Proteoform Patterns in the Samples of Hepatocellular Carcinoma: Aspects of Oncomarkers

This study aimed to generate comparative proteomics data, including various proteoforms, in hepatocellular carcinoma (HCC) and nonmalignant liver tissues. Using a panoramic, integrative top-down proteomics approach—sectional two-dimensional gel electrophoresis (2DE) coupled with liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS)—we obtained and visualized over 2,500 proteoform patterns for each sample type. This allowed us to identify specific protein signatures and common patterns distinguishing nonmalignant and malignant human liver cells. The results demonstrated that most proteoform patterns were highly similar, with the dominant peak matching the theoretical (unmodified) protein parameters. From these, 1,270 reproducibly detected protein patterns were selected for further analysis. Additionally, 38 proteins—including pyruvate kinase PKM (KPYM), annexin A2 (ANXA2), and others—showed pronounced differences in proteoform patterns between nonmalignant and malignant tissues and were prioritized for subsequent proteoform characterization.