A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics.

Area of Science:

• Proteomics
• Analytical Chemistry
• Biochemistry

Background:

• Mass spectrometry (MS) is crucial for quantitative proteomics.
• Multiplex isotope labeling improves accuracy, precision, and throughput in MS-based proteomics.
• Ratio-distortion is a key limitation in quantitative proteomics.

Purpose of the Study:

• To provide a comprehensive tutorial review of multiplex isotope labeling techniques in mass spectrometry.
• To detail the principles, advantages, and limitations of various labeling strategies.
• To highlight applications and future directions in quantitative proteomics.

Main Methods:

• Overview of precursor-based, mass defect-based, reporter ion-based, and hybrid labeling methods.
• Discussion of strategies to mitigate ratio-distortion.
• Review of current applications in diverse proteomic research areas.

Main Results:

• Detailed explanation of fundamental principles for each labeling technique.
• Identification of specific advantages and limitations associated with each method.
• Examples of successful applications in biomarker discovery, neuroproteomics, PTM analysis, cross-linking MS, and single-cell proteomics.

Conclusions:

• Multiplex isotope labeling is a powerful strategy for advancing quantitative proteomics.
• Understanding technique-specific limitations and mitigation strategies is essential for reliable results.
• This review serves as a guide for researchers selecting methods and highlights future trends in the field.