Quantitative proteomics is essential for understanding dynamic changes in protein abundance across different biological states, such as disease progression or drug treatment. Several key Quantitative Proteomics methodologies are employed, falling into two main categories: label-free and label-based approaches. Label-free quantification relies on comparing the intensity or spectral counts of peptides identified by the mass spectrometer across separate analytical runs. While simple and cost-effective, it is highly sensitive to technical variations.

Label-based methods use stable isotopes to chemically or metabolically tag proteins, allowing multiple samples to be mixed and analyzed simultaneously in a single mass spectrometry run, thus eliminating run-to-run variation. Examples include Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC), which tags proteins metabolically in vivo and is highly accurate for comparing cell-based samples. Isobaric tagging, such as Tandem Mass Tags (TMT), chemically tags peptides in vitro, allowing the simultaneous relative quantification of proteins across up to 18 different samples, increasing throughput for large-scale clinical studies.

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