Dataset Information

Identification and analysis of short open reading frame encoded peptides in different brain regions of mice

ABSTRACT: Here we used mass spectrometry-based proteomics technology to explore SEPs with potential function in five brain regions of the mouse. SEPs with unique peptides were identified in hippocampus, frontal cortex, temporal cortex, occipital cortex and parietal cortex.

ORGANISM(S): Mus Musculus

SUBMITTER: Cuihong Wan

PROVIDER: PXD036064 | iProX | Tue Aug 16 00:00:00 BST 2022

REPOSITORIES: iProX

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Publications

Identification and analysis of short open reading frame-encoded peptides in different regions of mouse brain.

Li Shengjie S Peng Die D Pan Ni N Wang Shaohui S Zhang Zheng Z Wan Cuihong C

iScience 20230317 4

Short open reading frame-encoded peptides (SEPs) are generally 2-100 amino acids in length and participate in various biological processes of the organism. The brain is the central hub of life activities, where different regions perform distinct functions. To characterize SEPs in brain regions, we analyzed SEPs in five mouse brain areas, including hippocampus, frontal cortex, temporal cortex, occipital cortex, and parietal cortex, with mass spectrometry-based proteomics. We obtained 1,095 protei ...[more]

PMID: 37034998

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Project description:The small proteins and short open reading frames encoded peptides (SEPs) are of fundamental importance because of their essential roles in biological processes. However, the annotation or identification of them is challenging, in part owing to the limitation of the traditional genome annotation pipeline and their inherent characteristics of low abundance and low molecular weight. To discover and characterize SEPs in Hep3B cell line, we developed an optimized peptidomic assay by combining different peptide extraction and separation methods. The organic solvent precipitation method in peptidomic showed promotion in the enrichment of low molecular proteins or peptides, and the data clearly showed a beneficial effect from the reduction of sample complexity, resulting in high-quality MS/MS spectra. Furthermore, different strategies exhibited good complementarity in improving the total amount of small proteins and their sequence coverage. In total, 1192 proteins within less than 100 amino acids were identified, including 271 newly discovered SEPs that been annotated in the OpenProt database and 147 SEPs of them encoded from ncRNA or lincRNA. Results in this work provide robust evidence to date that the human proteome is more complicated than previously appreciated, and this will be a benefit to discoveries of proteins without function annotation. SIGNIFICANCE: In this work, methods were optimized to identify SEPs in Hep3B. The organic solvent precipitation presents promotion in enrichment of low molecular proteins or peptides, and the data clearly showed a beneficial effect from the reduction of sample complexity, resulting in high quality MS/MS spectra. Different strategies exhibited good complementarity in improving total amount of small proteins and their sequence coverage. In total, 1192 proteins within less than 100 amino acids were identified, including 271 newly discovered SEPs that been annotated in the OpenProt database and 147 SEPs of them encoded from ncRNA or lincRNA. Furthermore, 22 SEPs generated from the uORF may has potential effect in translation control, and 149 newly identified SEPs have known functional domains or cross-species conservation. Results in this work present robust evidence for the coding potential of the ignored region of human genomes and may provide additional insights into tumor biology.

Dataset Information

Identification and analysis of short open reading frame encoded peptides in different brain regions of mice

Publications

Identification and analysis of short open reading frame-encoded peptides in different regions of mouse brain.

Similar Datasets

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