title: Chromosome-Based Proteomic Study for Identifying Novel Protein Variants from Human Hippocampal Tissue Using Customized neXtProt and GENCODE Databases.
abstract: The goal of the Chromosome-Centric Human Proteome Project (C-HPP) is to fully provide proteomic information from each human chromosome, including novel proteoforms, such as novel protein-coding variants expressed from noncoding genomic regions, alternative splicing variants (ASVs), and single amino acid variants (SAAVs). In the 144 LC/MS/MS raw files from human hippocampal tissues of control, epilepsy, and Alzheimer's disease, we identified the novel proteoforms with a workflow including integrated proteomic pipeline using three different search engines, MASCOT, SEQUEST, and MS-GF+. With a <1% false discovery rate (FDR) at the protein level, the 11 detected peptides mapped to four translated long noncoding RNA variants against the customized databases of GENCODE lncRNA, which also mapped to coding-proteins at different chromosomal sites. We also identified four novel ASVs against the customized databases of GENCODE transcript. The target peptides from the variants were validated by tandem MS fragmentation pattern from their corresponding synthetic peptides. Additionally, a total of 128 SAAVs paired with their wild-type peptides were identified with FDR <1% at the peptide level using a customized database from neXtProt including nonsynonymous single nucleotide polymorphism (nsSNP) information. Among these results, several novel variants related in neuro-degenerative disease were identified using the workflow that could be applicable to C-HPP studies. All raw files used in this study were deposited in ProteomeXchange (PXD000395).
authors.affiliation: Biomedical Omics Group, Korea Basic Science Institute , Chungbuk 28119, Republic of Korea.
authors.forename: Heeyoun
authors.initials: H
authors.lastname: Hwang
authors.affiliation: Biomedical Omics Group, Korea Basic Science Institute , Chungbuk 28119, Republic of Korea.|Graduate School of Analytical Science and Technology, Chungnam National University , Daejeon 34134, Republic of Korea.
authors.forename: Gun Wook
authors.initials: GW
authors.lastname: Park
authors.affiliation: Biomedical Omics Group, Korea Basic Science Institute , Chungbuk 28119, Republic of Korea.|Graduate School of Analytical Science and Technology, Chungnam National University , Daejeon 34134, Republic of Korea.
authors.forename: Kwang Hoe
authors.initials: KH
authors.lastname: Kim
authors.affiliation: Biomedical Omics Group, Korea Basic Science Institute , Chungbuk 28119, Republic of Korea.
authors.forename: Ju Yeon
authors.initials: JY
authors.lastname: Lee
authors.affiliation: Biomedical Omics Group, Korea Basic Science Institute , Chungbuk 28119, Republic of Korea.|Graduate School of Analytical Science and Technology, Chungnam National University , Daejeon 34134, Republic of Korea.
authors.forename: Hyun Kyoung
authors.initials: HK
authors.lastname: Lee
authors.affiliation: Biomedical Omics Group, Korea Basic Science Institute , Chungbuk 28119, Republic of Korea.
authors.forename: Eun Sun
authors.initials: ES
authors.lastname: Ji
authors.affiliation: Department of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92037, United States.
authors.forename: Sung-Kyu Robin
authors.initials: SK
authors.lastname: Park
authors.affiliation: Department of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92037, United States.
authors.forename: Tao
authors.initials: T
authors.lastname: Xu
authors.affiliation: Department of Chemical Physiology, The Scripps Research Institute , La Jolla, California 92037, United States.
authors.forename: John R
authors.initials: JR
authors.lastname: Yates
authors.affiliation: Biomedical Omics Group, Korea Basic Science Institute , Chungbuk 28119, Republic of Korea.
authors.forename: Kyung-Hoon
authors.initials: KH
authors.lastname: Kwon
authors.affiliation: Center for Cognition and Sociality, Institute for Basic Science , Daejeon 34047, Republic of Korea.
authors.forename: Young Mok
authors.initials: YM
authors.lastname: Park
authors.affiliation: Yonsei Proteome Research Center and Department of Integrated OMICS for Biomedical Science, and Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University , Seoul 03722, Republic of Korea.
authors.forename: Hyoung-Joo
authors.initials: HJ
authors.lastname: Lee
authors.affiliation: Yonsei Proteome Research Center and Department of Integrated OMICS for Biomedical Science, and Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University , Seoul 03722, Republic of Korea.
authors.forename: Young-Ki
authors.initials: YK
authors.lastname: Paik
authors.affiliation: Biomedical Omics Group, Korea Basic Science Institute , Chungbuk 28119, Republic of Korea.
authors.forename: Jin Young
authors.initials: JY
authors.lastname: Kim
authors.affiliation: Biomedical Omics Group, Korea Basic Science Institute , Chungbuk 28119, Republic of Korea.|Graduate School of Analytical Science and Technology, Chungnam National University , Daejeon 34134, Republic of Korea.
authors.forename: Jong Shin
authors.initials: JS
authors.lastname: Yoo
mesh_terms: D017398:Alternative Splicing; D000544:Alzheimer Disease / Q000235:genetics / Q000378:metabolism*; D000595:Amino Acid Sequence; D016022:Case-Control Studies; D002853:Chromatography, Liquid; D002877:Chromosomes, Human; D030541:Databases, Genetic; D030562:Databases, Protein; D004827:Epilepsy / Q000235:genetics / Q000378:metabolism*; D014644:Genetic Variation; D006624:Hippocampus / Q000378:metabolism* / Q000502:physiology; D006801:Humans; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D040901:Proteomics / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry; D057188:Workflow
keywords: C-HPP; alternative splice variants; hippocampus; novel proteoforms; single amino acid variants; translated lncRNA variants