SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream...

Area of Science:

• Proteomics
• Bioinformatics
• Computational Biology

Background:

• SWATH-MS is a targeted proteomics technique for high-throughput protein quantification.
• OpenSWATH is a widely used open-source software for SWATH-MS data analysis.
• Data transfer from OpenSWATH to downstream statistical tools is currently challenging.

Purpose of the Study:

• Introduce SWATH2stats, an R/Bioconductor package.
• Facilitate seamless data processing from OpenSWATH to downstream analysis tools.
• Enhance the analysis and quality control of SWATH-MS data.

Main Methods:

• Developed an R/Bioconductor package named SWATH2stats.
• Implemented functionalities for data conversion, annotation, and quality assessment.
• Integrated features for variation analysis, reproducibility assessment, FDR estimation, and advanced filtering.

Main Results:

• SWATH2stats enables direct data import into downstream statistical tools (e.g., MSstats, mapDIA, aLFQ).
• The package provides essential tools for analyzing measurement variation and reproducibility.
• Facilitates efficient quality control and filtering of SWATH-MS data prior to statistical analysis.

Conclusions:

• SWATH2stats streamlines the analysis pipeline for SWATH-MS data.
• Improves the efficiency and accessibility of large-scale targeted proteomics studies.
• Facilitates robust and reproducible quantitative proteomics research.