Strategies in relative and absolute quantitative mass spectrometry based proteomics

Area of Science:

• Proteomics
• Quantitative Mass Spectrometry
• Biochemistry

Background:

• Quantitative mass spectrometry is crucial for global proteome studies, offering various absolute and relative quantification techniques.
• Existing methods vary in accuracy, proteome coverage, complexity, and robustness.

Purpose of the Study:

• To review common relative and absolute quantification strategies in proteomics.
• To exemplify these strategies using three distinct experimental studies.

Main Methods:

• Label-free relative quantification for membrane proteome analysis (Mus musculus olfactory receptors).
• Stable Isotope Labeling by Amino acids in Cell culture (SILAC) for peroxisomal importomer studies (Saccharomyces cerevisiae).
• Absolute Quantification (AQUA) using stable isotopes for prenylome analysis under inhibitor influence.

Main Results:

• Demonstrated the utility of label-free quantification for deep proteome coverage.
• Showcased SILAC's effectiveness in identifying protein complexes and transient interactors.
• Highlighted AQUA's application in quantifying specific proteins affected by novel inhibitors.

Conclusions:

• Quantitative mass spectrometry offers diverse strategies for proteome analysis.
• The choice of method depends on specific research questions regarding accuracy, coverage, and complexity.
• These techniques are vital for advancing our understanding of biological systems and drug discovery.