Quantitative proteomics

Quantitative proteomics is an analytical chemistry technique for determining the amount of various proteins, including cofactors, in a sample. The methods for protein identification and separation are identical to those used in general qualitative proteomics, but include quantification as an additional dimension. Rather than just providing lists of proteins identified in a certain sample, quantitative proteomics yields information about the physiological differences between two biological samples. For example, this approach can be used to compare samples from healthy and diseased patients. Quantitative proteomics is mainly performed by two-dimensional gel electrophoresis (2-DE), preparative native PAGE, 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 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 structural changes and physiological functions.

Quantification using spectrophotometry The concentration of a certain protein in a sample may be determined using spectrophotometric procedures. The concentration of a protein can be determined by measuring the OD at 280 nm on a spectrophotometer, which can be used with a standard curve assay to quantify the presence of tryptophan, tyrosine, and phenylalanine. However, this method is not the most accurate because the composition of proteins can vary greatly and this method would not be able to quantify proteins that do not contain the aforementioned amino acids. This method is also inaccurate due to the possibility of nucleic acid contamination. Other more accurate spectrophotometric procedures for protein quantification include the Biuret, Lowry, BCA, and Bradford methods. An alternative method for label free protein quantification in clear liquid is cuvette-based SPR technique, that simultaneously measures the refractive index ranging 1.0 to 1.6 nD and concentration of the protein ranging from 0.5 μL to 2 mL in volume. This system consists of the calibrated optical filter with very high angular resolution and the interaction of light with this crystal forms a resonance at a wavelength which correlates to concentration and refractive index near the crystal.

Quantification using two dimensional electrophoresis Two-dimensional gel electrophoresis (2-DE) represents one of 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.

Quantification using mass spectrometry

Mass spectrometry (MS) represents one of the main technologies for quantitative proteomics with advantages and disadvantages. Quantitative MS has higher sensitivity but can provide only limited information about the intact protein. Quantitative MS has been used for both discovery and targeted proteomic analysis to understand global proteomic dynamics in populations of cells (bulk analysis) or in individual cells (single-cell analysis). Early approaches developed in the 1990s applied 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. This approach has been superseded by isobaric mass tags, which are also used for single-cell protein analysis.

Relative and absolute quantification Mass spectrometry is not inherently quantitative because of differences in the ionization efficiency and/or detectability of the many peptides in a given sample, which has sparked the development of methods to determine relative and absolute abundance of proteins in samples. The intensity of a peak in a mass spectrum is not a good indicator of the amount of the analyte in the sample, although differences in peak intensity of the same analyte between multiple samples accurately reflect relative differences in its abundance.

Stable isotope labeling in mass spectrometry

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