TMT vs Label Free

TMT (Tandem Mass Tag) Labeling

TMT is a chemical labeling method used for quantitative proteomics. Peptides from different samples are chemically labeled with different isotopic labels. These labels are designed to have the same mass, but when broken down in a mass spectrometer they will release different reporter ions. The relative abundance of peptides in different samples can be determined by comparing the intensities of these reporter ions.

 

1. Advantages

(1) Multiplexing: Multiple samples can be analyzed simultaneously, which can save time and reduce experimental variability.

(2) The use of isotopic labels adds to the reliability of peptide identification.

 

2. Disadvantages

(1) Increased complexity and cost associated with the labeling process.

(2) Ratio compression may occur due to co-isolation of interfering species.

 

Label-Free Quantification

Label-free quantification relies on comparing the intensity or counts of peptide MS signals in different runs to determine the relative abundance of peptides without using chemical labels.

 

1. Advantages

(1) Simplicity: No need for labeling, reducing sample handling steps and costs.

(2) The number of samples that can be compared is not limited as no multiplexing labels are needed.

 

2. Disadvantages

(1) More stringent normalization between runs is needed to take into account technical variability.

(2) More replicates are usually needed to achieve the same statistical power as labeled methods.

 

Comparison

While TMT offers the advantage of multiplexing and possibly increased accuracy due to the use of labels, label-free quantification is simpler and usually cheaper. The choice between these methods often depends on the specific requirements of the study, available resources, and the number of samples being analyzed.