A recent study using IonOpticks Aurora Series Columns compares the performance of widely used software and workflows for data-independent acquisition (DIA) proteomics and phosphoproteomics. The researchers generated a reference dataset for benchmarking and evaluated four popular software suites using various metrics. The results indicated that different software suites exhibit distinct strengths and weaknesses depending on the type of experiment, and there is no single “best” software for all DIA proteomics and phosphoproteomics applications. The researchers also provided recommendations for selecting software based on experimental needs and outlined the importance of transparency and reproducibility in DIA proteomics and phosphoproteomics research. Overall, this study provides valuable insights for researchers seeking to optimize their DIA proteomics and phosphoproteomics analyses. https://www.nature.com/articles/s41467-022-35740-1
Journal Article – Jan 2023 – Nature Communications
Authors
R. Lou; Y. Cao; S. Li; X. Lang; Y. Li; Y. Zhang; W. Shui
Title
Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics
