Interference of adjacent ion signals in CDMS: the effect on charge accuracy and potential correction algorithms

Importance of the Topic

The accuracy of charge detection mass spectrometry (CDMS) is essential for precise mass measurements of large biomolecules and assemblies. However, signals from adjacent ions oscillating at similar frequencies can interfere with charge assignment, reducing data reliability. The Selective Temporal Overview of Resonant Ions (STORI) method monitors ion conditions over time, offering a path to detect and correct these interference effects.

Objectives and Study Overview

This study investigates how neighboring ion signals affect charge accuracy in CDMS and assesses correction strategies. Artificial transients simulating coexisting ions in an Orbitrap analyzer were generated to characterize interference patterns. Two primary correction approaches were evaluated: frequency-domain windowing with different filter shapes and an iterative transient subtraction algorithm.

Methodology and Instrumentation

• Artificial transient generation: Custom Python scripts created single- and dual-ion signals with controlled lifetimes, amplitudes, frequency shifts, and disappearance times.
• STORI and misSTORI analysis: Extraction of real, imaginary, magnitude, and phase traces via brute-force convolution and efficient time-domain methods.
• Interference correction: Application of frequency-domain filters (box, Gaussian, half-sine, half-sine with flat top) and development of an interference subtraction loop that refines rough parameter estimates iteratively.

Main Results and Discussion

• Isolated ions: STORI slopes yielded accurate charge estimates matching the true state (e.g., +150 charges).
• Adjacent-ion interference: Ripple patterns in STORI plots caused underestimation of charge by up to two units when ions overlapped closely in frequency.
• Windowing filters: The flat-top half-sine window recovered correct charges for ions separated by several hertz but struggled when frequency gaps narrowed, filtering out desired signal information.
• Transient subtraction algorithm: Iterative removal of simulated interferent transients produced cleaner STORI plots and restored accurate charge assignments even for closely spaced ion frequencies.

Benefits and Practical Applications

Implementing robust interference-correction methods enhances CDMS performance in fields such as virology, proteomics, and polymer analysis. The transient subtraction approach can be integrated into data-processing pipelines to improve mass determination, support quality assurance, and enable more reliable structural characterization of macromolecules.

Future Trends and Potential Uses

• Advanced algorithms: Incorporation of machine-learning models to predict interference patterns and optimize filter parameters in real time.
• Hardware improvements: Development of analyzer designs with enhanced frequency resolution and ion attenuation to minimize interference at the source.
• High-throughput CDMS: Adaptation of STORI-based correction methods to faster acquisition schemes and multiplexed analyses.
• Broader analyzer compatibility: Extension of interference-correction workflows to time-of-flight and Fourier transform ion cyclotron resonance mass spectrometers.

Conclusion

Adjacent-ion signals pose a significant challenge for accurate charge detection in CDMS. While frequency-domain windowing offers a simple remedy, its performance diminishes for closely spaced frequencies. The proposed iterative transient subtraction algorithm provides a promising route to recover clean STORI plots and reliable charge assignments, supporting enhanced CDMS applications for complex analytes.

References

1. Goodwin MP et al Improved Signal Processing for Mass Shifting Ions in Charge Detection Mass Spectrometry J Am Soc Mass Spectrom 2024 35 4 658-662
2. Kafader JO et al STORI Plots Enable Accurate Tracking of Individual Ion Signals J Am Soc Mass Spectrom 2019 30 11 2200-2203