Abstract:Phosphoproteomics and ubiquitinomics data-independent
acquisition
(DIA) mass spectrometry (MS) data is typically analyzed by using a
data-dependent acquisition (DDA) spectral library. The performance
of various library-free strategies for analyzing phosphoproteomics
and ubiquitinomics DIA MS data has not been evaluated. In this study,
we systematically compare four commonly used DDA library-free approaches
including Spectronaut’s directDIA, DIA-Umpire, DIA-MSFragger,
and in silico-predicted library for analysi… Show more
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