What Methods are Used for Proteomics Differential Analysis?

Proteomics differential analysis typically involves a variety of techniques and methods, aimed at comparing the expression levels of proteins in different samples (such as different tissues, cell states, or treatment conditions).

 

Two-Dimensional Gel Electrophoresis (2D-GE)

2D-GE is a traditional method that separates proteins by isoelectric point in the first dimension and by molecular weight in the second dimension. Then, by staining and image analysis, gels from different samples are compared to identify significantly differentially expressed proteins.

 

Mass Spectrometry

(1) Mass spectrometry (MS) is one of the most powerful tools in proteomics research, especially in differential expression analysis.

(2) Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) is widely used in proteomics to identify and quantify proteins.

 

Labeling and Label-Free Quantitation Methods

(1) Labeling methods (such as SILAC, iTRAQ, TMT) distinguish proteins from different samples using different isotopes or chemical labels, and then perform quantitative comparisons in mass spectrometry.

(2) Label-free quantitation methods directly compare the MS signal intensities of proteins in different samples.

 

Protein Microarrays

Protein microarray technology allows simultaneous analysis of the relative expression levels of a large number of proteins or peptides. This method is often used for high-throughput screening of specific protein or antibody arrays.

 

Bioinformatics Analysis

Bioinformatics tools are used to process and analyze mass spectrometry or other experimental data to identify significantly differentially expressed proteins, and may perform functional annotation and pathway analysis.

 

Each method has its advantages and limitations, and the choice of appropriate method depends on the purpose of the specific experiment, sample type, available equipment and resources, and required data quality. Typically, these methods are combined to obtain more comprehensive and reliable results.