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 mor

SUBMITTER: Dou Y 

PROVIDER: S-EPMC10509223 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature