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

Abstract

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.

Translatomics: The Global View of Translation

“…In 2014, the Chinese Human Proteome Project completed the multi-omics level analysis of liver cancer cell lines [51]. From each cell line, more than 14,000 translating genes were detected and only 2/3 of the protein products were detected in MS, showing the high sensitivity of RNC-seq [22,51,132,133,134].…”

Utilising proteomic approaches to understand oncogenic human herpesviruses (Review)

“…In a recent effort to characterize all the missing proteins, an integrative OMICS approach was employed, combining MS-based proteomics, RNAseq and ribosome profiling, an emerging technique that identifies the translation potential of mRNAs present in a sample (120). This approach, utilising proteome, transcriptome and translatome data, reduced the as yet uncharacterised genes to ~15%, most of which are predicted to be tissue-specific.…”

Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry

“…6 Some missing proteins are also likely to be expressed only under certain stimulus or stress. 5 Recently, some mass spectrometry (MS) evidences were reported evidences to identify missing proteins from human brain tissues, 7 lung tissues and cell lines, 8 colorectal cancer samples, 9 and hepatocellular carcinoma samples 10 , showing the significance of clinical samples in detecting missing proteins. In addition, the distinct proteome profiles deciphered by the draft map of the human proteome 1 also revealed that missing proteins may even be expressed only during development in embryo or fetal tissues, with over 700 proteins having ten-fold increase in expression level compared to the adult counterparts.…”