From Peaks to Power: Systematic Evaluation of Chromatographic Sampling Reveals Determinants of Quantification and Biological Discovery in DIA Proteomics (opens in new tab)

Modern DIA proteomics increasingly emphasizes throughput and depth for large-cohort studies, but methods are often optimized using proxy metrics that can mask losses in quantifiable signal and statistical power. Here, we evaluate how datapoints per peak and other chromatographic features jointly contribute to quantification and downstream biological discovery. Using a matrix-matched calibration curve dataset, we checked how the number of datapoints per peak (DPPP) affects the limits of detect...