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Khalid MF, Iman K, Ghafoor A, Saboor M, Ali A, Muaz U, Basharat AR, Tahir T, Abubakar M, Akhter MA, Nabi W, Vanderbauwhede W, Ahmad F, Wajid B, Chaudhary SU. PERCEPTRON: an open-source GPU-accelerated proteoform identification pipeline for top-down proteomics. Nucleic Acids Res 2021; 49:W510-W515. [PMID: 33999207 PMCID: PMC8262694 DOI: 10.1093/nar/gkab368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/10/2021] [Accepted: 04/25/2021] [Indexed: 11/12/2022] Open
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).
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Affiliation(s)
- Muhammad Farhan Khalid
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Kanzal Iman
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Amna Ghafoor
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Mujtaba Saboor
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Ahsan Ali
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Urwa Muaz
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Abdul Rehman Basharat
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Taha Tahir
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Abubakar
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Momina Amer Akhter
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Waqar Nabi
- School of Computing Science, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Wim Vanderbauwhede
- School of Computing Science, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Fayyaz Ahmad
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
| | - Bilal Wajid
- Department of Electrical Engineering, University of Engineering and Technology, Lahore, Pakistan
- Department of Computer Science, University of Management and Technology, Lahore, Pakistan
- Division of Research and Development, Sabz-Qalam, Lahore, Pakistan
| | - Safee Ullah Chaudhary
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
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