Identification and Characterization of Proteins Encoded by Chromosome 12 as Part of Chromosome-centric Human Proteome Project

Chromosome-centric human proteome
project (C-HPP) is a global initiative
to comprehensively characterize proteins encoded by genes across all
human chromosomes by teams focusing on individual chromosomes. Here,
we report mass spectrometry-based identification and characterization
of proteins encoded by genes on chromosome 12. Our study is based
on proteomic profiling of 30 different histologically normal human
tissues and cell types using high-resolution mass spectrometry. In
our analysis, we identified 1,535 proteins encoded by 836 genes on
human chromosome 12. This includes 89 genes that are designated as
“missing proteins” by “neXtProt” as they
did not have any prior evidence either by mass spectrometry or by
antibody-based detection methods. We identified several variant peptides
that reflected coding SNPs annotated in dbSNP database. We also confirmed
the start sites of ∼200 proteins by identifying protein N-terminal
acetylated peptides. We also identified alternative start sites for
11 proteins that were not annotated in public databases until now.
Most importantly, we identified 12 novel protein coding regions on
chromosome 12 using our proteogenomics strategy. All of the 12 regions
have been annotated as pseudogenes in public databases. This study
demonstrates that there is scope for significantly improving annotation
of protein coding genes in the human genome using mass-spectrometry-derived
data. Individual efforts as part of C-HPP initiative should significantly
contribute toward enriching human protein annotation. The data have
been deposited to ProteomeXchange with identifier PXD000561.

以染色体为中心的人类蛋白质组计划（Chromosome-centric human proteome project, C-HPP）是一项全球性倡议，旨在由聚焦单条染色体的研究团队全面解析人类所有染色体上基因编码的蛋白质。在此，我们报道了基于质谱技术的人类12号染色体基因编码蛋白质的鉴定与表征研究。本研究采用高分辨率质谱技术，对30种组织学正常的人类组织与细胞类型开展蛋白质组学分析。经分析，我们共鉴定出人类12号染色体上836个基因编码的1535种蛋白质，其中包含89个被neXtProt列为“缺失蛋白质（missing proteins）”的基因——此前这些基因既无质谱检测证据，也无基于抗体的检测验证结果。我们还鉴定出多种反映dbSNP数据库中编码单核苷酸多态性（coding SNPs）的变异肽段。通过鉴定蛋白质N端乙酰化肽段，我们验证了约200种蛋白质的翻译起始位点；同时发现了11种此前未在公共数据库中注释的蛋白质可变起始位点。尤为重要的是，我们借助蛋白质基因组学（proteogenomics）策略，在12号染色体上鉴定出12个全新的蛋白质编码区域，这些区域此前在公共数据库中均被注释为假基因。本研究表明，利用质谱衍生数据可显著完善人类基因组蛋白质编码基因的注释工作。作为C-HPP倡议的组成部分，各项个体研究将极大丰富人类蛋白质注释体系。相关数据已以标识符PXD000561提交至ProteomeXchange数据库。