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

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.