Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics
Many software suites and spectral libraries have been developed for DIA proteomics data analysis. Here, the authors create benchmark data sets to evaluate four commonly used software tools combined with seven spectral libraries in both global proteomics and phosphoproteomics analysis.
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-01-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-022-35740-1 |
| _version_ | 1828069468757032960 |
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| author | Ronghui Lou Ye Cao Shanshan Li Xiaoyu Lang Yunxia Li Yaoyang Zhang Wenqing Shui |
| author_facet | Ronghui Lou Ye Cao Shanshan Li Xiaoyu Lang Yunxia Li Yaoyang Zhang Wenqing Shui |
| author_sort | Ronghui Lou |
| collection | DOAJ |
| description | Many software suites and spectral libraries have been developed for DIA proteomics data analysis. Here, the authors create benchmark data sets to evaluate four commonly used software tools combined with seven spectral libraries in both global proteomics and phosphoproteomics analysis. |
| first_indexed | 2024-04-11T00:21:33Z |
| format | Article |
| id | doaj.art-1ddc8e335f7b40868b2f2f3f64f66a60 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-04-11T00:21:33Z |
| publishDate | 2023-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-1ddc8e335f7b40868b2f2f3f64f66a602023-01-08T12:16:18ZengNature PortfolioNature Communications2041-17232023-01-0114111710.1038/s41467-022-35740-1Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomicsRonghui Lou0Ye Cao1Shanshan Li2Xiaoyu Lang3Yunxia Li4Yaoyang Zhang5Wenqing Shui6iHuman Institute, ShanghaiTech UniversityUniversity of Chinese Academy of SciencesiHuman Institute, ShanghaiTech UniversityiHuman Institute, ShanghaiTech UniversityInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of SciencesInterdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of SciencesiHuman Institute, ShanghaiTech UniversityMany software suites and spectral libraries have been developed for DIA proteomics data analysis. Here, the authors create benchmark data sets to evaluate four commonly used software tools combined with seven spectral libraries in both global proteomics and phosphoproteomics analysis.https://doi.org/10.1038/s41467-022-35740-1 |
| spellingShingle | Ronghui Lou Ye Cao Shanshan Li Xiaoyu Lang Yunxia Li Yaoyang Zhang Wenqing Shui Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics Nature Communications |
| title | Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics |
| title_full | Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics |
| title_fullStr | Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics |
| title_full_unstemmed | Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics |
| title_short | Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics |
| title_sort | benchmarking commonly used software suites and analysis workflows for dia proteomics and phosphoproteomics |
| url | https://doi.org/10.1038/s41467-022-35740-1 |
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