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Home > Overview of PepSeq


What is PepSeq?

PepSeq is a peptide sequencing simulation program, created to assist biochemistry students in understanding the basic principals involved in peptide sequencing. It covers the concepts of alkaline hydrolyses (composition analysis), enzymatic and chemical fragmentations, and exopetidase digestions. Originally written as a DOS based program, PepSeq has been re-written as an online service which provides many benefits.

How is PepSeq used?

PepSeq is provided as an online service to lecturers and students. Everything runs through the website, from setting up the class list, running the simulated experiments and viewing the results:

  1. The student list is created online and random peptide sequences are automatically generated
  2. Students log in and do their experiments online in their own time
  3. The lecturer then views student results online

Overview of PepSeq

PepSeq provides an easy way to learn peptide sequencing, without the cost and time of conducting real experiments. Students learn appropriate concepts to solve their peptide sequences, and gain a deeper understanding of the processes involved.

Both on-campus and distance students benefit from the flexibility of PepSeq as an online service. For example, the initial training session could be conducted at the University, then students can complete the remaining experiments from home or University. There is no software to install, which simplifies the setup for lecturers and students.

PepSeq does not explain the concepts of peptide sequencing in detail - this information is provided to students by their lecturer. However, once students learn the basic principals, PepSeq helps to reinforce these concepts with practical examples. This program looks at a specific part of the protein sequencing strategy. A general sample is given: 1

  1. Separate and purify chains if protein contains more than one polypeptide chain
  2. Cleave intrachain S-S (disulfide bridges) between Cystiene residues
  3. Determine amino acid composition of each polypeptide chain
  4. Identify N-terminus and C-terminus
  5. Cleave each polypeptide chain into smaller fragments, and repeat steps 3 & 4
  6. Generate overlapping sets of peptide fragments by using different cleavage procedures
  7. Reconstruct overall amino acid sequence from sequences in overlapping fragments
  8. Location positions of S-S cross linking between Cystiene residues

PepSeq assumes the students are provided with a polypeptide chain for each experiment, which they must determine sequence of. This means PepSeq simulates steps 3, 4 and 5 of the above process.

Read about the benefits of PepSeq for students and lecturers.

 

System Requirements

Web Browser

  • Internet Explorer
    4.0, 5.5, 6.0 (Windows)


References:

1. Garrett, R. H. & Grisham, C. M. (1995) "Biochemistry", Saunders College Publishing, Sydney.

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