Bashak, I am assuming that your CHAPS is from a 2D Gel cleanup protocol? Please do not stick to these protocols, they are often not compatible with ESI-MS. More to your question: please supply some indication of what kind of cell lines you are looking to analyze, what kind of MS equipment you are using (which will determine the quantitation approach, e.g. Spectral Counting, MSe. Top3 or similar) amd which software you have available for the task. Good advice on the protocol will partially depend on having complete information upfront.

In addition - there is a lot! of literature around this now.

Dear Chris, the CHAPs comes from the buffer I use to extract proteins from the whole cell lysate (I do not use gel spots) but the clean up kit should get rid of this. I am currently working with oral and oesophageal cancer cell lines. The whole protocol worked in someone else's hands from within our group before using the same oral cancer cell line but I seem to have CHAPs when I am processing the samples. I use Bruker Impact for ESI-MS but haven't got round to doing the quantitation yet. What I am doing now is purely optimizing the instrument by putting some complex samples through to get an idea about how the samples should look like. I have seen many protocols online but each one of them have different components so it made me wonder whether I should carry on using the protocol I have but get rid of CHAPs by using ZipTips or SCX cartridges.

Dear Bashak, ZipTips will definitely not help you with the CHAPS. Unless you are specifically after a subpopulation of proteins that is documented to require the CHAPS for solubilization, I would strongly suggest to change protocol. If you are looking for a global proteome, FASP and related techniques would be a good starting point. It is also worthwhile trying out different protocols at the beginning of a study to see which works best in your hands.