A deep learning framework for enhanced mass spectrometry data analysis and biomarker screening

Mass spectrometry (MS) serves as a powerful analytical technique in metabolomics. Traditional MS analysis workflows are heavily reliant on operator experience and are prone to be influenced by complex, high-dimensional MS data. This study introduces a deep learning framework designed to enhance the classification of complex MS data and facilitate biomarker screening. The proposed framework integrates preprocessing, classification, and biomarker selection, addressing challenges in high-dimensional MS analysis. Experimental results demonstrate significant improvements in classification tasks compared to other machine learning approaches. Additionally, the proposed peak-preprocessing module is validated for its potential in biomarker screening, identifying potential biomarkers from high-dimensional data.