Get hands-on experience using the Skyline peak boundary imputation feature for DIA experiments. Learn how missing values affect group comparisons in untargeted proteomics, explore the limitations of zero-substitution approaches, and see how Skyline transfers peak boundaries from high-confidence identifications (exemplary replicates) to replicates with missing peaks. Use the Score to Run Regression graph to understand retention time alignment and identify cases where imputation may not perform well. (19 pages)

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* - written on v26.0.9

On December 11, 2025, the Skyline Team produced Webinar #27: Peak Boundary Imputation for DIA Data, another great resource for this topic.
[webinar]