Monitoring host cell proteins (HCPs) is crucial for ensuring product safety and quality in biopharmaceutical development. In this webinar, Somar presents the application of label-free shotgun proteomics for HCP monitoring, benchmarking six prominent MS/MS search tools—Mascot, MaxQuant, SpectroMine, FragPipe, Byos, and PEAKS—utilizing trapped ion mobility spectrometry and ddaPASEF. The study employs Bayesian inference as a robust framework for evaluating tool performance, incorporating Markov Chain Monte Carlo modeling, Bayesian FDR control, and decision theory to balance differential abundance accuracy with uncertainty.

The webinar will highlight the strengths and trade-offs of each search tool, focusing on key metrics such as peptide and protein identifications, data extraction precision, fold change accuracy, linearity, and quantification trueness.