Quantitative proteomics

Quantitative proteomics is an analytical chemistry technique for determining the amount of proteins in a sample. Rather than just providing lists of proteins identified in a certain sample, quantitative proteomics yields information about differences between samples. For example, this approach can be used to compare samples from healthy and diseased patients. The methods for protein identification are identical to those used in general (i.e. qualitative) proteomics, but include quantification as an additional dimension. Quantitative proteomics is mainly performed by two-dimensional gel electrophoresis (2-DE) or mass spectrometry (MS). However, a recent developed method of Quantitative Dot Blot (QDB) analysis is able to measure both the absolute and relative quantity of an individual proteins in the sample in high throughput format, thus open a new direction for proteomic research. In contrast to 2-DE, which requires MS for the downstream protein identification, MS technology can identify and quantify the changes.

Mass spectrometry (MS) and two-dimensional gel electrophoresis (2-DE) represent the main technologies for quantitative proteomics with advantages and disadvantages. 2-DE provides information about the protein quantity, charge, and mass of the intact protein. It has limitations for the analysis of proteins larger than 150 kDa or smaller than 5kDa and low solubility proteins. Quantitative MS has higher sensitivity but does not provide information about the intact protein.

Classical 2-DE based on post-electrophoretic dye staining has limitations: at least three technical replicates are required to verify the reproducibility.Difference gel electrophoresis (DIGE) uses fluorescence-based labeling of the proteins prior to separation has increased the precision of quantification as well as the sensitivity in the protein detection. Therefore, DIGE represents the current main approach for the 2-DE based study of proteomes.

For quantitative MS, a commonly applied approach is isotope-coded affinity tags (ICAT), which uses two reagents with heavy and light isotopes, respectively, and a biotin affinity tag to modify cysteine containing peptides. This technology has been used to label whole Saccharomyces cerevisiae cells, and, in conjunction with mass spectrometry, helped lay the foundation of quantitative proteomics.

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