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  Home > JCE Print > Journal of Chemical Education > Issues > 2009  > August  >
In the Laboratory
Incorporating Biological Mass Spectrometry into Undergraduate Teaching Labs, Part 3: De Novo Peptide Sequencing Using Electrospray Tandem Mass Spectrometry
Isaac J. Arnquist and Douglas J. Beussman
Department of Chemistry, St. Olaf College, Northfield, MN 55057
Cover
August 2009
Vol. 86 No. 8
p. 966

Abstract
Tandem mass spectrometry (MS–MS) is an important technique routinely used to provide structural information about analytes of interest. One major application of tandem mass spectrometry is in the field of proteomics, which routinely uses MS–MS experiments to help identify peptides and proteins. In this experiment, students learn how to perform a tandem mass spectrometry experiment on a selected peptide ion using an ion-trap mass spectrometer and how to use the resulting data to sequence the peptide de novo. While the majority of protein and peptide identification done using mass spectrometry relies on database search algorithms, it is still important for a trained scientist to compare the computer results with the empirical data to make a judgment as to how well the two correlate. It is therefore important that students be exposed to peptide sequencing and learn how this can be done without a database to prepare them for research in the proteomics field. We have included several representative peptide fragmentation spectra, suitable for classroom use in the online material.
Supplement
Instructions for the students; Notes for the instructor; Spectra of five peptides
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Citation
Arnquist, Isaac J.; Beussman, Douglas J. J. Chem. Educ. 2009, 86, 966.
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Keywords
Analytical Chemistry; Bioanalytical Chemistry; Biochemistry; Hands-On Learning / Manipulatives; Instrumental Methods; Laboratory Instruction; Mass Spectrometry; Proteins / Peptides; Qualitative Analysis; Upper-Division Undergraduate
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History
Created:
Last Updated:
6/16/2009
6/30/2009
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Experiments, laboratory exercises, lecture demonstrations, and other descriptions of the use of chemicals, apparatus, instruments, computers, and computer interfaces are presented in the Journal of Chemical Education as illustrative of new or improved ideas or concepts in chemistry instruction and are directed at qualified teachers. Although every effort is made to assure and encourage safe practices and safe use of chemicals, the Journal of Chemical Education cannot assume responsibility for uses made of its published materials. Many chemicals are hazardous. Precautions for the safe use of hazardous chemicals and directions for their proper disposal are described in the Material Safety Data Sheets and on the labels. We strongly urge all those planning to use materials from our pages to make choices and to develop procedures for laboratory and classroom safety in accordance with local needs and situations.
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