I have started analysing cytochromes in bacteria by LC-MS using a C4 column, but have found it impossible to obtain responses from the hydrophobic cytochromes. Anybody have a clue?

First off, I think this question would be more appropriate in a mass spec forum. if the cytochrome is hydrophobic, you must be eluting the compound in a high concentration of organic which may not be a good environment for the protons needed for ionisation of the compound. I seem to recall a paper in a mass spec journal where the analyte was beta carotene. in order to ionise it a lewis acid had to be added, perhaps by postcolumn addition.