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

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DIALib: an automated ion library generator for data independent acquisition mass spectrometry analysis of peptides and glycopeptides.
Molecular Omics ( IF 3.0 ) Pub Date : 2020-02-27 , DOI: 10.1039/c9mo00125e
Toan K Phung ₁ , Lucia F Zacchi , Benjamin L Schulz

Affiliation

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.

中文翻译：

DIALib：一种自动离子库生成器，用于对肽和糖肽进行独立于数据的采集质谱分析。

数据独立采集（DIA）质谱（MS）工作流程允许对来自复杂蛋白质组的所有可检测肽段进行无偏测量，但需要离子库来查询目标肽段。这些DIA离子库可以是理论性的，也可以根据数据依赖采集（DDA）MS工作流程中的肽段识别数据构建。但是，来自经验数据的DDA库依赖于可靠的肽段鉴定，这对于携带复杂的翻译后修饰的肽段可能具有挑战性。在这里，我们介绍了DIALib，该软件可自动构建肽和糖肽数据独立采集离子库。我们表明DIALib理论离子库可以识别和测量酵母和哺乳动物糖蛋白中的各种N-和O-糖肽类，而无需对糖结构的现有知识。我们从中等复杂的酵母细胞壁糖蛋白组和哺乳动物糖蛋白的简单混合物中提供原理证明数据。我们还表明，仅由聚糖氧合子离子组成的DIALib文库可以快速，轻松地提供可检测的糖基蛋白质组“氧化基因组”的全局组成糖基化谱。DIALib将帮助使DIA糖蛋白组学成为DDA糖蛋白组学的补充分析方法。我们还表明，仅由聚糖氧合子离子组成的DIALib文库可以快速，轻松地提供可检测的糖基蛋白质组“氧化基因组”的全局组成糖基化谱。DIALib将帮助使DIA糖蛋白组学成为DDA糖蛋白组学的补充分析方法。我们还表明，仅由聚糖氧合子离子组成的DIALib文库可以快速，轻松地提供可检测的糖基蛋白质组“氧化基因组”的全局组成糖基化谱。DIALib将帮助使DIA糖蛋白组学成为DDA糖蛋白组学的补充分析方法。

更新日期：2020-02-18

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