Label-free and TMT-labeled proteomics methods to compare differences on normal liver + extra-celiac liver of Glyptosternum maculatum

Glyptosternum maculatum (G. maculatum) is a unique fish that lives in the middle and upper reaches of the Yarlung Zangbo River, with normal liver (NG) and Exo-celiac liver (WG). In this study, we compared the differences between NG and WG based on label-free and TMT-labeled proteomics methods. We detected a total of 643 and 107 differentially expressed proteins (DEPs) in the label-free and TMT-labeled groups. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and Protein structural domain (PSD) enrichment analysis were performed on these DEPs, respectively, and protein-protein interaction (PPI) networks were constructed. In terms of the number of DEPs, the labelling-free method is superior to the TMT-labeled method. TMT is better in terms of repeatability and accuracy. In the label-free and TMT-labeled groups, 7 common DEPs (co-DEPs) were selected through PPI network information. higher expression of evm.model.chr5.73, evm.model.chr18.610, evm.model.chr10.1201, and HIF-1 signaling pathway were associated with a hypoxic environment. evm.model.chr15.573, evm.model .chr5.320, evm.model.chr6.360, and evm.model.chr18.610 were associated with WG production. The myosin11 not only responds to low temperature and low oxygen, but may also lead to WG production through Tight junction. NG may be more sensitive than WG in stress response to cancer and viral infections. Significant expression of Ubiquitin-like protein 4A and Heat shock 70 kDa protein protects liver cells from injury in a hypothermic and hypoxic environment. This paper provides a theoretical basis for the adaptation of G. maculatum in the plateau region with low temperature and low oxygen.