Dataset Information

Identification of phosphorylated SEPs in Hep3B cells by LC/MS/MS

ABSTRACT: We identified phosphorylated SEPs in Hep3B cells. ACN precipitation, thermo precipitation and HCl precipitation were used to enrich SEPs. Three materials (nmTiO2, umTiO2, IMAC) were used to enrich phosphorylated peptides.

ORGANISM(S): Homo Sapiens

SUBMITTER: Cuihong Wan

PROVIDER: PXD047431 | iProX | Mon Apr 15 00:00:00 BST 2024

REPOSITORIES: iProX

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Publications

Identification of phosphorylated small ORF-encoded peptides in Hep3B cells by LC/MS/MS.

Peng Mingbo M Zhou Yutian Y Wan Cuihong C

Journal of proteomics 20240531

Small ORF-encoded peptides (SEPs) are a class of low molecular weight proteins and peptides comprising <100 amino acids with important functions in various life activities. Although the sequence length is short, SEPs might also have post-translational modification (PTM). Phosphorylation is one of the most essential PTMs of proteins. In this work, we enriched phosphopeptides with IMAC and TiO<sub>2</sub> materials and analyzed the phosphorylated SEPs in Hep3B cells. A total of 24 phosphorylated S ...[more]

PMID: 38823442

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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 of phosphorylated SEPs in Hep3B cells by LC/MS/MS

Publications

Identification of phosphorylated small ORF-encoded peptides in Hep3B cells by LC/MS/MS.

Similar Datasets

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