Chemical Sciences: A Manual for CSIR-UGC National Eligibility Test for Lectureship and JRF/Quantitative proteomics

The aim of quantitative proteomics is to obtain quantitative information about all 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.

Mass spectrometry-based proteomics

Due to differences in ionization efficiency and/or detectability the intensity of a peak in a mass spectrum is not a good indicator of the amount of the analyte. However, differences in peak intensity of the same analyte accurately reflect differences in its abundance. Therefore, in mass spectrometry-based proteomics relative quantification is used to compare protein abundance between samples. This can be achieved by labeling one sample with stable isotopes alone or incorporated into protein crosslinkers like D4-BS3, which leads to a mass shift in the mass spectrum. Differentially labeled samples are combined and analyzed together. The differences in the peak intensities of the isotope pairs accurately reflect difference in the abundance of the corresponding proteins. Current methods include:

• Isotope-Coded Affinity Tags (ICAT))
• Isobaric labeling
  • Tandem mass tags (TMT)
  • Isobaric tags for relative and absolute quantitation (iTRAQ)
• Label-free quantification / No Label Quantitation
• Metal Coded Tags (MeCATs)
• N-Terminal Labelling
• Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC)

MeCAT can be used in combination with element mass spectrometry ICP-MS allowing first-time absolute quantification of the metal bound by MeCAT reagent to a protein or biomolecule. Thus it is possible to determine the absolute amount of protein down to attomol range using external calibration by metal standard solution. It is compatible to protein separation by 2D electrophoresis and chromatography in multiplex experiments. Protein identification and relative quantification can be performed by MALDI-MS/MS and ESI-MS/MS.

Two-dimensional gel electrophoresis

Modern day gel electrophoresis research often leverages software-based image analysis tools primarily to analyze bio-markers by quantifying individual, as well as showing the separation between one or more protein "spots" on a scanned image of a 2-DE product. Differential staining of gels with fluorescent dyes (difference gel electrophoresis) can also be used to highlight differences in the spot pattern.