Mass spectrometry-based proteomics is a powerful technique for the analyses of thousands of proteins, fueling biomarker research and drug discovery. With the rich complex data from each precious sample and large cohorts, new developments in the field of deep learning with the INFERYS platform deliver improved confidence in proteomics results. Its application to large amounts of high-quality training data can unlock this dimension and enable novel data analysis workflows on readily available CPU and end-user infrastructure.  Fusing deep learning approaches with established toolchains allows the extraction of more identifications from difficult proteomic samples measured label-free or using tandem mass tags.