Proteome Analysis of Human Plasma with the ProteomeLab™ PF 2D System
Michael H. Simonian, Ph.D., and Edna Betgovargez
Beckman Coulter, Inc.
Figure 1 shows the ProteomeLab PF 2D hardware. Starting from the left side, the 1st dimension consists of a single piston pump (HPCF Module), manual injector for sample introduction into the system, pH monitor, and UV detector.
Figure 1. Hardware components of the ProteomeLab PF 2D System
The hardware is controlled by 32 Karat™ software. In the software, there is a default method for the ProteomeLab PF 2D that has been optimized for separation in the 1st and 2nd dimensions.
Two-dimensional chromatographic fractionation by the ProteomeLab PF 2D has been used to compare two states of the human plasma proteome, namely fasting vs. non-fasting states. The first dimension separation based on pI did not reveal any significant differences in protein profiles between fasting and non-fasting plasma samples. Comparing the second dimension separations of the pI fractions did reveal significant quantitative and qualitative differences for several peaks in the fasting and non-fasting fractions with a pI boundary between 4.80 and 5.10.
When comparing states of a proteome, qualitative differences between the states can be the easiest to be exploited because their occurrence is definitive. However, accurate quantitative differences between states of a proteome require a technology that has resolution and reproducibility. The ProteomeLab PF 2D has both of these characteristics and, therefore, uncovers quantitative differences between proteomes. Finally, the proteome fractionated by the ProteomeLab PF 2D is in a liquid form, which lends itself to subsequent analysis, such as mass spectrometry, without further extraction or solubilization of the sample as with other fractionation techniques.
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