SWPepNovo : an efficient de novo peptide sequencing tool for large-scale MS/MS spectra analysis
Tandem mass spectrometry (MS/MS)-based de novo peptide sequencing is a powerful method for high-throughput protein analysis. However, the explosively increasing size of MS/MS spectra dataset inevitably and exponentially raises the computational demand of existing de novo peptide sequencing methods,...
| Main Authors: | , , , , |
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| Format: | Journal Article |
| Language: | English |
| Published: |
2020
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| Online Access: | https://hdl.handle.net/10356/142187 |
| _version_ | 1811683108320182272 |
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| author | Li, Chuang Li, Kenli Li, Keqin Xie, Xianghui Lin, Feng |
| author2 | School of Computer Science and Engineering |
| author_facet | School of Computer Science and Engineering Li, Chuang Li, Kenli Li, Keqin Xie, Xianghui Lin, Feng |
| author_sort | Li, Chuang |
| collection | NTU |
| description | Tandem mass spectrometry (MS/MS)-based de novo peptide sequencing is a powerful method for high-throughput protein analysis. However, the explosively increasing size of MS/MS spectra dataset inevitably and exponentially raises the computational demand of existing de novo peptide sequencing methods, which is an issue urgently to be solved in computational biology. This paper introduces an efficient tool based on SW26010 many-core processor, namely SWPepNovo, to process the large-scale peptide MS/MS spectra using a parallel peptide spectrum matches (PSMs) algorithm. Our design employs a two-level parallelization mechanism: (1) the task-level parallelism between MPEs using MPI based on a data transformation method and a dynamic feedback task scheduling algorithm, (2) the thread-level parallelism across CPEs using asynchronous task transfer and multithreading. Moreover, three optimization strategies, including vectorization, double buffering and memory access optimizations, have been employed to overcome both the compute-bound and the memory-bound bottlenecks in the parallel PSMs algorithm. The results of experiments conducted on multiple spectra datasets demonstrate the performance of SWPepNovo against three state-of-the-art tools for peptide sequencing, including PepNovo+, PEAKS and DeepNovo-DIA. The SWPepNovo also shows high scalability in experiments on extremely large datasets sized up to 11.22 GB. The software and the parameter settings are available at https://github.com/ChuangLi99/SWPepNovo. |
| first_indexed | 2024-10-01T04:07:29Z |
| format | Journal Article |
| id | ntu-10356/142187 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T04:07:29Z |
| publishDate | 2020 |
| record_format | dspace |
| spelling | ntu-10356/1421872020-06-17T03:36:36Z SWPepNovo : an efficient de novo peptide sequencing tool for large-scale MS/MS spectra analysis Li, Chuang Li, Kenli Li, Keqin Xie, Xianghui Lin, Feng School of Computer Science and Engineering Engineering::Computer science and engineering Large-scale MS/MS Spectra Analysis De Novo Peptide Sequencing Tandem mass spectrometry (MS/MS)-based de novo peptide sequencing is a powerful method for high-throughput protein analysis. However, the explosively increasing size of MS/MS spectra dataset inevitably and exponentially raises the computational demand of existing de novo peptide sequencing methods, which is an issue urgently to be solved in computational biology. This paper introduces an efficient tool based on SW26010 many-core processor, namely SWPepNovo, to process the large-scale peptide MS/MS spectra using a parallel peptide spectrum matches (PSMs) algorithm. Our design employs a two-level parallelization mechanism: (1) the task-level parallelism between MPEs using MPI based on a data transformation method and a dynamic feedback task scheduling algorithm, (2) the thread-level parallelism across CPEs using asynchronous task transfer and multithreading. Moreover, three optimization strategies, including vectorization, double buffering and memory access optimizations, have been employed to overcome both the compute-bound and the memory-bound bottlenecks in the parallel PSMs algorithm. The results of experiments conducted on multiple spectra datasets demonstrate the performance of SWPepNovo against three state-of-the-art tools for peptide sequencing, including PepNovo+, PEAKS and DeepNovo-DIA. The SWPepNovo also shows high scalability in experiments on extremely large datasets sized up to 11.22 GB. The software and the parameter settings are available at https://github.com/ChuangLi99/SWPepNovo. Published version 2020-06-17T03:36:36Z 2020-06-17T03:36:36Z 2019 Journal Article Li, C., Li, K., Li, K., Xie, X., & Lin, F. (2019). SWPepNovo : an efficient de novo peptide sequencing tool for large-scale MS/MS spectra analysis. International Journal of Biological Sciences, 15(9), 1787-1801. doi:10.7150/ijbs.32142 1449-2288 https://hdl.handle.net/10356/142187 10.7150/ijbs.32142 31523183 2-s2.0-85071009731 9 15 1787 1801 en International Journal of Biological Sciences © 2019 The Author(s). This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). See http://ivyspring.com/terms for full terms and conditions. application/pdf |
| spellingShingle | Engineering::Computer science and engineering Large-scale MS/MS Spectra Analysis De Novo Peptide Sequencing Li, Chuang Li, Kenli Li, Keqin Xie, Xianghui Lin, Feng SWPepNovo : an efficient de novo peptide sequencing tool for large-scale MS/MS spectra analysis |
| title | SWPepNovo : an efficient de novo peptide sequencing tool for large-scale MS/MS spectra analysis |
| title_full | SWPepNovo : an efficient de novo peptide sequencing tool for large-scale MS/MS spectra analysis |
| title_fullStr | SWPepNovo : an efficient de novo peptide sequencing tool for large-scale MS/MS spectra analysis |
| title_full_unstemmed | SWPepNovo : an efficient de novo peptide sequencing tool for large-scale MS/MS spectra analysis |
| title_short | SWPepNovo : an efficient de novo peptide sequencing tool for large-scale MS/MS spectra analysis |
| title_sort | swpepnovo an efficient de novo peptide sequencing tool for large scale ms ms spectra analysis |
| topic | Engineering::Computer science and engineering Large-scale MS/MS Spectra Analysis De Novo Peptide Sequencing |
| url | https://hdl.handle.net/10356/142187 |
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