Chromosome-Based Proteomic Study for Identifying Novel Protein Variants from Human Hippocampal Tissue Using...

Area of Science:

• Proteomics
• Genomics
• Neuroscience

Background:

• The Chromosome-Centric Human Proteome Project (C-HPP) aims to comprehensively map human proteomic information.
• Identifying novel proteoforms, including variants from noncoding regions and alternative splicing, is crucial for understanding human biology and disease.

Purpose of the Study:

• To identify novel proteoforms, such as long noncoding RNA variants, alternative splicing variants (ASVs), and single amino acid variants (SAAVs), in human hippocampal tissues.
• To apply and validate a proteomic workflow for the C-HPP initiative.

Main Methods:

• Utilized 144 LC/MS/MS raw files from human hippocampal tissues (control, epilepsy, Alzheimer's disease).
• Employed an integrated proteomic pipeline with MASCOT, SEQUEST, and MS-GF+ search engines.
• Used customized databases (GENCODE lncRNA, GENCODE transcript, neXtProt with nsSNP information) and validated peptides via tandem MS.

Main Results:

• Identified 11 peptides mapping to four translated long noncoding RNA variants.
• Discovered four novel ASVs and 128 SAAVs with <1% FDR at the protein or peptide level.
• Identified novel variants potentially related to neurodegenerative diseases.

Conclusions:

• The developed workflow successfully identified novel proteoforms, contributing to the C-HPP goals.
• The findings provide valuable proteomic insights applicable to neurodegenerative disease research.
• This study demonstrates the utility of integrated proteomic analysis for comprehensive human proteome mapping.