Enhancing mass spectrometry data analysis: A novel framework for calibration, outlier detection, and classification

Weili Peng, Tao Zhou, Yuanyuan Chen

Abstract: Highlights•Novel framework integrates three steps for MS data analysis.•Deep AE removes batch effects, while an ensemble approach removes outliers.•Transformer captures intrinsic relationships in MS data for accurate classification.•The framework provides a comprehensive solution to improve classification accuracy.•The framework also facilitates reliable biological insights.