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].
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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MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
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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].
Figures
Mass spectrometry experimental protocol flowchart. OD = optical density; MOI = multiplicity of infection; LC-MS/MS = liquid chromatography-tandem mass spectrometry; ORF = open reading frame.

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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.
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.

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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.
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.

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.