Differences of Labeled and Label-free Quantitative Proteomics

Labeled quantification and label-free quantification are two major quantitative strategies in proteomics for comparing protein abundance under different samples or treatment conditions.

 

Labeled Quantification

In the sample preparation stage, a certain labeling technique is used to chemically label proteins or protein digestion peptides. These labels usually have different masses. After mixing, the samples are analyzed by mass spectrometry, which allows the quantification of proteins in different samples based on these mass differences.

 

Label-Free Quantification

No chemical labels are used. Instead, quantification is achieved by comparing the signal intensities (such as the peak area or peak height of peptides) of the same protein in different samples through multiple repeat experiments.

 

In labeled quantification methods, a certain labeling technique, such as ICAT, iTRAQ, or TMT, is used to chemically label proteins or protein digestion peptides during the sample preparation stage. These labels usually have different masses, allowing the mixed samples to be quantified by mass spectrometry based on these mass differences. The advantage of this method is that samples can be mixed before mass spectrometry analysis, reducing variations caused by experimental operations or machine analysis. However, the drawback is that additional steps are required for labeling, which may increase the experimental cost and complexity.

 

On the other hand, label-free quantification methods do not use any chemical labels. Instead, quantification is achieved by comparing the signal intensities of the same protein in different samples, such as the peak area or peak height of peptides. This method is simpler to operate and does not require additional labeling steps, thereby reducing costs. However, to ensure comparability between experiments, it requires more stringent sample handling and mass spectrometry analysis conditions.