I have a list of DNA sequences which I assume are bound by proteins. Now, I would like to identify the proteins that bind to these DNA sequences. I imagine this should be (theoretically) possible by using the DNA as a kind of fishing pole (as, e.g., immobilized on beads) in cell lysate, "catching" a protein and subsequent mass spectrometry. However, I'm not able to find papers that did something like this - can anybody point me to literature on this or to reasons why this will not work? Thank you very much in advance!
If you google "gel shift mass spec" you find a number of papers there the influence of DNA binding proteins on the electrophoretic mobility of a labelled DNA probe has been used to identify proteins that bind to a gicen DNA (or RNA) sequence, and that have then been identified by mass spectrometry analysis,
e.g http://cshprotocols.cshlp.org/content/2012/1/pdb.top067470.abstract
or https://www.mcponline.org/content/5/9/1697
You may start with this one.
Article Rapid identification of DNA-binding proteins by mass spectrometry
The required MALDI TOF is available at the core facility in Marburg
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