Automated SWATH Data Analysis Using Targeted Extraction of Ion Chromatograms

Area of Science:

• Proteomics
• Analytical Chemistry
• Biochemistry

Background:

• Targeted mass spectrometry methods like Selected Reaction Monitoring (SRM) and SWATH MS enable sensitive and accurate protein quantification.
• These techniques rely on specific mass spectrometric coordinates (assays) for reproducible protein detection.

Purpose of the Study:

• To describe a standard workflow for analyzing SWATH MS data for targeted protein monitoring.
• To provide guidance on ensuring maximal coverage, reproducibility, and quantitative accuracy in large-scale proteomic studies.

Main Methods:

• Standard SWATH MS analysis workflow.
• Manual data analysis for quality control using Skyline.
• Automated data analysis with error rate control using the OpenSWATH workflow.

Main Results:

• A reproducible method for analyzing SWATH MS data to monitor thousands of proteins across numerous samples.
• Implementation of quality control measures for data analysis.
• Strategies for controlling error rates in automated analysis.

Conclusions:

• The described workflow facilitates reproducible and accurate quantification of proteins using SWATH MS.
• The protocol supports large-scale proteomic analyses requiring high sensitivity and coverage.
• Considerations for maximizing data quality in targeted proteomics are discussed.