Proteomics - lesson plan

Learning outcomes

• Understand protein translation & genetic code
• Understand impact of alphabet size in matching
• Understand basics of mass spectrometry
• Understand how mass spectrometry can help sequence a peptide
• Able to develop a brute force algorithm for peptide sequencing
• Able to speed up brute force algorithms through branch and bound strategies
• Reason about impact of errors on algorithm
• Understand the spectrum deconvolution method
• Select appropriate datastructures for task.

Class plan

• Discuss DNA versus protein matching
• Work on peptide encoding problem - how does it influence algorithm for matching peptides to genome?
• Discuss mass spectrometry and data it produces
• Discuss why circular peptides are different from linear peptides.and how that impacts mass spectrometry data
• Cyclopeptide sequencing algorithm - discuss and analyze
• Discuss data-structures
• Extension to errors
• Use of deconvolution method

Exercises

Rosalind section 2

2B

2E