Hello,
I have to come up with a research project for university and I am planning to find possible binding partners of a specific signalling molecule in Drosophila. I have an antibody against the protein so I can co-precipitate the protein and its binding partners. Now my question, can I do the usal MALDI-TOF or would the data too hard to anaylse since there might be many mayn binding partners. Should I purify it before with a 2D gel to get results that I can easier interprete?

Thanks in advance
Tina

If you do an immuno-precipitation assay like that, you usually pull down quite a few protein unspecifcially. However, often a 1d gel with digest is able to resolve that. Direct MALDI MS can work sometimes, especially if your target is very dominant part of your original lysate. However, I would not bet on that. If you have access to a decent LC-MS you can omit the gel.