Benchmark of different library-free DIA strategies

Abstract

Abstract Motivation: Proteomics is advancing rapidly and testing and comparing recently published mass spectrometry acquisition and data analysis methods is the best way to keep up with the advances as well as to improve and generate the highest quality data possible at the mass spectrometry facility. Results: The use of variable isolation windows is the DIA (Data Independent Acquisition) strategy that performs best in our group from the ones we have tested. But depending on the window scheme it can also perform worse than other strategies. Dia-NN is better than Spectronaut for library-free searches and when used with a specific window scheme method the results are even greater.