Proteomics Label Free, TMT, and iTRAQ

Proteomics is the science of studying the expression, function, and structure of all proteins in cells or tissues. This field utilizes various experimental methods to identify and quantify proteins, as well as to study their interactions and dynamic changes. Label-free and TMT/iTRAQ (isotope tagging) technologies are three commonly used methods in quantitative proteomics research, each with its own advantages and application scenarios.

 

Label-Free Technology

Label-Free, also known as unmarked technology, is a method of analyzing quantitative analysis of proteomes without relying on chemical tags. This technology mainly relies on mass spectrometry (MS), analyzing by comparing the relative abundance of proteins or peptides in different samples. The advantage of the unmarked method is that it is more direct and simple, does not require complex chemical treatment, thereby reducing the potential for variation in the sample processing process.

 

1. Advantages

(1) Simple and fast, no additional tagging steps are needed.

(2) Suitable for large-scale proteome analysis, especially when sample volume is limited.

(3) Reduces the potential bias introduced in the experiment.

 

2. Disadvantages

(1) Sensitivity and quantitative accuracy may not be as good as tagging methods.

(2) For complex samples, data analysis may be more challenging.

 

TMT/iTRAQ Technology

Tandem Mass Tags (TMT) and Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) are two different isotope tagging technologies widely used in quantitative analysis of proteomics. Both methods use heavy isotope tagging of proteins or peptides, then quantify protein expression levels through mass spectrometry analysis. TMT and iTRAQ allow for simultaneous analysis of multiple samples, improving the throughput and accuracy of comparative analysis.

 

1. Advantages

(1) High throughput: Able to simultaneously analyze protein expression of up to 16 (TMT) or 8 (iTRAQ) different samples.

(2) Improved accuracy and repeatability, especially in complex samples.

(3) Applicable for absolute and relative protein quantification.

 

2. Disadvantages

(1) More sample processing and chemical tagging steps are required in the early stage of the experiment.

(2) Tagging reagent cost is high.

(3) Variations in isotope tagging efficiency may occur during the analysis process.

 

Choosing Label-Free or TMT/iTRAQ technology depends on the specific research objectives, sample type, budget, and demand for accuracy and throughput. Unmarked technology is suitable for preliminary exploratory research due to its convenience and lower cost, while TMT/iTRAQ technology is suitable for in-depth quantitative analysis and large-scale comparative proteome research due to its high throughput and accuracy.