RT Journal Article
SR Electronic
T1 DIALib: an automated ion library generator for data independent acquisition mass spectrometry analysis of peptides and glycopeptides
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 696518
DO 10.1101/696518
A1 Toan K. Phung
A1 Lucia F Zacchi
A1 Benjamin L. Schulz
YR 2019
UL http://biorxiv.org/content/early/2019/07/10/696518.abstract
AB Data Independent Acquisition (DIA) Mass Spectrometry (MS) workflows allow unbiased measurement of all detectable peptides from complex proteomes, but require ion libraries for interrogation of peptides of interest. These DIA ion libraries can be theoretical or built from peptide identification data from Data Dependent Acquisition (DDA) MS workflows. However, DDA libraries derived from empirical data rely on confident peptide identification, which can be challenging for peptides carrying complex post-translational modifications. Here, we present DIALib, software to automate the construction of peptide and glycopeptide Data Independent Acquisition ion Libraries. We show that DIALib theoretical ion libraries can identify and measure diverse N- and O-glycopeptides from yeast and mammalian glycoproteins without prior knowledge of the glycan structures present. We also show that DIALib libraries consisting only of glycan oxonium ions can quickly and easily provide a global glycosylation profile of the “oxoniome” of glycoproteomes. DIALib also enables the study of post-translational modifications beyond glycosylation, in isolation or combination, in complex proteomes from diverse biological and clinical samples.