Mass Spectrometry as a Tool to Enhance “-omics” Education †
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Authors:
Michael J. Wolyniak1,*,
Nathan S. Reyna2,
Ruth Plymale2,
Welkin H. Pope3,
Daniel E. Westholm4
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Received 27 August 2017 Accepted 27 November 2017 Published 16 February 2018
- ©2018 Author(s). Published by the American Society for Microbiology
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[open-access] This is an Open Access article distributed under the terms of the Creative Commons Attribution-Noncommercial-NoDerivatives 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/ and https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode), which grants the public the nonexclusive right to copy, distribute, or display the published work.
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†Supplemental materials available at http://asmscience.org/jmbe
- *Corresponding author. Mailing address: Department of Biology, Hampden-Sydney College, Box 183, Hampden-Sydney, VA 23943. Phone: 434-223-6175. E-mail: [email protected].
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Affiliations:
1: Department of Biology, Hampden-Sydney College, Hampden-Sydney, VA 23943;
2: Department of Biology, Ouachita Baptist University, Arkadelphia, AR 71998;
3: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260;
4: Department of Biology, The College of St. Scholastica, Duluth, MN 55811
AUTHOR AND ARTICLE INFORMATION
AUTHOR AND ARTICLE INFORMATION
Source:
J. Microbiol. Biol. Educ.
February 2018
vol. 19 no. 1 doi:10.1128/jmbe.v19i1.1459
MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
Abstract:
The rise of "-omics" related technologies makes it essential for students to have experience working with large bioinformatics data sets. Although”-omic” datasets are complex and abstract, effective instruction can be improved when students see the direct connections between the data on a computer screen and the results of "wet lab" experimentation. Here we describe the use of protein mass spectrometry as a means for students to gain experience in connecting bioinformatic data with work done at the lab bench. Course-based Research Experiences (CREs) based on these techniques are accessible to institutions of all types as a result of rapidly declining costs for whole genome and proteome analysis. Our implementation is within a CRE based on viral infection of a bacterial host; however, this basic paradigm may be applied to other experimental systems of interest.
References & Citations
Supplemental Material
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Appendix 1: Experimental protocol for mass spectrometry of M. smegmatis cell pellet infected by mycobacteriophage
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2020-11-30
Abstract:
The rise of "-omics" related technologies makes it essential for students to have experience working with large bioinformatics data sets. Although”-omic” datasets are complex and abstract, effective instruction can be improved when students see the direct connections between the data on a computer screen and the results of "wet lab" experimentation. Here we describe the use of protein mass spectrometry as a means for students to gain experience in connecting bioinformatic data with work done at the lab bench. Course-based Research Experiences (CREs) based on these techniques are accessible to institutions of all types as a result of rapidly declining costs for whole genome and proteome analysis. Our implementation is within a CRE based on viral infection of a bacterial host; however, this basic paradigm may be applied to other experimental systems of interest.
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Author and Article Information
-
Received 27 August 2017 Accepted 27 November 2017 Published 16 February 2018
- ©2018 Author(s). Published by the American Society for Microbiology
-
[open-access] This is an Open Access article distributed under the terms of the Creative Commons Attribution-Noncommercial-NoDerivatives 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/ and https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode), which grants the public the nonexclusive right to copy, distribute, or display the published work.
-
†Supplemental materials available at http://asmscience.org/jmbe
- *Corresponding author. Mailing address: Department of Biology, Hampden-Sydney College, Box 183, Hampden-Sydney, VA 23943. Phone: 434-223-6175. E-mail: [email protected].
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Mass Spectrometry as a Tool to Enhance “-omics” Education
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Citation:
Wolyniak M, Reyna N, Plymale R, Pope W, Westholm D. 2018. Mass spectrometry as a tool to enhance “-omics” education
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. J. Microbiol. Biol. Educ. 19(1): doi:10.1128/jmbe.v19i1.1459
/content/jmbe/10.1128/jmbe.v19i1.1459.f1-jmbe-19-8
FIGURE 1
Mass spectrometry experimental protocol flowchart. OD = optical density; MOI = multiplicity of infection; LC-MS/MS = liquid chromatography-tandem mass spectrometry; ORF = open reading frame.
jmbe/19/1/jmbe-19-8f1_thmb.gif
jmbe/19/1/jmbe-19-8f1.gif
Click to view
FIGURE 1
Mass spectrometry experimental protocol flowchart. OD = optical density; MOI = multiplicity of infection; LC-MS/MS = liquid chromatography-tandem mass spectrometry; ORF = open reading frame.
Source:
J. Microbiol. Biol. Educ.
February 2018
vol. 19 no. 1 doi:10.1128/jmbe.v19i1.1459
/content/jmbe/10.1128/jmbe.v19i1.1459.f2-jmbe-19-8
FIGURE 2
SCAFFOLD Viewer Sample display window. Gene product names beginning with CDS are linked to the mycobacteriophage Brusacoram. All others are of host Mycobacterium smegmatis or other origin.
jmbe/19/1/jmbe-19-8f2_thmb.gif
jmbe/19/1/jmbe-19-8f2.gif
Click to view
FIGURE 2
SCAFFOLD Viewer Sample display window. Gene product names beginning with CDS are linked to the mycobacteriophage Brusacoram. All others are of host Mycobacterium smegmatis or other origin.
Source:
J. Microbiol. Biol. Educ.
February 2018
vol. 19 no. 1 doi:10.1128/jmbe.v19i1.1459
/content/jmbe/10.1128/jmbe.v19i1.1459.f3-jmbe-19-8
FIGURE 3
SCAFFOLD Viewer output for a representative bacteriophage infection experiment using the bacteriophage Brusacoram. (A) Representative recovered peptide from the mass spectrometry reading. Yellow highlights indicate that LC-MS/MS detected peptide overlap with the gene product. Green highlights indicate modified amino acids. (B) In this case, a much smaller percentage of the predicted ORF was detected. Here, four peptides were detected that overlap with this ORF. A minimum of two detected peptides are required to confirm protein expression. ORF = open reading frame; LC-MS/MS = liquid chromatography-tandem mass spectrometry.
jmbe/19/1/jmbe-19-8f3_thmb.gif
jmbe/19/1/jmbe-19-8f3.gif
Click to view
FIGURE 3
SCAFFOLD Viewer output for a representative bacteriophage infection experiment using the bacteriophage Brusacoram. (A) Representative recovered peptide from the mass spectrometry reading. Yellow highlights indicate that LC-MS/MS detected peptide overlap with the gene product. Green highlights indicate modified amino acids. (B) In this case, a much smaller percentage of the predicted ORF was detected. Here, four peptides were detected that overlap with this ORF. A minimum of two detected peptides are required to confirm protein expression. ORF = open reading frame; LC-MS/MS = liquid chromatography-tandem mass spectrometry.
Source:
J. Microbiol. Biol. Educ.
February 2018
vol. 19 no. 1 doi:10.1128/jmbe.v19i1.1459
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