Brett Larsen

TL;DR: DIA-Umpire enables targeted extraction of quantitative information based on peptides initially identified in only a subset of the samples, resulting in more consistent quantification across multiple samples.

TL;DR: This study demonstrates that the acquisition of reproducible quantitative proteomics data by multiple labs is achievable, and broadly serves to increase confidence in SWATH-mass spectrometry data acquisition as a reproducible method for large-scale protein quantification.

TL;DR: It is established that NUDC family cochaperones specifically associate with structurally related but evolutionarily distinct β-propeller folds, providing a framework for deciphering the proteostasis network and its regulation in development and disease and expand the use of chaperones as sensors for drug-target engagement.

TL;DR: It is shown that AP-SWATH is a robust label-free approach to characterize changes in protein-protein interactions imparted by the HSP90 inhibitor NVP-AUY922 or melanoma-associated mutations in the human kinase CDK4 and proposed a scalable pipeline for systems biology studies.

TL;DR: In this article, changes to protein interactomes as a result of mutations to the bait protein or addition of a pharmacological inhibitor are robustly monitored with affinity purification coupled with data-independent acquisition-based mass spectrometry and an automated data analysis pipeline.