Influence of extraction windows for data-independent acquisition on feature annotation during suspect screening

Area of Science:

• Environmental chemistry
• Analytical chemistry
• Mass spectrometry

Background:

• Non-target analysis (NTA) using high-resolution mass spectrometry is vital for identifying unknown chemicals.
• Data-independent acquisition (DIA), such as SWATH-MS, is essential for comprehensive NTA.
• Acquisition parameters in DIA methods can significantly impact the detection and annotation of chemical features.

Purpose of the Study:

• To evaluate how different DIA settings influence the confident annotation and identification of chemical features.
• To assess the impact of acquisition window number and size on NTA in diverse sample matrices.
• To determine matrix-specific optimal DIA parameters for improved chemical screening.

Main Methods:

• Analysis of environmental (river water, PSE), wastewater, and biological (urine) samples.
• Utilized 11 different Sequential Windowed Acquisition of all THeoretical Mass Spectra (SWATH-MS) methods with 5-15 variable acquisition windows.
• Evaluated true positive annotation rates, number of annotated features, and library score variations.

Main Results:

• True positive annotation rates varied by matrix, with higher rates observed in urine and wastewater using more windows (15).
• The number of annotated features was maximized in PSE and urine with specific window counts (9 and 14, respectively).
• Less complex matrices showed higher annotation rates with fewer windows (5-6), indicating matrix-dependent optimal settings.

Conclusions:

• Optimization of DIA parameters, particularly the number of acquisition windows, is critical and matrix-dependent for effective non-target analysis.
• The variability in library scores necessitates carefully curated libraries and optimized methods for reliable chemical identification.
• Achieving the best ratio of total to true positive annotations is key for successful NTA outcomes.