Proteomics-based detection methods

Another area where TOF-MS has an advantage is in high-mass analysis where its mass range is nearly unlimited. In MALDI-TOF, for example, it is not unusual to detect proteins with molecular weights exceeding 100,000. The ability for high-mass analysis is expected to increase in importance as clinical laboratories embrace proteomic-based diagnostic methods. 

AuNPs have been considered suitable for in vivo studies, due to well-known characterized biocompatibility. For AuNPs, many different strategies have been described for surface functionalization with drugs, peptides, and so on, which are very useful to perform systematic cytotoxic studies. AuNPs are used in proteomics because of its physicochemical properties (e.g., optical features, electromagnetic or photothermal properties), which are very useful for label-based detection methods (23,24). 

The popularity of aptamer-based assays has risen over the last several years in proteomics (25). Typical aptamers are single-stranded nucleic acids that can recognize target molecules. The general basis is similar to immuno-based methods. These aptamers are found by screening large libraries of nucleic acid sequences. This technology has been applied to several proteome-level detections (26-29). 

R 645 L. Zeng, C. H. Chen, M. Muller and M. -M. Zhou, Structure-Based Rational Design of Chemical Ligands for AMPA-Subtype Glutamate Receptors , J. Mol. Neurosci., 2003,20, 345 R 646 S. Zhou, Separation and Detection Methods for Covalent Drug-Protein Adducts , J. Chromatogr., B, 2003,797, 63 R 647 I. Zhukov and A. Ejchart, NMR Spectroscopy in Structural Proteomics. NMR-Based Protein Structure Determination , Polimery (Warsaw, Poland), 2003, 48, 28... 

Other PTMs may involve changes in the chemical nature of amino acids (e.g., citrullination or deimination). Because many of these modifications result in mass changes that are measurable by MS, they are amenable to detection by MS-based approaches. A number of emerging MS-based strategies allow the identification of PTMs. Several MS-based methods to determine the types and sites of protein phosphorylation and ubiquitination have been developed. Phosphorylation occurs mainly on serine, threonine, and tyrosine residues at a frequency ratio of 1800 200 1 in vertebrates.70 Although the phosphorylation of tyrosine residues occurs less frequently in the proteome, it has been extensively studied. 

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