Quantitative Proteomics Analysis

Quantitative studies comparing the relative abundances of proteins in different cellular states may be performed with MS. Methods such as 2D-GE have been utilized extensively with great success and differentially represent spots excised and then subjected to MS/MS for final identification of the differentially expressed proteins. 2D-GE requires approximately 50 pg of starting material and is limited by its bias toward high abundance proteins and propensity to detect proteins with extreme pi values. Furthermore, proteins at both extremes of molecular weight and those associated with membrane fractions are not well represented by 2D-GE.10 

---

Griffin, T. J. Han, D. K. Gygi, S. R Rist, B. Lee, H. Aebersold, R. Parker, K. C. Toward a high-throughput approach to quantitative proteomic analysis Expression-dependent protein identification by mass spectrometry. J. Am. Soc. Mass. Spectrom. 2001,12,1238-1246. 

Jain MR, Liu T, Hu J, et al. Quantitative proteomic analysis of formahn fixed paraffin embedded oral HPV lesions from HIV patients. Open Proteomics J. 2008 1 40-45. 

Aebersold, R. (2003) Quantitative proteome analysis Methods and applications. /. Infect. Dis. 187 (Suppl. 2), S315-S320. 

Zhou, H., Ranish, J.A., Watts, J.D., and Aebersold, R. (2002) Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nat. Biotechnol. 20, 512-515. 

Gygi, S. P., Rist, B., and Aebersold, R., Measuring gene expression by quantitative proteome analysis, Curr. Opin. Biotechnol., 11, 396, 2000. 

R. Aebersold. Quantitative Proteome Analysis Methods and Applications. J. Infect. Dis., 187, Suppl 2(2003) S315-20. 

Wolf-Yadlin, A., Hautaniemi, S., Lauffen-burger, D.A. and White, E.M. (2007) Multiple Reaction Monitoring for Robust Quantitative Proteomic Analysis of Cellular Signaling Networks. Proc Natl Acad Sci, 104, 5860-5865. 

Li C, Hong Y, Tan YX et al. Accurate qualitative and quantitative proteomic analysis of clinical hepatocellular carcinoma using laser capture microdissection coupled with isotope-coded affinity tag and two-dimensional liquid chromatography mass spectrometry. Mo/ Cell Proteomics 2004,3399-409. 

Smolka MB, Zhou H, Purkayastha S, Aebersold R. 2001. Optimization of the isotope-coded affinity tag-labeling procedure for quantitative proteome analysis. Anal Biochem 297 25-31. 

Shen, Y, Moore, R. J., Anderson, D. J., Zhang, R., Calvano, S. E., etal. (2005). Quantitative proteome analysis of human plasma following in vivo lipo-polysaccharide administration using 160/180 labeling and the accurate mass and time tag approach. Mol. Cell Proteomics 4, 700-709. 

Gupta, N., Wollscheid, B., Watts, J.D., Scheer, B., Aebersold, R. and Defranco, A.L. (2006) Quantitative proteomic analysis of B cell lipid rafts reveals that ezrin regulates antigen receptor-mediated lipid raft dynamics. Nat. Iimnunol. 7, 625-633. 

Maclellan, D.L., Steen, H., Adam, R.M., Garlick, M., Zurakowski, D., Gygi, S.P., Freeman, M.R. and Solomon, K.R. (2005) A quantitative proteomic analysis of growth factor-induced compositional changes in lipid rafts of human smooth muscle cells. Proteomics 5, 4733-4742, Published on-line. 

Wolf-YadUn A, Hautaniemi S, Lauffenburger DA, White FM. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc Natl Acad Sci U. S. A. 2007 104 5860-5865. 

J, Kearney RE, Nilsson T, Bergeron JIM. Quantitative proteomic analysis of the secretory pathway. Cell 2006 127 1265-1281. 

Gilchrist A, Au CE, Hiding J, Bell AW, Femandez-Rodriguez J, Lesimple S, Nagaya H, Roy L, Gosline SJ, Hallett M, et al. Quantitative proteomics analysis of the secretory pathway. Cell 2006 127 1265-1281. 

Y.H. Lee, H. Han, S.-B. Chang, S.-W. Lee, Isotope-coded N-terminal sulfonation of peptides allows quantitative proteomic analysis with increased de novo peptide sequencing capability. Rapid Commun. Mass Spectrom., 18 (2004) 3019. 

Macdonald N, Chevalier S, Tonge R, Davison M, Rowlinson R, Young J, Rayner S, Roberts R. Quantitative proteomic analysis of mouse liver response to the peroxisome proliferator diethylhexylphthalate (DEHP). Arch Toxicol 2001 75(7) 415-24. 

PTMs of proteins enable many important functions in organisms (139). Proteins with PTMs can be enriched in a variety of ways antibody-based, chemical derivatization, and ionic interaction-based (89). Antibodies that are highly specific to a particular PTM site help functional assays greatly. Antibodies that preferably bind a class of PTM (e.g., proteins carrying phosphotyrosine residues) make possible the in-depth quantitative proteomic analysis of these proteins. The substoichiometric nature of PTMs yields a low concentration of modified proteins. Enrichment of these proteins allows for improved analysis. 

Since light and heavy amino acids are chemically identical, the labeling process will not affect the chemical properties of the peptides and therefore differentially labeled peptides will co-elute from the HPLC column. However, these peptides are isotopically distinct from each other the peaks from light and heavy labeled peptides can be accurately distinguished and quantified by using mass spectrometry. An example of a study using SILAC includes the quantitative proteomic analysis of 495 proteins in renal cells towards the exploration of molecular mechanisms of calcineurin-inhibitors induced nephrotoxicity [82], In a second study, a... 

Lamoureux F, Mestre E, Essig M, Sauvage FL, Marquet P, Gastinel LN (2011) Quantitative proteomic analysis of cyclosporine-induced toxicity in a human kidney cell line and comparison with tacrolimus. J Proteomics 75(2) 677-694... 

Shiio, Y., Suh, K. S., Lee, H., Yuspa, S. H., Eisenman, R. N., Aeber-sold, R. (2006). Quantitative proteomic analysis of myc-induced apoptosis a direct role for Myc induction of the mitochondrial chloride ion channel, mtCLIC/CLIC4. The Journal of Biological Chemistjy, 281, 2750-2756. 

Guina, T., Purvine, S.O., Yi, E.C., Eng, J., Goodlett, D.R., Aehersold, R., and Miller, S.l. 2003, Quantitative proteomic analysis indictes increased synthesis of a quinolone by Pseudomonas aeruginosa isolates cystic fibrosis airways. Proc Natl Acad Sci USA 100 2771-2776. 

---