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.