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

Bruderer R, Bernhardt OM, Gandhi T, Miladinović SM, Cheng L, Messner S, Ehrenberger T, Zanotelli V, Butscheid Y, Escher C, Vitek O, Rinner O, Reiter L. MCP.

In this work, Biognosys and collaborators compared proteome coverage and quantification performance of the emerging DIA/SWATH method against the long-established shotgun DDA. The hyper reaction monitoring (HRM) workflow presented in this work combined DIA acquisition and retention-time-normalized (iRT) spectral libraries for targeted data extraction using Spectronaut. HRM showed higher precision, accuracy and less missing values compared to DDA and was proposed for large-scale quantitative proteome profiling.

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