Proteomics antibody-based

Uhlen M, Ponten F. Antibody-based proteomics for human tissue profiling. Mol Cell Proteomics 2005 4(4) 384-393. Review. 

Ohara, O., Mann, M., Jensen, O. N., Pandey, a. (2002). A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-spedfic antibodies identification of a novel protein, Frigg, as a protein kinase A substrate. Mol. Cell Proteomics 1, 517-527. 

Figure 7 (a) Capillary electrophoresis (CE) for ABPP. The probe-labeled proteome is trypsinized and peptide fragments are analyzed via CE. (b) General strategy for antibody-based ABPP microarrays. Proteomes are labeled in solution with fluorescent activity-based probes and captured on glass slides arrayed with enzyme-specific antibodies. Reproduced by permission of The Royal Society of Chemistry. 

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. 

Armexin A1 emerged as a promising antigen for the radiolabeled antibody-based imaging and therapy of cancer [100]. In our laboratory, we use terminal perfusion protocols featuring active esters of biotin for the selective chemical labeling of accessible proteins in vascular structures. Biotinylated proteins are then purified from different organs (collected separately) and are submitted to a comparative proteomic analysis [106]. 

The focus of Chapters 11 and 12 is on measuring autoantibody expression for tissue-based proteomic research. Chapter 11 depicts the use of arrayed transcription factors to identify serum autoantibodies that may be used as biomarkers and reporters of aberrantly regulated transcription factors. Similarly, Chapter 12 presents a novel and useful method for detecting autoantibody expression to a wide variety of native intracellular antigens that are immobilized on a monoclonal antibody microarray. 

Microarray-based proteomics, where antibodies or other molecules that have been arrayed onto a surface to seleetively eapture proteins, has been presented and covered in a number of reviews. 

Chen, S.L., Wu, S.L., Huang, L.J., et al. (2013) A global comparability approach for biosinular monoclonal antibodies using LC-tandem MS based proteomics. J Pharm BiomedAnal, 80,126-135. 

Ngundi, M.M., Kulagina, N.V., Anderson, G.P., et al, 2006. Non antibody-based recognition alternative molecules for detection of pathogens. Expert Rev. Proteomics 3, 511-524. 

Uhlen M, Bjorling E, Agaton C, et al. A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol. Cell. Proteomics 2005 4 1920-1932. 

Fujita Y, Nakanishi T, Fliramatsu M et al. Proteomics-based approach identifying auto-antibody against peroxiredoxin Vt as a novel serum marker in esophageal squamous cell carcinoma. Clin Cancer Res 2006 12 6415-6420. 

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