A Scoring Algorithm for the Automated Analysis of Glycosaminoglycan MS/MS Data
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J. Am. Soc. Mass Spectrom. (2019) DOI: 10.1007/s13361-019-02338-9
RESEARCH ARTICLE
A Scoring Algorithm for the Automated Analysis of Glycosaminoglycan MS/MS Data Jiana Duan, Lauren Pepi, I. Jonathan Amster Department of Chemistry, University of Georgia, Athens, GA 30602, USA
Scores Histogram
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Abstract. The role of glycosaminoglycans (GAGs) in major biological functions is numerous (CH ) NH and diverse, yet structural characterization of NS NS 2S 2S NS 3S 6S 6S 6S them by mass spectrometric techniques proves (CH ) NH NS 2S 2S 3S NS 6S 6S to be challenging. Characterization of GAG struc(CH ) NH 2S 3S NS 2S NS 3S ture from tandem mass spectrometry is a tedious 6S 6S 6S (CH ) NH NS 3S 2S 3S 2S and time-consuming process but one that can be 6S 6S (CH ) NH automated in a database-independent, high3S 2S NS 3S 3S 2S 6S 6S 6S (CH ) NH throughput fashion through the assistance of soft2S 3S 2S 3S 3S score(x) ware implementing a genetic algorithm (J. Am. Soc. Mass Spectrom. 29, 1802–1911, 2018). This work presents the manner in which this data is interpreted by the software, specifically addressing the development of a scoring algorithm. The significance of glycosidic and cross-ring fragment ions and the implications that specific fragments provide for assigning the positions of modifications are discussed. The scoring algorithm is tested for statistical merit using the widely accepted expectation value as the criterion for quality. Using MS/MS data for well-characterized standards, this scoring approach is shown to assign the correct structure, with a low likelihood (1 in 1012 chances) that the assigned structure matches the data due to random chance. The integrated software that automates the structure assignment is called Glycosaminoglycan-Unambiguous Identification Technology (G-UNIT). Keywords: Glycosaminoglycans, Fourier transform mass spectrometry, Automation, Software, Automated data analysis 6S
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(CH2)5NH2
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Received: 17 August 2018/Revised: 20 August 2019/Accepted: 20 August 2019
Introduction
G
lycosaminoglycans (GAGs) are linear, polydisperse carbohydrates that are ubiquitous among living cells, and are responsible for a multitude of biological interactions including cell signaling, energy generation, protein binding conformation changes, and molecular recognition [1–4]. Structurally, GAGs are composed of a repeating linear disaccharide backbone of a uronic sugar and amino sugar residue. Structural differentiation occurs based on three primary forms of modifications: Osulfation, N-deacetylation/sulfation, and uronic sugar epimerization. Recent studies suggest that patterns of sulfation have a profound effect on protein binding [5, 6]. Moreover, Electronic supplementary material The online version of this article (https:// doi.org/10.1007/s13361-019-02338-9) contains supplementary material, which is available to authorized users. Correspondence to: I.
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