Yongchao’s paper SEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics has been published in Nature Communications. Shotgun proteomics is crucial for identifying and quantifying proteins in biomedical research. However, characterizing protein isoforms is challenging due to shared peptides among proteins. We introduce SEPepQuant, a graph theory-based method to tackle this challenge. SEPepQuant addresses limitations of existing methods, enhancing isoform characterization, identifying isoform-level regulation events, and facilitating cross-study comparisons. Our results support a significant role of protein isoform regulation in normal and disease processes, making SEPepQuant valuable for biological and translational research. Source code is available in the Zhang Lab GitHub.
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