically binding with complementary oligonucleotide sequences of Barcode. This method breaks through the limitations of the number of visible light spectrum fluorescence imaging channels and can simultaneously detect and analyze up to 50 or even more protein targets. In addition, this technology also has the advantages of high throughput, high spatial resolution, and flexible application, so it is widely used in tumor microenvironment and tumor immunity, drug research and development, and efficacy evaluation.