Protein abundance index

Label-free quantification is a very attractive method, because there are no extra costs involved. Instead, there are much higher demands on the reproducibility of technical parameters, such as sample loading, chromatography, and mass accuracy, and more experimental replicates are needed. In the following sections, different approaches to label-free quantification will be discussed the extracted ion chromatogram (XIC), spectral counting (SC), the protein abundance index (PAI), and the LCMS method. 

Ishihama, Y Oda, Y. Tabata, T. Sato, T. Nagasu, T. Rappsilber, J. Mann, M. Exponentially modified protein abundance index (emPAl) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 2005, 4, 1265-1272. 

The total rate of gut metabolism includes all the enzymes (i.e., individual CYPs and CYP abundances, index i) that exist in the gut enterocyte compartments (index j) (Gastroplus 5.0, SimulationsPlus, Inc., Lancaster, CA). The CYP450 enzymes are present in the gut in smaller quantities ( 20 times less) than in the liver however, in some cases their contribution to metabolism is similar to what occurs in the liver. This is true for drugs that are highly bound to plasma proteins and have limited access to liver hepatocyte enzymes (Agoram et al. 2001). GastroPlus Manual version 6.0 describes the metabolic activity of aU gut enzymes in (8). 

The Voronoi calculation can be performed on protein atoms buried at interfaces as well as inside proteins. However, the procedure has a serious limitation a Voronoi polyhedron can be drawn around an atom only if it is completely surrounded by other atoms. At interfaces, only about one-third of the atoms that contribute to the interface area B have zero accessible surface area. These atoms are located mostly at the center of the interface, which biases the F/Fq ratio in an opposite way to the gap index, which is biased toward the periphery. However, high-resolution X-ray structures usually report positions for immobilized water molecules, which are abundant at interfaces (see Section II,D). These molecules may also be used to close the polyhedra, making the evaluation of Voronoi volumes possible for atoms which are surrounded by both protein atoms and immobilized water molecules (Fig. 4). On average, there are as many such interface atoms as there are completely buried atoms. Thus, a Voronoi calculation taking into account the crystallographic water molecules applies to two-thirds of the interface atoms on average instead of only one-third and up to 90% in specific cases (Lo Conte et al., 1999). 

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