Deep Quantitative Proteomics of Biological Samples via iTRAQ/TMT

iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) and TMT (Tandem Mass Tag) are two commonly used mass spectrometry labeling techniques for protein quantification analysis in proteomics research. These techniques quantify protein expression levels in different samples by using chemical labels and are particularly useful for comparing biological samples under different conditions, such as disease vs normal state, or cells before and after drug treatment.

 

iTRAQ Technology

iTRAQ is an isotope-based labeling technique used to simultaneously quantify proteins in up to 8 different samples. It achieves protein quantification by adding isotope tags to the N-terminus and lysine residues of the peptides. The iTRAQ tagged peptides are recognized and broken down in the mass spectrometer, generating unique reporter ions, the intensities of which reflect the abundance of the corresponding proteins in the original sample.

 

TMT Technology

Similarly, TMT is a mass spectrometry labeling strategy used to compare the relative expression of proteins in different samples. TMT labels covalently bind to the peptides of the protein, allowing for the simultaneous analysis of up to 16 different samples. Similar to iTRAQ, the TMT tagged peptides generate specific reporter ions during the mass spectrometry analysis, the intensities of which are used to calculate the relative expression of the proteins.

 

iTRAQ vs TMT

1. Sample Handling Capacity

TMT technology generally can handle more samples (up to 16), while iTRAQ can handle up to 8 samples.

 

2. Quantification Accuracy

Although both techniques provide highly accurate quantitative data, improvements in TMT technology and its higher multiplexing capacity may make it more precise in some cases.

 

3. Cost-Effectiveness

The cost of iTRAQ is usually lower than TMT, especially when the number of samples analyzed is small.

 

4. Scope of Application

Both techniques are widely used in biomedical research, discovery of disease markers, identification of drug targets, and systems biology research.

 

5. Data Processing

The data processing workflow of TMT and iTRAQ is similar, but data processing might be more complex for TMT because it can analyze more samples.

 

Both iTRAQ and TMT technologies have their advantages, and the choice of which technology to use depends on the research objective, the number of samples, and available resources. They are both indispensable tools in current proteomics research, providing strong support for a deeper understanding of biological systems and disease mechanisms. With the continuous advancement of mass spectrometry technology, these methods will continue to play a crucial role in the field of biomedical research.