Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics
- Journal:
- Nature Communications
- Published:
- DOI:
- 10.1038/s41467-022-35740-1
- Affiliations:
- 6
- Authors:
- 7
Research Highlight
Testing software for analysing mass-spectrometry protein data
© Nitat Termmee/Moment/Getty Images
Four software suites for processing mass-spectrometry data on proteins have been put through their paces to evaluate their performance in analysing complex biological data.
Mass spectrometry is routinely used to analyse all the proteins active in biological processes. Emerging techniques for analysing mass-spectrometry data that are independent of data offer significant advantages over more conventional data-dependent ones.
However, many software suites have been developed, and it is not known how the choice of software affects the results.
Now, a team led by researchers from ShanghaiTech University in China has evaluated four commonly used software suites using benchmark data for thousands of proteins, which mimics the complexity seen in biological systems.
The team found that two of the four software suites performed particularly well in analyzing the data, although they note that all four suites are subject to ongoing improvement.
References
- Nature Communications 14, 94 (2023). doi: 10.1038/s41467-022-35740-1