Differences between Labeling Quantification and Label-Free Quantification in Proteomics
Labeled quantification and label-free quantification are two primary quantification strategies in proteomics used to compare protein abundance across different samples or treatment conditions.
The main differences between them are as follows:
1. Labeled Quantification:
In the sample preparation stage, a labeling technique is used to chemically label proteins or protein enzymatic peptides, which usually have different masses. After mixing, these mass differences can be used to quantify proteins in different samples through mass spectrometry analysis.
Figure 1. Workflow of relative quantification using 10plex TMT (Zhang et al., 2017)
2. Label-Free Quantification:
No chemical labels are used; instead, quantification is achieved by comparing the signal intensity of the same protein in different samples (such as peak area or peak height of peptides) through multiple repeated experiments.
Figure 2. Workflow of Label-Free Quantitative Proteomics
Labeled quantification methods involve using certain labeling techniques, such as ICAT, iTRAQ, or TMT, to chemically label proteins or protein enzymatic peptides in the sample preparation stage. These labels typically have different masses, allowing samples to be quantified by mass differences using mass spectrometry after mixing. 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 it requires additional steps for labeling, which may increase experimental costs and complexity.
On the other hand, label-free quantification methods do not use any chemical labeling. Instead, they achieve quantification by comparing the signal intensity 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, thus reducing costs. However, to ensure comparability between experiments, it requires stricter sample handling and mass spectrometry analysis conditions.
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