We have developed our tool DeepMRM as an external tool for Skyline. We would like to make our tool available to Skyline users through the Skyline External Tool Store.
DeepMRM is a data interpretation tool for quantitative analysis of targeted proteomics based on deep learning.
DeepMRM supports multiple reaction monitoring (MRM), parallel reaction monitoring (PRM), and data-independent acquisition (DIA) data with an accuracy comparable to that of human experts. It detects peak groups across multiple transitions of endogenous (light) and stable isotope labeled (heavy) peptides, and estimates their qualities and abundances. DeepMRM can significantly reduce the burden of manual inspection in clinical proteomics laboratories.