MGMS2：用于多微生物样本的膜糖脂质质谱模拟器。

MGMS2: Membrane glycolipid mass spectrum simulator for polymicrobial samples.

机构信息

School of Community Health Sciences, University of Nevada, Reno, NV, USA.

Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD, USA.

出版信息

Rapid Commun Mass Spectrom. 2020 Aug 30;34(16):e8824. doi: 10.1002/rcm.8824.

DOI:10.1002/rcm.8824

PMID:32384576

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7466374/

Abstract

RATIONALE

Polymicrobial samples present unique challenges for mass spectrometric identification. A recently developed glycolipid technology has the potential to accurately identify individual bacterial species from polymicrobial samples. In order to develop and validate bacterial identification algorithms (e.g. machine learning) using this glycolipid technology, generating a large number of various polymicrobial samples can be beneficial, but it is costly and labor-intensive. Here, we propose an alternative cost-effective approach that generates realistic in silico polymicrobial glycolipid mass spectra.

METHODS

We introduce MGMS2 (membrane glycolipid mass spectrum simulator) as a simulation software package that generates in silico polymicrobial membrane glycolipid matrix-assisted laser desorption/ionization time-of-flight mass spectra. Unlike currently available simulation algorithms for polymicrobial mass spectra, the proposed algorithm considers errors in m/z values and variances of intensity values, occasions of missing signature ions, and noise peaks. To our knowledge, this is the first stand-alone bacterial membrane glycolipid mass spectral simulator. MGMS2 software and its manual are freely available as an R package. An interactive MGSM2 app that helps users explore various simulation parameter options is also available.

RESULTS

We demonstrated the performance of MGSM2 using six microbes. The software generated in silico glycolipid mass spectra that are similar to real polymicrobial glycolipid mass spectra. The maximum correlation between in silico mass spectra generated by MGMS2 and the real polymicrobial mass spectrum was about 87%.

CONCLUSIONS

We anticipate that MGMS2, which considers spectrum-to-spectrum variation, will advance the bacterial algorithm development for polymicrobial samples.

摘要

原理

混合微生物样本给质谱鉴定带来了独特的挑战。最近开发的糖脂技术有可能从混合微生物样本中准确鉴定单个细菌物种。为了使用这种糖脂技术开发和验证细菌鉴定算法（例如机器学习），生成大量各种混合微生物样本可能是有益的，但这既昂贵又费力。在这里，我们提出了一种替代的具有成本效益的方法，可以生成逼真的计算机模拟混合微生物糖脂质荷比质谱。

方法

我们引入了 MGMS2（膜糖脂质荷比质谱模拟器）作为一种模拟软件包，用于生成计算机模拟的混合微生物膜糖脂质基质辅助激光解吸/电离飞行时间质谱。与目前可用的混合微生物质荷比光谱模拟算法不同，所提出的算法考虑了 m/z 值的误差、强度值的方差、特征离子的缺失情况和噪声峰。据我们所知，这是第一个独立的细菌膜糖脂质荷比质谱模拟器。MGMS2 软件及其手册可作为 R 包免费获得。还提供了一个交互式的 MGSM2 应用程序，帮助用户探索各种模拟参数选项。