Proteomics: Protein Identification Using On-Line Databases

Overview & Concepts

Students will become familiar with proteomic databases and how they can be used to determine the identity of an unknown protein using laboratory data files created from yeast proteins.

Grade Level: 

Concepts Covered: 

bioinformatics, proteomics, mass spectrometry, PAGE, proteins, peptides, yeast

Prior Knowledge Required: 

Students will need to have an understanding of the basic structures and properties of amino acids, proteins, and enzymes. They will also need to know how electrophoresis can separate molecules by their size and charge and how a mass spectrometer can be used to determine molecular masses. The teacher can either present this information to the students in a traditional fashion or they can visit tutorial websites to learn about these topics. A link to an informative tutorial from the Children's Hospital Boston is listed below.

Activity Notes

Days to Teach: 

2-3 45 minute periods or 1-2 80-90 minute block(s)

Materials: 

  • student handout
  • computers with internet access
  • mass spectrometry data files (mgf files) provided below in the Student Attachments section

Teaching Tips / Activity Overview: 

  1. Students will learn how to search proteomic databases to determine the identity, functions and 3D structure of an unknown yeast protein.
  2. Mass spectrometry data files, prepared by undergraduate students at Franklin and Marshall College, will be uploaded into a proteomic search engine that will query protein databases and return a report of possible identifications for the unknown protein.
  3. Students will be able to determine the primary structure of their identified protein, learn about its function and view an interactive 3D model of its structure.

Assessment: 

  • Post-assessment: Evaluation of completed reports, printout of protein structure, problems on unit test, potential for presentations.

Extensions: 

Resources: 

Acknowledgements: 

This activity was produced by Chris Eurich and Peter Fields.

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