Considering the technical limitations of mass spectrometry in
protein identification, the mRNAs bound to ribosomes (RNC-
mRNA) are assumed to reflect the mRNAs participating in the translational process. The RNC-
mRNA data are reasoned to be useful for appraising the missing
proteins. A set of the multiomics data including free-mRNAs, RNC-mRNAs, and
proteomes was acquired from three
liver cancer cell lines. On the basis of the missing
proteins in neXtProt (release 2014-09-19), the bioinformatics analysis was carried out in three phases: (1) finding how many neXtProt missing
proteins have or do not have
RNA-seq and/or MS/MS evidence, (2) analyzing specific physicochemical and
biological properties of the missing
proteins that lack both
RNA-seq and MS/MS evidence, and (3) analyzing the combined properties of these missing
proteins. Total of 1501 missing
proteins were found by neither RNC-
mRNA nor MS/MS in the three
liver cancer cell lines. For these missing
proteins, some are expected higher hydrophobicity, unsuitable detection, or sensory functions as properties at the
protein level, while some are predicted to have nonexpressing
chromatin structures on the corresponding gene level. With further integrated analysis, we could attribute 93% of them (1391/1501) to these causal factors, which result in the expression products scarcely detected by
RNA-seq or MS/MS.