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?