Systematic Analysis of Missing Proteins Provides Clues to Help Define All of the Protein-Coding Genes on Human Chromosome 1

Our
first proteomic exploration of human chromosome 1 began in
2012 (CCPD 1.0), and the genome-wide characterization of the human
proteome through public resources revealed that 32–39% of proteins
on chromosome 1 remain unidentified. To characterize all of the missing
proteins, we applied an OMICS-integrated analysis of three human liver
cell lines (Hep3B, MHCC97H, and HCCLM3) using mRNA and ribosome nascent-chain
complex-bound mRNA deep sequencing and proteome profiling, contributing
mass spectrometric evidence of 60 additional chromosome 1 gene products.
Integration of the annotation information from public databases revealed
that 84.6% of genes on chromosome 1 had high-confidence protein evidence.
Hierarchical analysis demonstrated that the remaining 320 missing
genes were either experimentally or biologically explainable; 128
genes were found to be tissue-specific or rarely expressed in some
tissues, whereas 91 proteins were uncharacterized mainly due to database
annotation diversity, 89 were genes with low mRNA abundance or unsuitable
protein properties, and 12 genes were identifiable theoretically because
of a high abundance of mRNAs/RNC-mRNAs and the existence of proteotypic
peptides. The relatively large contribution made by the identification
of enriched transcription factors suggested specific enrichment of
low-abundance protein classes, and SRM/MRM could capture high-priority
missing proteins. Detailed analyses of the differentially expressed
genes indicated that several gene families located on chromosome 1
may play critical roles in mediating hepatocellular carcinoma invasion
and metastasis. All mass spectrometry proteomics data corresponding
to our study were deposited in the ProteomeXchange under the identifiers
PXD000529, PXD000533, and PXD000535.