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bioRxiv · 10.1101/726273

Analyzing data independent acquisition mass spectrometry with noiseless ion-networks

Willems, S.·Daled, S.·Van Puyvelde, B.·De Clerck, L.·Vande Casteele, S.·Van Nieuwerburgh, F.·Deforce, D.·Dhaenens, M.
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Abstract

Data-independent acquisition (DIA) mass spectrometry (MS) has introduced deter-ministic, periodic and simultaneous acquisition of all fragment ions. Despite the chimeric side-effects associated with this unprecedented data integrity, DIA data analysis approaches still use conventional spectra and extracted ion chromatograms (XICs) that represent individual precursors and fragments. Here, we introduce ion-networks, an alternative data format wherein nodes correspond to reproducible fragment ions from multiple runs and edges correspond to consistent co-elution. Each ion-network represents a complete experiment and computationally eliminates chimericy based on reproducibility without sacrificing data integrity.

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Willems, S., Daled, S., Van Puyvelde, B., De Clerck, L., Vande Casteele, S., Van Nieuwerburgh, F., Deforce, D., Dhaenens, M.. 2019-08-21. Analyzing data independent acquisition mass spectrometry with noiseless ion-networks. https://doi.org/10.1101/726273

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