Dataset Information

SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics

ABSTRACT: Shotgun proteomics is essential for protein identification and quantification in biomedical research, but protein isoform characterization is challenging due to the extensive number of peptides shared across proteins, hindering our understanding of protein isoform regulation and their roles in normal and disease biology. We systematically assess the challenge and opportunities of shotgun proteomics-based protein isoform characterization using in silico and experimental data, and then present SEPepQuant, a graph theory-based approach to maximize isoform characterization. Using published data from one induced pluripotent stem cell study and two human hepatocellular carcinoma studies, we demonstrate the ability of SEPepQuant in addressing the key limitations of existing methods, providing more comprehensive isoform-level characterization, identifying hundreds of isoform-level regulation events, and facilitating streamlined cross-study comparisons. Our analysis provides solid evidence to support a widespread role of protein isoform regulation in normal and disease processes, and SEPepQuant has broad applications to biological and translational research.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Liver

SUBMITTER: Yongchao Dou

LAB HEAD: Bing Zhang

PROVIDER: PXD044809 | Pride | 2023-10-24

REPOSITORIES: Pride

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			Action	DRS
	20230329_HFX_ZHW_zhangbing_PRM_sample_heavy_HCC_211.raw	Raw
	20230329_HFX_ZHW_zhangbing_PRM_sample_heavy_HCC_212.raw	Raw
	20230329_HFX_ZHW_zhangbing_PRM_sample_heavy_HCC_221.raw	Raw
	20230329_HFX_ZHW_zhangbing_PRM_sample_heavy_HCC_222.raw	Raw
	20230329_HFX_ZHW_zhangbing_PRM_sample_heavy_HCC_227.raw	Raw

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SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics.

Dou Yongchao Y Liu Yuejia Y Yi Xinpei X Olsen Lindsey K LK Zhu Hongwen H Gao Qiang Q Zhou Hu H Zhang Bing B

Nature communications 20230919 1

Shotgun proteomics is essential for protein identification and quantification in biomedical research, but protein isoform characterization is challenging due to the extensive number of peptides shared across proteins, hindering our understanding of protein isoform regulation and their roles in normal and disease biology. We systematically assess the challenge and opportunities of shotgun proteomics-based protein isoform characterization using in silico and experimental data, and then present SEP ...[more]

PMID: 37726316

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