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本文引用的文献

1
Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function.将 MALDI-TOF 质谱蛋白质分析与特色代谢物分析相结合，可快速区分细菌功能。
Proc Natl Acad Sci U S A. 2018 May 8;115(19):4981-4986. doi: 10.1073/pnas.1801247115. Epub 2018 Apr 23.
2
Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists.基于基质辅助激光解吸/电离飞行时间质谱（MALDI-TOF MS）的微生物鉴定：微生物生态学家面临的挑战与机遇
Front Microbiol. 2016 Aug 30;7:1359. doi: 10.3389/fmicb.2016.01359. eCollection 2016.
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Application of MALDI Mass Spectrometry in Natural Products Analysis.基质辅助激光解吸电离质谱在天然产物分析中的应用。
Planta Med. 2016 May;82(8):671-89. doi: 10.1055/s-0042-104800. Epub 2016 Apr 28.
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Evaluation of the Bruker MALDI Biotyper for identification of Gram-positive rods: development of a diagnostic algorithm for the clinical laboratory.使用布鲁克基质辅助激光解吸电离飞行时间质谱仪鉴定革兰氏阳性杆菌的评估：临床实验室诊断算法的开发
J Clin Microbiol. 2014 Apr;52(4):1089-97. doi: 10.1128/JCM.02399-13. Epub 2014 Jan 22.
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A cross-platform toolkit for mass spectrometry and proteomics.一个用于质谱和蛋白质组学的跨平台工具包。
Nat Biotechnol. 2012 Oct;30(10):918-20. doi: 10.1038/nbt.2377.
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MALDI TOF MS profiling of bacteria at the strain level: a review.基质辅助激光解吸电离飞行时间质谱技术在细菌种水平上的分析：综述。
Mass Spectrom Rev. 2013 May-Jun;32(3):188-217. doi: 10.1002/mas.21359. Epub 2012 Sep 19.
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mzML--a community standard for mass spectrometry data.mzML--质谱数据的社区标准。
Mol Cell Proteomics. 2011 Jan;10(1):R110.000133. doi: 10.1074/mcp.R110.000133. Epub 2010 Aug 17.
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Phylogenetic classification and identification of bacteria by mass spectrometry.通过质谱法对细菌进行系统发育分类和鉴定。
Nat Protoc. 2009;4(5):732-42. doi: 10.1038/nprot.2009.37.
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ProteoWizard: open source software for rapid proteomics tools development.ProteoWizard：用于快速蛋白质组学工具开发的开源软件。
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10
Rapid identification of intact whole bacteria based on spectral patterns using matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry.使用基质辅助激光解吸/电离飞行时间质谱法基于光谱模式快速鉴定完整的全细菌。
Rapid Commun Mass Spectrom. 1996;10(10):1227-32. doi: 10.1002/(SICI)1097-0231(19960731)10:10<1227::AID-RCM659>3.0.CO;2-6.

使用开源基质辅助激光解吸电离飞行时间质谱微生物鉴定数据库管道分析微生物蛋白质和特殊代谢物数据。

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data.

作者信息

Clark Chase M, Costa Maria S, Conley Erin, Li Emma, Sanchez Laura M, Murphy Brian T

机构信息

Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago.

Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago; Faculty of Pharmaceutical Sciences, University of Iceland.

出版信息

J Vis Exp. 2019 May 15(147). doi: 10.3791/59219.

DOI:10.3791/59219
PMID:31157770
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7204650/
Abstract

In order to visualize the relationship between bacterial phylogeny and specialized metabolite production of bacterial colonies growing on nutrient agar, we developed IDBac-a low-cost and high-throughput matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) bioinformatics pipeline. IDBac software is designed for non-experts, is freely available, and capable of analyzing a few to thousands of bacterial colonies. Here, we present procedures for the preparation of bacterial colonies for MALDI-TOF MS analysis, MS instrument operation, and data processing and visualization in IDBac. In particular, we instruct users how to cluster bacteria into dendrograms based on protein MS fingerprints and interactively create Metabolite Association Networks (MANs) from specialized metabolite data.

摘要

为了可视化在营养琼脂上生长的细菌菌落的系统发育与特殊代谢产物产生之间的关系，我们开发了IDBac——一种低成本、高通量的基质辅助激光解吸/电离飞行时间质谱（MALDI-TOF MS）生物信息学流程。IDBac软件是为非专业人员设计的，可免费获取，并且能够分析少量到数千个细菌菌落。在此，我们介绍用于MALDI-TOF MS分析的细菌菌落制备、质谱仪操作以及IDBac中的数据处理和可视化的流程。特别是，我们指导用户如何根据蛋白质质谱指纹将细菌聚类成树状图，并根据特殊代谢产物数据交互式创建代谢产物关联网络（MANs）。