| Chromosome-centric human proteome project(C-HPP) has made great progress of finding protein evidence(PE) for missing proteins in PE2-4 categories as defined by the ne Xt Prot. However, identifying the rest missing proteins becomes increasingly challenging. As a majority of samples tested in this field were from adult tissues/cells, the developmental stage specific or relevant proteins could be missed due to the unavailability of biological sample sources. We posit that epigenetic interventions may help to partially bypass such a limitation by stimulating the expression of the “silenced†genes in adult cells, leading to the increased chance of finding missing proteins.Aim:To identify “missing proteins†from epigenetically manipulated human cells with stringent quality criteria.Methods: We established in vitro human cell models to modify the histone acetylation, demethylation, and methylation under near physiological conditions. To validate the physiological state of the cells, we performed the molecular experiments and confirmed that the cell membrane integrity was not compromised at the MED in all cases, then identified the missing proteins with m RNA-seq and Label-free MS analysis. Then we investigated whether the identified missing proteins differed in any physical or chemical properties and functions by biostastical analysis.Results: We found that histone modifications resulted in overall increases of expressed genes in an even distribution manner across different chromosomes anf identified 27 PE2-4 and 5 PE5 proteins were identified from the epigenetically modified cells; among them, 19 PE2-4 and 3 PE5 proteins passed FDR < 1% at both peptide and protein levels. Gene ontology analyses revealed that the PE2-4 proteins were significantly involved in development and spermatogenesis, although their chemical-physical features had no statistical difference from the background. In addition, we presented an example of suspicious PE5 peptide spectrum matched with unusual AA substitutions related to post-translational modification. In conclusion, the epigenetically manipulated cell models should be a useful tool for finding missing proteins in C-HPP. |
