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

被引：13
作者：
Fisher, Amanda [1 ]
Sekera, Emily [1 ]
Payne, Jill [2 ]
Craig, Paul [1 ]
机构：
[1] Rochester Inst Technol, Sch Chem & Mat Sci, Rochester, NY 14623 USA
[2] Rochester Inst Technol, Dept Comp Sci, Rochester, NY 14623 USA
来源：
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION | 2012年 / 40卷 / 06期
关键词：
Biotechnology education; computational biology; computers in research and teaching; genomics proteomics bioinformatics; laboratory exercises; using simulation and internet resources for teaching; IDENTIFICATION; CHEMISTRY; EXERCISE;
D O I：
10.1002/bmb.20651
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
In proteomics, complex mixtures of proteins are separated (usually by chromatography or electrophoresis) and identified by mass spectrometry. We have created 2DE Tandem MS, a computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations-2D electrophoresis and tandem mass spectrometry. The two simulations are integrated together and are designed to teach the concept of proteome analysis of prokaryotic and eukaryotic organisms. 2DE-Tandem MS can be used as a freestanding simulation, or in conjunction with a wet lab, to introduce proteomics in the undergraduate classroom. 2DE Tandem MS is a free program available on Sourceforge at https://sourceforge.net/projects/jbf/. It was developed using Java Swing and functions in Mac OSX, Windows, and Linux, ensuring that every student sees a consistent and informative graphical user interface no matter the computer platform they choose. Java must be installed on the host computer to run 2DE Tandem MS. Example classroom exercises are provided in the Supporting Information. (c) 2012 by The International Union of Biochemistry and Molecular Biology
引用
收藏
页码：393 / 399
页数：7
相关论文
共 24 条
  • [1] Identifying Gel-separated Proteins Using In-gel Digestion, Mass Spectrometry, and Database Searching
    Albright, Jessica C.
    Dassenko, David J.
    Mohamed, Essa A.
    Beussman, Douglas J.
    [J]. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 2009, 37 (01) : 49 - 55
  • [2] [Anonymous], BIOCH ED
  • [3] COMPUTER-ASSISTED-INSTRUCTION IN BIOCHEMISTRY
    APOSTOLIDES, Z
    [J]. BIOCHEMICAL EDUCATION, 1987, 15 (03): : 129 - 133
  • [4] Reorganizing the protein space at the Universal Protein Resource (UniProt)
    Apweiler, Rolf
    Martin, Maria Jesus
    O'Donovan, Claire
    Magrane, Michele
    Alam-Faruque, Yasmin
    Antunes, Ricardo
    Casanova, Elisabet Barrera
    Bely, Benoit
    Bingley, Mark
    Bower, Lawrence
    Bursteinas, Borisas
    Chan, Wei Mun
    Chavali, Gayatri
    Da Silva, Alan
    Dimmer, Emily
    Eberhardt, Ruth
    Fazzini, Francesco
    Fedotov, Alexander
    Garavelli, John
    Castro, Leyla Garcia
    Gardner, Michael
    Hieta, Reija
    Huntley, Rachael
    Jacobsen, Julius
    Legge, Duncan
    Liu, Wudong
    Luo, Jie
    Orchard, Sandra
    Patient, Samuel
    Pichler, Klemens
    Poggioli, Diego
    Pontikos, Nikolas
    Pundir, Sangya
    Rosanoff, Steven
    Sawford, Tony
    Sehra, Harminder
    Turner, Edward
    Wardell, Tony
    Watkins, Xavier
    Corbett, Matt
    Donnelly, Mike
    van Rensburg, Pieter
    Goujon, Mickael
    McWilliam, Hamish
    Lopez, Rodrigo
    Xenarios, Ioannis
    Bougueleret, Lydie
    Bridge, Alan
    Poux, Sylvain
    Redaschi, Nicole
    [J]. NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) : D71 - D75
  • [5] GenBank
    Benson, Dennis A.
    Karsch-Mizrachi, Ilene
    Lipman, David J.
    Ostell, James
    Sayers, Eric W.
    [J]. NUCLEIC ACIDS RESEARCH, 2011, 39 : D32 - D37
  • [6] THE FOCUSING POSITIONS OF POLYPEPTIDES IN IMMOBILIZED PH GRADIENTS CAN BE PREDICTED FROM THEIR AMINO-ACID-SEQUENCES
    BJELLQVIST, B
    HUGHES, GJ
    PASQUALI, C
    PAQUET, N
    RAVIER, F
    SANCHEZ, JC
    FRUTIGER, S
    HOCHSTRASSER, D
    [J]. ELECTROPHORESIS, 1993, 14 (10) : 1023 - 1031
  • [7] An introduction to mass spectrometry applications in biological research
    Finehout, EJ
    Lee, KH
    [J]. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 2004, 32 (02) : 93 - 100
  • [8] ExPASy: the proteomics server for in-depth protein knowledge and analysis
    Gasteiger, E
    Gattiker, A
    Hoogland, C
    Ivanyi, I
    Appel, RD
    Bairoch, A
    [J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (13) : 3784 - 3788
  • [9] The NCBI BioSystems database
    Geer, Lewis Y.
    Marchler-Bauer, Aron
    Geer, Renata C.
    Han, Lianyi
    He, Jane
    He, Siqian
    Liu, Chunlei
    Shi, Wenyao
    Bryant, Stephen H.
    [J]. NUCLEIC ACIDS RESEARCH, 2010, 38 : D492 - D496
  • [10] On the convenience of using a computer simulation to teach enzyme kinetics to undergraduate students with biological chemistry-related curricula
    González-Cruz, J
    Rodríguez-Sotres, R
    Rodríguez-Penagos, M
    [J]. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 2003, 31 (02) : 93 - 101
123