Proteomics

Dataset Information

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NextPP for chromosome-based proteomic research using neXtProt and GENCODE databases

ABSTRACT: In this study, we introduce a streamlined pipeline using customized and concatenated GENCODE and neXtProt databases with controlled false discovery rate (FDR) for finding GENCODE ASVs and missing proteins while mapping onto single amino acid variants (SAAVs) from Hippocampal dataset.

INSTRUMENT(S): LTQ Orbitrap, Orbitrap Fusion, LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Jong Shin Yoo  

PROVIDER: MSV000081385 | MassIVE | Tue Jul 25 19:53:00 BST 2017

SECONDARY ACCESSION(S): PXD007166

REPOSITORIES: MassIVE

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Publications

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

Hwang Heeyoun H   Park Gun Wook GW   Kim Kwang Hoe KH   Lee Ju Yeon JY   Lee Hyun Kyoung HK   Ji Eun Sun ES   Park Sung-Kyu Robin SK   Xu Tao T   Yates John R JR   Kwon Kyung-Hoon KH   Park Young Mok YM   Lee Hyoung-Joo HJ   Paik Young-Ki YK   Kim Jin Young JY   Yoo Jong Shin JS  

Journal of proteome research 20151116 12

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 integra  ...[more]

PMID: 26549206

Publication: 1/4

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