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J Proteome Res. 2018 Dec 7;17(12):4085-4096. doi: 10.1021/acs.jproteome.8b00386. Epub 2018 Oct 2.

Next Steps on in Silico 2DE Analyses of Chromosome 18 Proteoforms.

Author information

1
Institute of Biomedical Chemistry of Russian Academy of Medical Sciences , Pogodinskaya 10 , Moscow 119121 , Russia.
2
Petersburg Nuclear Physics Institute , National Research Center "Kurchatov Institute" , Leningrad Region , Gatchina 188300 , Russia.

Abstract

In the boundaries of the chromosome-centric Human Proteome Project (c-HPP) to obtain information about proteoforms coded by chromosome 18, several cell lines (HepG2, glioblastoma, LEH), normal liver, and plasma were analyzed. In our study, we have been using proteoform separation by two-dimensional electrophoresis (2DE) (a sectional analysis) and a semivirtual 2DE with following shotgun mass spectrometry using LC-ESI-MS/MS. Previously, we published a first draft of this research, where only HepG2 cells were tested. Here, we present the next step using more detailed analysis and more samples. Altogether, confident (2 significant sequences minimum) information about proteoforms of 117 isoforms coded by 104 genes of chromosome 18 was obtained. The 3D-graphs showing distribution of different proteoforms from the same gene in the 2D map were generated. Additionally, a semivirtual 2DE approach has allowed for detecting more proteoforms and estimating their pI more precisely. Data are available via ProteomeXchange with identifier PXD010142.

KEYWORDS:

ESI LC−MS/MS; chromosome 18; chromosome-centric; inventory; mass spectrometry; proteoforms; proteome; two-dimensional electrophoresis

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