Tutorial 4: Peptide fingerprinting questions

December 4, 2006

A- Use Aldente or MS-Fit to identify the following proteins.

  1. A protein that was identified on a 2D-gel with an approximate MW of 35 kDa and an isoelectric point of 8.4.
    After trypsin digestion and MS analysis, the following masses were obtained:

    1261.59
    1211.4
    1111.64
    963.48
    950.49
    871.54
    842.54
    751.5
    721.354
    609.33

  2. During a co-immunoprecipitation experiment (what is it?), a protein with a MW around 50 kDa and pI about 5, was identified to bind to HSP 60.
    The peptide fingerprinting results were as follow:

    1272.24
    702.352
    645.36
    1076.5
    1115.7
    861.32
    1169.7
    1323.6
    1471.2
    1405.7
    1588.644

    There was a closely related form of the protein with the following, slightly different peptide masses:

    872.41
    702.352
    645.36
    1076.5
    1115.7
    701.39
    1169.7
    1323.6
    1471.2
    1405.7
    1428.7117

    Identify the protein and explain the slight differences in MS results.

  3. Have you noticed differences between Aldente and MS-FIT? Discuss the differences…
  4. How does the choice of search database affect peptide fingerprinting results?
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Hello world!

November 29, 2006

This weblog will allow  the communication between instructors, students and trainees during the workshops on bioinformatics and systems biology.

We hope that the blog will be a part of our future EGYBIO website.