Deep learning is the most popular research area in the field of machine learning in recent years, especially in image and speech recognition, natural language processing, and automatic driving．Biological mass spectrometry is an important research tool in the field of life sciences and plays a key role in proteomics, metabolomics, and biopharmaceuticals．In recent years, based on the development of deep learning methods, the big data analysis in proteomics centered on biological mass spectrometry will usher into a new era．This article reviews the latest applications of deep learning methods in the analysis of biological mass spectrometry data and proteomics research.