Mass spectrometry targeted proteomics

Opiteck, G.J. and Scheffler, J.E. (2004). Target class strategies in mass spectrometry-based proteomics, Exp. Rev. Proteom, 1(1), 57-66. 

Warscheid, B. Fenselau, C. A targeted proteomics approach to the rapid identification of bacterial cell mixtures by MALDI mass spectrometry. Proteomics 2004, 4, 2877-2892. 

Lewis TS et al. Identification of novel MAP kinase pathway signaling targets by functional proteomics and mass spectrometry. Mol Cell 2000 6 1343-1354. 

The sustained attractiveness of photolabeling is apparent from its prominence in studies of y-secretase, an intramembrane protease that contributes to forming amyloid-p peptides and is a major target in Alzheimer s disease [60-62]. y-Secretase is a complex of at least four different polypeptides, and is difficult to engage with high-resolution structural methods. However, in a case of this kind that involves a known target, immunodetection of proteins can often specify the target of y-secretase inhibitor photoaffinity probes such as 19, and proteomic mass spectrometry is not needed. 

Many diseases are characterized by the expression of specific proteins1 in some cases, malignant cells yield unique protein profiles when total cellular protein extracts are analyzed by proteomic methods such as two-dimensional gel electrophoresis or matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS).2 High-throughput proteomic studies may be useful to differentiate normal cells from cancer cells, to identify and define the use of biomarkers for specific cancers, and to characterize the clinical course of disease. Proteomics can also be used to isolate and characterize potential drug targets and to evaluate the efficacy of treatments. 

High-throughput proteomic methods hold great promise for the discovery of novel protein biomarkers that can be translated into practical interventions for the diagnosis, treatment, and prevention of disease. These approaches may also facilitate the development of therapeutic agents that are targeted to specific molecular alterations in diseases such as cancer. In many cases, malignant cells yield unique protein profiles when total protein extracts from such cells are analyzed by 2-D gel electrophoresis or mass spectrometry (MS) methods. Such proteomic studies have the potential to provide an important complement to the analysis of DNA and mRNA extracts from these tissues.1... 

B. Warscheid and C. Fenslau. A Targeted Proteomics Approach to the Rapid Identification of Bacterial Cell Mixtures by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Proteomics, 4(2004) 2877-2892. 

If the scope of mass spectrometry is limitless, why are the applications of clinical MS almost completely small molecules The answer is that most clinical tests analyze small molecules, biomarkers that are either metabolites or steroids and, hence, mass spectrometers would target those first. Perhaps a more complete answer would also include that methods must be very robust, easily reproduced in different labs, reliable, and subjected to an extensive array of validation tests. Although peptide and protein analysis is increasing rapidly in clinical labs, the MS approaches to these assays is lagging behind somewhat. MS techniques targeting these peptides and proteins exist, but they are primarily in the research stage, with few systems and methods subjected to the clinical rigors of validation. Once the necessary validations occur and methods simplified, it will only be a short time before MS is used routinely in clinical proteomics. 

Keshishian H, Addona T, Burgess M, Mani DR, Shi X, Kuhn E et al (2009) Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution. Mol Cell Proteomics 8 2339-2349... 

Fig. 4 Identification of alkyne-tagged P-lactone probes that target ClpP in S. aureus using click-chemistry, in-gel fluorescence and mass spectrometry. Subsequently, lead compounds were administered to 5. aureus and changes to the global bacterial proteome monitored. Particularly, changes to the levels of haemolysis and proteolysis enzymes (haemolysins, proteases, lipases and...

Significant improvements in the technologies of high-resolution two-dimensional Polyacrylamide Gel Electrophoresis (2-D PAGE) and Mass Spectrometry (MS) have marked the start of proteome analysis. Proteomics permits the analysis of thousand of proteins simultaneously, and have the potential to identify markers for early detection, classification and prognosis of diseases, as well as pinpointing targets for improved treatment outcomes [42]. 

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