Simulation of two dimensional electrophoresis and tandem mass spectrometry for teaching proteomics

Polyacrylamide gel electrophoresis (PAGE) is the most classical technique favored worldwide for resolution of macromolecules in many biochemistry laboratories due to its incessant advanced developments and wide modifications. These ever-growing advancements in the basic laboratory equipments lead to emergence of many expensive, complex, and tricky laboratory equipments. Practical courses of biochemistry at high school or undergraduate levels are often affected by these complications. Two dimensional gel electrophoresis technique (2D-PAGE) used for resolving thousands of proteins in a gel is a combination of isoelectric focusing (first dimension gel electrophoresis technique) and sodium-dodecylsulphate PAGE (second dimension gel electrophoresis technique or SDS-PAGE). Two different laboratory equipments are needed to carry out effective 2D-PAGE technique, which also invites extra burden to the school laboratory. Here, we describe a low cost, time saving and simple gel cassette for protein 2D-PAGE technique that uses easily fabricated components and routine off-theshelf materials. The performance of the apparatus was verified in a practical exercise by a group of high school students with positive outcomes. V C 2018 by The International

Section: Resultsmentioning

confidence: 99%

Simple and rapid system for two‐dimensional gel electrophoresis technique: A laboratory exercise for high school students

Maurye

Basu

Biswas

et al. 2018

“…After some discussion, I sent her home for the summer with the suggestion, “Learn to write Java code.” So she did. Over the next 2 years, she added a simulation of tandem mass spectrometry for protein sequence determination (Figure 1b) to the 2D electrophoresis application 8 . The simulation suite, JBioFramework, can be downloaded from Sourceforge (https://sourceforge.net/projects/jbf/) and includes 1D electrophoresis, 2D electrophoresis, the tandem mass spectrometer and an embedded version of Marvin Sketch from Chemaxon (https://chemaxon.com/; included with permission from the authors).…”

Section: Protein Separation Simulationsmentioning

confidence: 99%

Developing and applying computational resources for biochemistry education

Craig

2020

Biochemistry is about structure and function, but it is also about data and this is where computers come in. From my time as a graduate student and post doc, whenever I encountered data I thought, "I can work this up by hand, but I think a computer could do a better job." Since that time, I have been working at the interface of biochemistry and computers, by attracting talented students and collaborating with colleagues with complementary skills. This has resulted in several exciting projects: a simulation of 2D electrophoresis and tandem mass spectrometry, the human visualization project, and two different programs that enable biochemists to search protein structures for enzyme active sites: ProMOL (promol.org) and Moltimate (moltimate.appspot.com). The human side of software development for education involved finding the right students and colleagues, communicating effectively across disciplines, building and managing effective teams and the importance of serendipity throughout the process. K E Y W O R D S computational biology, genomics proteomics bioinformatics, integration of research into undergraduate teaching, molecular visualization, using simulation and internet resources for teaching

“…Fisher et al . created a computer program “2DE Tandem MS” to help students to understand proteomic concepts .…”

Section: Introductionmentioning

confidence: 99%

An integrated course based on two dimensional‐electrophoresis and mass spectrometry analysis to teach proteomic techniques for undergraduate students

Sha

Jia

Xin

et al. 2018

Here, we developed an integrated course based on two dimensional-electrophoresis and spectrometry mass (2DE-MS) technique for undergraduate students to help them learn proteomic techniques. The soluble proteins in wild type and gene knockout bacteria were separated by 2DE and the differently expressed proteins were identified by MS analysis. The proteomic data was finally confirmed by RT-PCR detection. The separated experiments of 2DE, MS, RNA isolation, RT-PCR, as well as essential bioinformatic analysis, were integrated into a one-week course, which provided students an opportunity to systematically understand the proteomic techniques and their applications in current scientific research. © 2018 by The International Union of Biochemistry and Molecular Biology, 46:354-360, 2018.