title: Identification and characterization of proteins encoded by chromosome 12 as part of chromosome-centric human proteome project.
abstract: 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.
authors: Institute of Bioinformatics, International Technology Park , Bangalore 560066, India.
authors: Srikanth Srinivas
authors: SS
authors: Manda
authors: Raja Sekhar
authors: RS
authors: Nirujogi
authors: Sneha Maria
authors: SM
authors: Pinto
authors: Min-Sik
authors: MS
authors: Kim
authors: Keshava K
authors: KK
authors: Datta
authors: Ravi
authors: R
authors: Sirdeshmukh
authors: T S Keshava
authors: TS
authors: Prasad
authors: Visith
authors: V
authors: Thongboonkerd
authors: Akhilesh
authors: A
authors: Pandey
authors: Harsha
authors: H
authors: Gowda
mesh_terms: D000328:Adult; D000595:Amino Acid Sequence; D001483:Base Sequence; D002874:Chromosome Mapping; D002881:Chromosomes, Human, Pair 12 / Q000235:genetics*; D005260:Female; D006801:Humans; D008297:Male; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D020641:Polymorphism, Single Nucleotide; D020543:Proteome / Q000235:genetics* / Q000502:physiology; D022661:RNA, Untranslated / Q000235:genetics; D053719:Tandem Mass Spectrometry
chemical_list: D020543:Proteome; D022661:RNA, Untranslated