Dynamic Data-Independent Acquisition Mass Spectrometry with Real-Time Retrospective Alignment

Area of Science:

• Proteomics
• Analytical Chemistry
• Mass Spectrometry

Background:

• Data-independent acquisition (DIA) mass spectrometry offers reproducible and rigorous quantitative analysis.
• Traditional DIA methods can be inefficient, dedicating instrument time to MS/MS spectra lacking useful data, which impacts sensitivity.
• Optimizing MS/MS acquisition is crucial for enhancing DIA performance.

Purpose of the Study:

• To develop an advanced DIA strategy that dynamically adjusts MS/MS windows during chromatographic separation.
• To improve quantitative sensitivity and lower the limit of quantification in mass spectrometry.
• To maximize the utility of instrument time by focusing on relevant mass ranges.

Main Methods:

• Developed a novel DIA strategy with dynamic MS/MS window adjustment.
• Implemented real-time adaptation of acquisition windows based on chromatographic elution.
• Focused MS/MS acquisition on the most relevant mass-to-charge ratio ranges at each time point.

Main Results:

• Achieved an improved average lower limit of quantification.
• Demonstrated enhanced quantitative sensitivity without compromising the number of detected peptides.
• Showcased the effectiveness of dynamic windowing in maximizing data quality.

Conclusions:

• The developed dynamic DIA strategy significantly enhances quantitative performance in mass spectrometry.
• This method optimizes instrument utilization, leading to better sensitivity and quantification.
• Dynamic window adjustment represents a key advancement for reproducible and sensitive proteomics analysis.