Perceptron is a freely available web-based proteoform search and identification platform for top-down proteomics (TDP). Perceptron search pipeline brings together algorithms for intact mass tuning, de novo sequencing, identification of chemical and post-translational modifications and candidate protein scoring. High-throughput performance is achieved through the execution of multiple search threads in parallel, on graphical processing units (GPUs) using NVidia Compute Unified Device Architecture (CUDA) framework. The accuracy and performance of the tool have been validated on several TDP datasets and against available TDP software. Specifically, results obtained from searching three published TDP datasets demonstrate that Perceptron outperforms all other tools by at least 71% in terms of reported proteins and 80% in terms of runtime. Together, the proposed software significantly enhances the state-of-the-art in TDP search software and is publically available at http://perceptron.lums.edu.pk. Users can also create in-house deployments of the tool by building code available at the GitHub repository (http://github.com/BIRL/Perceptron).