دورية أكاديمية
WOMBAT-P: benchmarking label-free proteomics data analysis workflows
| العنوان: | WOMBAT-P: benchmarking label-free proteomics data analysis workflows |
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| المؤلفون: | Bouyssié, D., Altiner, P., Capella-Gutierrez, S., Fernández, J.M., Hagemeijer, Y.P., Horvatovich, P., Hubálek, M., Levander, F., Mauri, P., Palmblad, M., Raffelsberger, W., Rodríguez-Navas, L., Silvestre, D. di, Kunkli, B.T., Uszkoreit, J., Vandenbrouck, Y., Vizcaíno, J.A., Winkelhardt, D., Schwämmle, V. |
| المصدر: | Journal of Proteome Research |
| سنة النشر: | 2023 |
| المجموعة: | Leiden Repository (Leiden University) |
| مصطلحات موضوعية: | workflow, data analysis, benchmarking, label-free proteomics, quality metrics |
| الوصف: | The inherent diversity of approaches in proteomics research has led to a wide range of software solutions for data analysis. These software solutions encompass multiple tools, each employing different algorithms for various tasks such as peptide-spectrum matching, protein inference, quantification, statistical analysis, and visualization. To enable an unbiased comparison of commonly used bottom-up label-free proteomics workflows, we introduce WOMBAT-P, a versatile platform designed for automated benchmarking and comparison. WOMBAT-P simplifies the processing of public data by utilizing the sample and data relationship format for proteomics (SDRF-Proteomics) as input. This feature streamlines the analysis of annotated local or public ProteomeXchange data sets, promoting efficient comparisons among diverse outputs. Through an evaluation using experimental ground truth data and a realistic biological data set, we uncover significant disparities and a limited overlap in the quantified proteins. WOMBAT-P not only enables rapid execution and seamless comparison of workflows but also provides valuable insights into the capabilities of different software solutions. These benchmarking metrics are a valuable resource for researchers in selecting the most suitable workflow for their specific data sets. The modular architecture of WOMBAT-P promotes extensibility and customization. The software is available at https://github.com/wombat-p/WOMBAT-PipelinesTest. ; Proteomics |
| نوع الوثيقة: | article in journal/newspaper |
| وصف الملف: | application/pdf |
| اللغة: | English |
| العلاقة: | lumc-id: 186717214; https://hdl.handle.net/1887/3729604Test |
| DOI: | 10.1021/acs.jproteome.3c00636 |
| الإتاحة: | https://doi.org/10.1021/acs.jproteome.3c00636Test https://hdl.handle.net/1887/3729604Test |
| رقم الانضمام: | edsbas.C2D20B90 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1021/acs.jproteome.3c00636 |
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