Benchmarking DIA data analysis workflows

• DOI: 10.1101/2023.06.02.543441
• Publication Date: 2023-06-06T22:05:24Z
• Authors: An Staes; Teresa Maia; Sara Dufour; Robbin Bouwmeester; Ralf Gabriels; Lennart Martens; Francis Impens; Simon Devos
• Keywords: Benchmarking; Ground truth; Mode (computer interface)

Abstract Data independent acquisition (DIA) has become a well-established method in LC-MS driven proteomics. Nonetheless, there are still lot of possibilities at the data analysis level. By benchmarking different DIA workflows using ground-truth sample, consisting differential spike-in UPS2 constant yeast background, we provide roadmap for shotgun samples based on whether sensitivity, precision or accuracy is essence. Three commonly used software tools (DIA-NN, EncyclopeDIA and Spectronaut TM ) were tested both spectral library mode library-free mode. In prediction PROSIT MS2PIP together with DeepLC, next to classical DDA-based libraries. total benchmarked 12 workflows. DIA-NN silico predicted libraries, mode, shows highest sensitivity maintaining high reproducibility accuracy. general, best reproducibility, while comparable all