Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we
present a fast and sensitive approach for direct peptide identification from DIA data,
MSFragger-DIA, which leverages the unmatched speed of the fragment ion indexing-based
search engine MSFragger. Different from most existing methods, MSFragger-DIA conducts a
database search of the DIA tandem mass (MS/MS) spectra prior to spectral feature detection …

Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we
present a fast and sensitive approach for direct peptide identification from DIA data,
MSFragger-DIA, which leverages the unmatched speed of the fragment ion indexing-based
search engine MSFragger. MSFragger-DIA conducts a database search of the DIA tandem
mass (MS/MS) spectra prior to spectral feature detection and peak tracing across the LC …