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Keshishian et al. reported a 1000-fold improfement of limit of detection (LOD) upon depletion of seven high abundant plasma proteins by strong cation exchange chromatography [123].
Just after the pulse excitation, where the carrier density is high, abundant high-energy carriers in the weakly localized states recombine rapidly.
Therefore, depletion of high abundant protein may also deplete some biologically important proteins.
However, many proteins, no matter large or small, are binding to or associated with high abundant protein such as albumin.
In this regard, we chose not to deplete the high abundant protein before 2-DE analysis [47].
Analysis of unfiltered sets of identified proteins in stromal samples suggested that the cTP success rate was much lower for low abundant proteins than for high abundant proteins.
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This is attributed partially to the existence of high-abundant protein.
Using a specifically designed chromatographic apparatus, the high-abundant fractions were filtered prior to LC MS analysis.
Both data indicate that high-abundant proteins tend to be less hydrophobic than low-abundant.
The average GRAVY scores are −0.24 and −0.36 for low- and high-abundant proteins, respectively.
This suggests that in high-abundant polypeptides, these residues are preferentially located at the surface in the folded conformation.
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