PERCEPTRON: an open-source GPU-accelerated proteoform identification pipeline for top-down proteomics

Abstract

PERCEPTRON is a next-generation freely available web-based proteoform identification and characterization platform for top-down proteomics (TDP). PERCEPTRON search pipeline brings together algorithms for (i) intact protein mass tuning, (ii) de novo sequence tags-based filtering, (iii) characterization of terminal as well as post-translational modifications, (iv) identification of truncated proteoforms, (v) in silico spectral comparison, and (vi) weight-based candidate protein scoring. High-throughput performance is achieved through the execution of optimized code via multiple threads in parallel, on graphics processing units (GPUs) using NVidia Compute Unified Device Architecture (CUDA) framework. An intuitive graphical web interface allows for setting up of search parameters as well as for visualization of results. The accuracy and performance of the tool have been validated on several TDP datasets and against available TDP software. Specifically, results obtained from searching two published TDP datasets demonstrate that PERCEPTRON outperforms all other tools by up to 135% in terms of reported proteins and 10-fold in terms of runtime. In conclusion, the proposed tool significantly enhances the state-of-the-art in TDP search software and is publicly available at https://perceptron.lums.edu.pk. Users can also create in-house deployments of the tool by building code available on the GitHub repository (http://github.com/BIRL/Perceptron).

Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection

“…We selected four top-down search engines that were capable of truncation searches and could be installed for use on local computers (see Figure 1 and Table 2 ). Algorithms that did not completely fulfill these criteria (Perceptron, 37 Mascot Top-Down, 38 MetaMorpheus, 14 and PIITA 39 were not included in our comparison. Perceptron requires a high-end nVidia graphics card and several development kits for installation, which were not available to us.…”