Your question is so broad and without context (to do what with, for which protein, in what, to resolve it from what, at what levels or concentrations, does it need to be intact... and run HPLC for what purpose or goal?) that a constructive answer is not possible. Before asking for help, please take the time to understand and research (on your own) what it is you wish to do, and why. Additionally, HPLC is a technique that requires many years of professional experience just to achieve a basic level of proficiency. Get some local help from an experienced chromatographer at your University for this project. They will be able to guide you in a plan that is realistic to achieve your goal.
Once you have articulated the details of your task, please try a keyword search on the web to find related articles, white papers, application notes, journal references with more information and examples.
PS: a water soluble protein may be dissolved and run in a large number of possible aqueous based mobile phases. The question is not the mobile phase (though understanding solubility is very important), but which HPLC column would be most appropriate for the proposed analysis (which was not identified). As your are a student at school, please get some local help to answer these questions and you will start off your project in positive direction.
Just ran across the discussion, this is where you always start. The solution also depends on the matrix, your peptide and its properties. Check pubmed with respective key words. Typically gives good leads.
You will have to define what this means; "to perform various characterizations using HPLC" before you can proceed. That is an extremely general statement and provide no goals for method development. Characterize it from what?
Since you know what the compound is, please try a keyword search on the web to find related articles, white papers, application notes, journal references with more information and examples.