Tutorial 4: Peptide fingerprinting questions

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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2 Responses to Tutorial 4: Peptide fingerprinting questions

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