Journal of Proteomics & Bioinformatics
Open Access
ISSN: 0974-276X
ISSN: 0974-276X
Stanislav Naryzhny
Institute of Biomedical Chemistry, Russia
Petersburg Nuclear Physics Institute, Russia
Scientific Tracks Abstracts: J Proteomics Bioinform
Here, we show that a combination of virtual and experimental two-dimensional gel electrophoresis (2DE) together with ESI LCMS/ MS allows to performing convenient analysis of human proteome. First, proteins from human cells (HepG2) and human blood plasma were run by 2DE. After protein staining and identification in spots the most abundant proteins (by MALDI-TOF massspectrometry), 2D protein maps were generated. Next, deeper analysis of spots by ESI LC-MS/MS was performed, and all proteins presented in spots were identified. Second, theoretical parameters (pI/Mw) of identified proteins were extracted from NeXtprot database. Then correlation plots between theoretical and experimental parameters (pI or Mw) were built. It was revealed from these plots that the most abundant proteoforms in the cell line have pI/Mw parameters similar to theoretical values. In opposite, the minor proteoforms often have very different from theoretical (pI/Mw) parameters. The similar situation is also observed in plasma, but in much higher degree. It shows that in plasma less abundant proteoforms are higher modified and processed than in cell. This information can be very useful in case of biomarkers identification in plasma. All these aspects are better revealed by separate representation of proteoforms coded by the same gene. In particular, graphs for potential cancer biomarkers were built. In these graphs, we often see the chains of spots with a shift by mass and pI that is characteristic for glycosylation or phosphorylation, or sets of spots corresponding to cleaved products. Such a representation is a starting point for their further analysis, and these graphs can be used as a source of better (more specific) biomarkers.
Stanislav Naryzhny has completed his PhD from the Biophysics Institute in Pushchino, Russia and postdoctoral studies from St. Petersburg Nuclear Physics Institute (PNPI), Gatchina, Russia and from the Northeastern Ontario Regional Cancer Centre, Sudbury, Canada. He is the Head of Proteomics Laboratory of Petersburg Nuclear Physics Institute at National Research Center "Kurchatov Institute" and also Chief Scientist at Institute of Biomedical Chemistry, Moscow, Russia. He is a Protein Biochemist with extensive hands-on experience in academia with strong background in protein structure-function theory and expertise in processes involved in DNA replication, DNA stability and tumorigenesis; protein, protein structure and proteomics analysis employing a wide variety of biophysical and biochemical methods. His favorite area of research is two-dimensional gel electrophoresis (2DE) based proteomics, where he has published more than 40 papers in reputed journals.
Email: snaryzhny@mail.ru