PERCEPTRON is a freely available web-based proteoform identification pipeline for Top-Down Proteomics (TDP). Top-down proteomics is an emerging experimental protocol for analysis of intact proteoforms. PERCEPTRON search pipeline brings together algorithms for: (i) intact mass tuning, (ii) de novo peptide sequence tag extraction, (iii) in silico spectral comparison, (iv) identification of post-translational modifications as well as truncated proteins, and (v) a novel composite scoring scheme for candidate protein scoring. PERCEPTRON achieves high performance by leveraging NVIDIA GPU technology coupled with Microsoft ASP.NET and ANGULAR frameworks. The search results obtained include a list of proteins, their scores and details on the matching information. This information can be visualized as well as downloaded. Overall, PERCEPTRON is aimed at filling the crucial void of open-source and open-architecture protein identification software for TDP data, employing state-of-the-art algorithms.