title: Chromosome 18 transcriptome profiling and targeted proteome mapping in depleted plasma, liver tissue and HepG2 cells.
abstract: The final goal of the Russian part of the Chromosome-centric Human Proteome Project (C-HPP) was established as the analysis of the chromosome 18 (Chr 18) protein complement in plasma, liver tissue and HepG2 cells with the sensitivity of 10(-18) M. Using SRM, we have recently targeted 277 Chr 18 proteins in plasma, liver, and HepG2 cells. On the basis of the results of the survey, the SRM assays were drafted for 250 proteins: 41 proteins were found only in the liver tissue, 82 proteins were specifically detected in depleted plasma, and 127 proteins were mapped in both samples. The targeted analysis of HepG2 cells was carried out for 49 proteins; 41 of them were successfully registered using ordinary SRM and 5 additional proteins were registered using a combination of irreversible binding of proteins on CN-Br Sepharose 4B with SRM. Transcriptome profiling of HepG2 cells performed by RNAseq and RT-PCR has shown a significant correlation (r = 0.78) for 42 gene transcripts. A pilot affinity-based interactome analysis was performed for cytochrome b5 using analytical and preparative optical biosensor fishing followed by MS analysis of the fished proteins. All of the data on the proteome complement of the Chr 18 have been integrated into our gene-centric knowledgebase ( www.kb18.ru ).
authors.affiliation: Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Russia.
authors.forename: Victor G
authors.initials: VG
authors.lastname: Zgoda
authors.forename: Arthur T
authors.initials: AT
authors.lastname: Kopylov
authors.forename: Olga V
authors.initials: OV
authors.lastname: Tikhonova
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Moisa
authors.forename: Nadezhda V
authors.initials: NV
authors.lastname: Pyndyk
authors.forename: Tatyana E
authors.initials: TE
authors.lastname: Farafonova
authors.forename: Svetlana E
authors.initials: SE
authors.lastname: Novikova
authors.forename: Andrey V
authors.initials: AV
authors.lastname: Lisitsa
authors.forename: Elena A
authors.initials: EA
authors.lastname: Ponomarenko
authors.forename: Ekaterina V
authors.initials: EV
authors.lastname: Poverennaya
authors.forename: Sergey P
authors.initials: SP
authors.lastname: Radko
authors.forename: Svetlana A
authors.initials: SA
authors.lastname: Khmeleva
authors.forename: Leonid K
authors.initials: LK
authors.lastname: Kurbatov
authors.forename: Aleksey D
authors.initials: AD
authors.lastname: Filimonov
authors.forename: Nadezhda A
authors.initials: NA
authors.lastname: Bogolyubova
authors.forename: Ekaterina V
authors.initials: EV
authors.lastname: Ilgisonis
authors.forename: Aleksey L
authors.initials: AL
authors.lastname: Chernobrovkin
authors.forename: Alexis S
authors.initials: AS
authors.lastname: Ivanov
authors.forename: Alexei E
authors.initials: AE
authors.lastname: Medvedev
authors.forename: Yury V
authors.initials: YV
authors.lastname: Mezentsev
authors.forename: Sergei A
authors.initials: SA
authors.lastname: Moshkovskii
authors.forename: Stanislav N
authors.initials: SN
authors.lastname: Naryzhny
authors.forename: Elena N
authors.initials: EN
authors.lastname: Ilina
authors.forename: Elena S
authors.initials: ES
authors.lastname: Kostrjukova
authors.forename: Dmitry G
authors.initials: DG
authors.lastname: Alexeev
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Tyakht
authors.forename: Vadim M
authors.initials: VM
authors.lastname: Govorun
authors.forename: Alexander I
authors.initials: AI
authors.lastname: Archakov
mesh_terms: D001798:Blood Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D002887:Chromosomes, Human, Pair 18 / Q000235:genetics / Q000378:metabolism; D030562:Databases, Protein; D015870:Gene Expression; D015894:Genome, Human; D056945:Hep G2 Cells; D006801:Humans; D008099:Liver / Q000378:metabolism; D013058:Mass Spectrometry; D020543:Proteome / Q000032:analysis*; D059467:Transcriptome
chemical_list: D001798:Blood Proteins; D020543:Proteome