Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

Short summary

A novel data-independent acquisition (DIA) method called Hyper Reaction Monitoring (HRM) achieved over 98% peptide detection reproducibility, significantly outperforming shotgun proteomics (49% reproducibility) in identifying and quantifying proteins. HRM was applied to acetaminophen-treated liver microtissues, revealing early proteome changes at subtoxic doses and identifying human NAPQI-protein adducts for the first time.

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