Issue 2, 2020

DIALib: an automated ion library generator for data independent acquisition mass spectrometry analysis of peptides and glycopeptides

Abstract

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 present proof-of-principle data from a moderately complex yeast cell wall glycoproteome and a simple mixture of mammalian glycoproteins. We also show that DIALib libraries consisting only of glycan oxonium ions can quickly and easily provide a global compositional glycosylation profile of the detectable “oxoniome” of glycoproteomes. DIALib will help enable DIA glycoproteomics as a complementary analytical approach to DDA glycoproteomics.

Graphical abstract: DIALib: an automated ion library generator for data independent acquisition mass spectrometry analysis of peptides and glycopeptides

Supplementary files

Article information

Article type
Research Article
Submitted
31 Jul 2019
Accepted
17 Feb 2020
First published
18 Feb 2020

Mol. Omics, 2020,16, 100-112

DIALib: an automated ion library generator for data independent acquisition mass spectrometry analysis of peptides and glycopeptides

T. K. Phung, L. F. Zacchi and B. L. Schulz, Mol. Omics, 2020, 16, 100 DOI: 10.1039/C9MO00125E

To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements