How does the ratio compression in TMT-labeling quantitative proteomics occur, what impact does this characteristic have? Why can TMT only perform relative quantification and not absolute quantification?
1. The Emergence and Impact of Ratio Compression
In TMT-labeled quantitative proteomics, ratio compression is a common issue. It primarily arises during mass spectrometry analysis when multiple different peptides are ionized simultaneously and enter the mass spectrometer detector. This leads to ion signals at the same m/z value being shared by isotopic tags from different peptides. Since the ion abundance of TMT tags can vary slightly between samples, these minor differences are often averaged or diminished during mixed analysis, ultimately leading to the compression of signal ratios between TMT tags.
The result of ratio compression is an underestimation of differences between samples, particularly those with significant actual differences. The signal ratio may be compressed to nearly 1:1. This phenomenon not only affects the precision of the experiment but may also obscure biologically meaningful changes, leading to misinterpretations of protein expression levels.
To address this issue, researchers often employ correction methods, such as ratio compression correction algorithms or normalization-based methods, to reduce the impact of ratio compression on quantitative results.
2. Why TMT Can Only Perform Relative Quantification, Not Absolute Quantification
TMT is an isotopic labeling method that achieves relative quantification of multiple samples by labeling peptides with different isotopic tags. Its principle relies on comparing the signal intensities of labeled peptides between different samples, rather than measuring the absolute abundance of a particular peptide or protein.
-
Lack of internal standards: TMT-labeled quantification typically lacks absolute quantification internal standards or calibration curves, making it impossible to directly measure the absolute abundance of proteins.
-
Inconsistencies in instrument response: The mass spectrometric response factors (i.e., the response intensity of the mass spectrometer to different peptides) may vary for different proteins or peptides. This variability makes it impossible to directly infer the absolute content of proteins.
BiotechPack, A Biopharmaceutical Characterization and Multi-Omics Mass Spectrometry (MS) Services Provider
Related Services:
Quantitative Proteomics Analysis
Label-Free Quantitative Proteomics Analysis
Label-Based Protein Quantification Technologies - iTRAQ, TMT, SILAC
TMT/iTRAQ/MultiNotch Quantitative Proteomics Analysis
SILAC/Dimethyl Labeling-Based Quantitative Proteomics Analysis
How to order?
