Here, we established a comprehensive database profiling the proteome of total proteins and those containing nine major PTMs: phosphorylation, acetylation, crotonylation, lactylation, ubiquitination, succinylation, malonylation, β-hydroxybutyrylation, and N-glycosylation in the normal adjacent tissues (NATs) and tumor tissues of HCC patients. This multiomics study robustly identified thousands of PTM sites and proteins, including 7,637 proteins; 28,849 phosphosites; 4,035 N-glycosyl sites; 8,098 acetyl sites; 19,713 crotonyl sites; 6,663 β-hydroxybutyryl sites; 3,191 malonyl sites; 5,692 succinyl sites; 6,535 lactosyl sites; and 21,453 ubiquitinated sites. Among these, 6,262 proteins; 6,776 phosphosites; 1,500 N-glycosyl sites; 2,746 acetyl sites; 7,874 crotonyl sites; 2,793 β-hydroxybutyryl sites; 1,072 malonyl sites; 2,107 succinyl sites; 1,107 lactosyl sites; and 2,765 ubiquitinated sites were quantified, with less than 50% missing values across samples.