My main problem with the prospectus was the organization of it. I had a few example research proposals from grants my advisor had submitted, but those were not helpful. I ended up re-arranging the entire document several times. So, based on my experience, and the helpful suggestions of fellow graduate students, I've put together a list of prospectus tips.
Tips for writing your Prospectus
1. Start reading early. The first portion of your prospectus is likely a literature review. Or a long winded introduction to your topic. Either way, you will need a lot of references for this. The good news is that you can use these references over and over throughout your career. They should be the fundamental papers in your field, and some more specific ones that comment directly on your topic. The bad news is that you have to find and read them all now. Don't despair. As soon as you know your topic, start reading up on it. Make sure you take notes! By the time you get to your prospectus, you should have a wealth of paper summaries to populate the introduction.
2. Define an audience. Before you start writing, take a moment and define your audience. Yes, your committee members will probably be the only ones reading your prospectus. And they probably already know a lot about your topic. However, their goal is to see what you know. I started by assuming a basic knowledge of concepts, but no knowledge about my specific field. In oceanography, this translates to knowing the key ideas about oceanography, but not knowing the oceanography of my region of interest. When in doubt, go by this rule: If it was on your qualifying/candidacy exam, don't explain it. Or, pretend you are talking to someone who just graduated from your department, but with a completely different research project. Any base knowledge you expect them to have doesn't need to be mentioned, but the specifics of your project should be explained.
3. Tell a story. This part was hard for me because my prospectus seemed to be two different parts - an information dump, and a research proposal. There needs to be a sense of flow to your writing. I suggest approaching it like a story. Begin with a broad overview: you are introducing your audience to the topic. Then, increase in specifics and lead up to the most recent research in your field. The idea is to state it in such a way that what you plan to do comes as an obvious next step to addressing an important issue or question. This is how you can transition to the research proposal part. Now, state your research questions, describe the methods you will use to answer them, indicate any preliminary results, and finish up by stating the significance of your research. Note that I haven't given you specific section titles. Get it written first so it flows, then divide it up later as needed for your topic.
4. Be specific. AKA, how to be a scientist for real. I made the mistake in my first draft of not being specific about what I was researching. Mostly because I hadn't thought enough about it. I know better now. If you have some vague idea in your head, such as "I'm want to know more about such and such area", forget it. That does not count as a research goal. Set out extremely specific questions you want to answer, and think about exact methods you can use to answer those. It doesn't matter if you change your mind later and use a different method. Or end up answering a different question. Your committee wants to see that you can scientifically think through a problem. You also need to specifically consider potential problems or issues. Maybe the method you want to use has known failings. If you state specifically what those are and how you will deal with them, not a problem. This forces you to really consider your research and define it, which gives it a scope, and more importantly, a finishing point.
5. Write steadily. Now that you know what to write and how to write it, go write! Avoid burnout by writing for a set amount of time each day, say an hour or two. It is always easier to go back and edit than it is to write new material. If you aren't sure about a fact or figure, write it down anyways. Then, go back later and look up the reference to fix the sentence. I ended up working in a cycle. One session was spent writing. I would get to a point where I wouldn't know details or have references to back myself up. So the next session would be looking up more papers. I'd use those papers to correct what I had already written and then move on to more writing. Just remember, its not always about how much you get done in a day, but that you worked on it each day.
I hope these tips help you out as you write your prospectus. It's much more than just a writing document - its ordering your thoughts and really defining your research project.
Remember though, any comments or instructions from your advisor and committee always trump. If you aren't 100% happy, but they are, let it go. They are the ones that grant you your degree in the end. Just think of it as a lesson in collaboration.
Did you have to write a prospectus as part of your degree? Was it anything like what I've described here? Tell me if there are any tips you think I missed!