Quantitative proteomics absolute quantitation

Quantitation and qualification of large molecules follow similar principles as procedures for small molecules but involve different foci and approaches. The quantitation of proteins and peptides includes relative and absolute amount evaluations. Most proteomic applications in drug discovery are concerned with relative abundances of proteins. 

M. A. Kuzyk, D. Smith, J. Yang, T. J. Cross, A. M. Jackson, D. B. Hardie, N. L. Anderson, and C. H. Borchers, Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma, Mol. Cell. Proteomics, 8 (2009) 1860-1877. 

Isobaric tags for relative and absolute quantitation of proteins in proteomic research Janus kinase c-Jun iV-terminal kinase... 

In the previous sections, comparative quantitative proteomics is discussed. This is aiming at relative quantification of protein levels in various cell states. In some applications, absolute rather than relative quantification of proteins is relevant, e.g., as an alternative to immunoaffinity methods for quantitative bioanalysis of protein dmgs. This requires different strategies. 

B.M. Mayr, O. Kohlbacher, K. Reinert, M. Sturm, C. Gropl, E. Lange, C. Klein, C.G. Huber, Absolute myoglobin quantitation in serum by combining 2D-LC-ESI-MS and novel data analysis algorithms, J. Proteome Res., 5 (2006) 414. 

AQUA allows for direct comparison of proteomic data obtained on different instruments and in different laboratories. The need to measure the absolute abundance of proteins is achievable using a targeted quantitation approach. A synthetic, isotopically labeled peptide is used as the IS. This peptide is the isotopic counterpart of a signature peptide, which represents a 1 1 ratio... 

Mayr BM, Kohlbacher O, Reinert K, Sturm M, Gropl C, Lange E, Klein C, Huber CG. Absolute myoglobin quantitation in serum by combining two-dimensional liquid chromatography electrospray ionization mass spectrometry and novel data analysis algorithms. J Proteome Res 2006 5(2) 414—421. 

The objective in many proteomic experiments is to identify proteins whose abundance differs across two or more related samples. This may include variations in absolute protein levels or variations in the stoichiometry of different forms of modification, such as phosphorylation. At the current time, protein quantitation in proteomics relies primarily on the use of... 

Some popular quantitative methods in proteomics are based on derivatization with agents containing a stable isotope. In this respect, isotope-coded affinity tags (ICAT) have been widely used [121], as have isobaric tags for relative and absolute quantitation (iTRAQ) [122]. 

Obviously, the combination of element labeling and then detection by element mass spectrometry is still in its infancy for quantitative proteomics. However, this is such a promising method for metallomics and metallopro-teomics, because of the unique advantages (1) results can be validated due to the traceability of ICP-MS measurement (2) multiplexed analysis is easy to implement because of the availability of so many isotopes for labeling and (3) absolute quantification at a very low concentration allows comparison between the results from different laboratories. 

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