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 ...»»»»
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.^^^^