dc.contributor |
Háskóli Íslands |
dc.contributor |
University of Iceland |
dc.contributor.author |
Clark, Chase M. |
dc.contributor.author |
Costa, Maria Sofia |
dc.contributor.author |
Conley, Erin |
dc.contributor.author |
Li, Emma |
dc.contributor.author |
Sanchez, Laura M. |
dc.contributor.author |
Murphy, Brian T. |
dc.date.accessioned |
2020-04-29T14:12:11Z |
dc.date.available |
2020-04-29T14:12:11Z |
dc.date.issued |
2019-05-15 |
dc.identifier.citation |
Clark, C. M., Costa, M. S., Conley, E., Li, E., Sanchez, L. M., Murphy, B. T. Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data. J. Vis. Exp. (147), e59219, doi:10.3791/59219 (2019). |
dc.identifier.issn |
1940-087X |
dc.identifier.uri |
https://hdl.handle.net/20.500.11815/1754 |
dc.description |
Publisher's version (útgefin grein) |
dc.description.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 (MALDITOF 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. |
dc.description.sponsorship |
This work was supported by National Institute of General Medical Sciences Grant R01 GM125943, National Geographic Grant CP-044R-17; Icelandic Research Fund Grant 152336-051; and University of Illinois at Chicago startup funds. Also, we thank the following contributors: Dr. Amanda Bulman for assistance with MALDI-TOF MS protein acquisition parameters; Dr. Terry Moore and Dr. Atul Jain for recrystallizing alpha-cyano-4-hydroxycinnamic acid matrix (CHCA). |
dc.format.extent |
e59219 |
dc.language.iso |
en |
dc.publisher |
MyJove Corporation |
dc.relation.ispartofseries |
Journal of Visualized Experiments;2019(147) |
dc.rights |
info:eu-repo/semantics/openAccess |
dc.subject |
Biochemistry |
dc.subject |
Bioinformatics |
dc.subject |
MALDI-TOF MS |
dc.subject |
Mass spectrometry |
dc.subject |
Microbiology |
dc.subject |
Natural products |
dc.subject |
Specialized metabolites |
dc.subject |
Lífefnafræði |
dc.subject |
Litrófsgreining |
dc.subject |
Örverufræði |
dc.subject |
Opinn hugbúnaður |
dc.title |
Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data |
dc.type |
info:eu-repo/semantics/article |
dcterms.license |
This content is Open Access under Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported
License |
dc.description.version |
Peer Reviewed |
dc.identifier.journal |
Journal of Visualized Experiments |
dc.identifier.doi |
10.3791/59219 |
dc.relation.url |
https://www.jove.com/video/59219/using-open-source-maldi-tof-ms-idbac-pipeline-for-analysis-microbial |
dc.contributor.department |
Lyfjafræðideild (HÍ) |
dc.contributor.department |
Faculty of Pharmaceutical Sciences (UI) |
dc.contributor.school |
Heilbrigðisvísindasvið (HÍ) |
dc.contributor.school |
School of Health Sciences (UI) |