title: Combination of virtual and experimental 2DE together with ESI LC-MS/MS gives a clearer view about proteomes of human cells and plasma.
abstract: Virtual and experimental 2DE coupled with ESI LC-MS/MS was introduced to obtain better representation of the information about human proteome. The proteins from HEPG2 cells and human blood plasma were run by 2DE. After staining and protein spot identification by MALDI-TOF MS, the protein maps were generated. The experimental physicochemical parameters (pI/Mw) of the proteoforms further detected by ESI LC-MS/MS in these spots were obtained. Next, the theoretical pI and Mw of identified proteins were calculated using program Compute pI/Mw (http://web.expasy.org/compute_pi/pi_tool-doc.html). Accordingly, the relationship between theoretical and experimental parameters was analyzed, and the correlation plots were built. Additionally, virtual/experimental information about different protein species/proteoforms from the same genes was extracted. As it was revealed from the plots, the major proteoforms detected in HepG2 cell line have pI/Mw parameters similar to theoretical values. In opposite, the minor protein species have mainly very different from theoretical pI and Mw parameters. A similar situation was observed in plasma in much higher degree. It means that minor protein species are heavily modified in cell and even more in plasma proteome.
authors.affiliation: Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow, Russia.|B.P. Konstantinov Petersburg Nuclear Physics Institute, National Research Center "Kurchatov Institute,", Gatchina, Leningrad district, Russia.
authors.forename: Stanislav N
authors.initials: SN
authors.lastname: Naryzhny
authors.affiliation: Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow, Russia.
authors.forename: Victor G
authors.initials: VG
authors.lastname: Zgoda
authors.affiliation: Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow, Russia.
authors.forename: Maria A
authors.initials: MA
authors.lastname: Maynskova
authors.affiliation: Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow, Russia.
authors.forename: Svetlana E
authors.initials: SE
authors.lastname: Novikova
authors.affiliation: Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow, Russia.
authors.forename: Natalia L
authors.initials: NL
authors.lastname: Ronzhina
authors.affiliation: Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow, Russia.
authors.forename: Igor V
authors.initials: IV
authors.lastname: Vakhrushev
authors.affiliation: Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow, Russia.
authors.forename: Elena V
authors.initials: EV
authors.lastname: Khryapova
authors.affiliation: Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow, Russia.
authors.forename: Andrey V
authors.initials: AV
authors.lastname: Lisitsa
authors.affiliation: Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow, Russia.
authors.forename: Olga V
authors.initials: OV
authors.lastname: Tikhonova
authors.affiliation: Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow, Russia.
authors.forename: Elena A
authors.initials: EA
authors.lastname: Ponomarenko
authors.affiliation: Orekhovich Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow, Russia.
authors.forename: Alexander I
authors.initials: AI
authors.lastname: Archakov
mesh_terms: D001798:Blood Proteins / Q000032:analysis*; D002853:Chromatography, Liquid; D015180:Electrophoresis, Gel, Two-Dimensional; D056945:Hep G2 Cells; D006801:Humans; D020543:Proteome / Q000032:analysis*; D040901:Proteomics; D021241:Spectrometry, Mass, Electrospray Ionization; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D053719:Tandem Mass Spectrometry
chemical_list: D001798:Blood Proteins; D020543:Proteome
keywords: 2DE; ESI LC-MS/MS; Mass spectrometry; Protein species