BROWSE

Related Scientist

park,youngmok's photo.

park,youngmok
사회성뇌과학그룹
more info

ITEM VIEW & DOWNLOAD

Chromosome-Based Proteomic Study for Identifying Novel Protein Variants from Human Hippocampal Tissue Using Customized neXtProt and GENCODE Databases

Cited 4 time in webofscience Cited 4 time in scopus
1,337 Viewed 353 Downloaded
Title
Chromosome-Based Proteomic Study for Identifying Novel Protein Variants from Human Hippocampal Tissue Using Customized neXtProt and GENCODE Databases
Author(s)
Heeyoun Hwang; Gun Wook Park; Kwang Hoe Kim; Ju Yeon Lee; Hyun Kyoung Lee; Eun Sun Ji; Sung-Kyu Robin Park; Tao Xu; John R. Yates; Kyung-Hoon Kwon; Young Mok Park; Hyoung-Joo Lee; Young-Ki Paik; Jin Young Kim; Jong Shin Yoo
Subject
alternative splice variants, ; C-HPP, ; hippocampus, ; Novel proteoforms, ; single amino acid variants, ; translated lncRNA variants
Publication Date
2015-12
Journal
JOURNAL OF PROTEOME RESEARCH, v.14, no.12, pp.5028 - 5037
Publisher
AMER CHEMICAL SOC
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). © 2015 American Chemical Society
URI
https://pr.ibs.re.kr/handle/8788114/1823
DOI
10.1021/acs.jproteome.5b00472
ISSN
1535-3893
Appears in Collections:
Center for Cognition and Sociality(인지 및 사회성 연구단) > Social Neuroscience Group(사회성 뇌과학 그룹) > 1. Journal Papers (저널논문)
Files in This Item:
2015_JPR_cHPP_HH-park.pdfDownload

qrcode

  • facebook

    twitter

  • Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.
해당 아이템을 이메일로 공유하기 원하시면 인증을 거치시기 바랍니다.

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

Browse