Mass spectroscopy proteomics

Griffin, T.J. and Abersold, R., Advances in proteomic analysis by mass spectroscopy, /. Biol. Chem., 276, 45497-45500, 2001. 

Figure 6 The SELDI technology. This type of proteomic analytical tool is a class of mass spectroscopy instrument that is useful in high-throughput proteomic fingerprinting of serum. Using a robotic sample dispenser, 1 p,L of serum is applied to the surface of a protein-binding chip. A subset of the proteins in the sample binds to the surface of the chip. The bound proteins are treated with a matrix-assisted laser desorption and ionization matrix and are washed and dried. The chip, which contains multiple patient samples, is inserted into a vacuum chamber where it is irradiated with a laser. The laser desorbs the adherent proteins and causes them to be launched as ions. The TOF of the ion before detection by an electrode is a measure of the mass-to-charge (m/z) value of the ion. The ion spectra can be analyzed by computer-assisted tools that classify a subset of the spectra by characteristic patterns of relative intensity (adapted from www.evmsdoctors.com).

Combining affinity chromatography, two-dimensional electrophoresis, and mass spectroscopy, Becamel and colleagues pioneered a global proteomic approach to 5-HT receptosomes (Chapter 7). These groundbreaking studies employed either the entire or partial carboxyl terminus of the 5-HT2 receptors as bait and heralded the discovery of multiple FRAPs (14,15). Since then, the proteomic strategy has been successfully applied to other 5-HT receptor subtypes (16,17). 

Genomes and proteomes are not the only omes. At the close of the twentieth century a number of methods for capturing data (e.g., mass spectroscopy and expression arrays) and a growing interest in systems biology emerged as a plethora of omes. These and other omes important to the medical record will be discussed in Chapter 4. 

The 2D gel or Iso-Dalt is the most commonly used method in proteomics because of its relatively easy use, automation, high reproducibility, high resolution of proteins, and applicability to analysis by mass spectroscopy. Furthermore, protein bands separated by Iso-Dalt are readily amenable to Edman degradation or to the amino acid composition analysis. 

Plasma Proteome. The plasma proteome has been studied extensively. Plasma can be obtained readily from individuals by drawing blood using a simple procedure that is considered noninvasive. Plasma proteins have been characterized routinely by 2D gel followed by affinity chromatography, tandem mass spectroscopy, and comparison of protein sequence data in the protein databank. Some proteins such as albumin and transferrin, which are predominantly present in serum, are removed by affinity depletion chromatography to enrich the presence of other low-bundance proteins in plasma. More than 4000 proteins have been identified from human plasma, which are being developed to be used as a biomarker for several human diseases. 

Bottom-up proteomics based on two-dimensional (2D) gel electrophoresis followed by the tryptic digestion of spots and analysis by mass spectroscopy (MS). ... 

---