Large-Scale Proteome Quantification of Hepatocellular Carcinoma Tissues by a Three-Dimensional Liquid Chromatography Strategy Integrated with Sample Preparation

Hepatocellular
carcinoma is one of the most fatal cancers worldwide.
In this study, a reversed-phase–strong cation exchange–reversed-phase
three-dimensional liquid chromatography strategy was established and
coupled with mass spectrometry to investigate the differential proteome
expression of HCC and normal liver tissues. In total, 2759 proteins
were reliably quantified, of which, 648 proteins were dysregulated
more than 3-fold in HCC liver tissues. Some important proteins that
relate to HCC pathology were significantly dysregulated, such as NAT2
and AKR1B10. Furthermore, 2307 phosphorylation sites from 1264 phosphoproteins
were obtained in our previous phosphoproteome quantification, and
the nonphosphorylated counterparts of 445 phosphoproteins with 983
phosphorylation sites were reliably quantified in this work. It was
observed that 337 (34%) phosphorylation sites exhibit significantly
different expression trends from that of their corresponding nonphosphoproteins.
Some novel phosphorylation sites with important biological functions
in the progression of HCC were reliably quantified, such as the significant
downregulation of pT185 for ERK2 and pY204 for ERK1.