As you're using coomassie G250, I'm assuming you're trying to run a Blue Native PAGE gel. These have worked well for me in the past, but I must admit I have only run a few of these, so I'm no expert.

This was a relatively new technique when I used it a couple of years ago and I didn't find any cheap, ready made gels or marker mixes, so I made my own gels and marker mix. You can't use the same marker mix you use for you denaturing SDS PAGE gels if it is already prestained as the proteins will already be covered with other types of coomassie. I guess you could potentially use an unstained mix as long as the marker proteins are all monomeric, but most SDS-PAGE gel marker mixes don't tend to have any proteins larger than 200 kDa in them. If your protein forms multimers beyond that size, you won't have any marker as a reference on your gel. Therefore I made my own mix by using proteins from a size exclusion chromatography calibration kit, which generally contain monomeric proteins such as Catalase (~230 kDa),  Ferritin (~450 kDa) and Thyroglobulin (~670 kDa).

Hi thank you for your answer.

I think I have decided to exclude a marker because I'm not too worried about sizing my bands at this stage. But your advice is much appreciated and I will bear that in mind for the future. 

I am using a pre-cast Bis-Tris gel 3-12% from Invitrogen but hoping to use my own sample buffer because I don't have coomassie G250. My own sample buffer is Tris-HCl, glycerol and BPB. My concern was that my protein would waft away and not run properly through the gel. 

I should add that the pH is 6.8 for the sample buffer. 

I don't think I will be much help in this case, Laura.

The reason I run BN-PAGE gels is that the pI of the protein becomes irrelevant and even mixtures of different proteins will run down the gel according to size, rather than up or down the gel according to size AND charge as in old fashioned native gels.

If you're not using coomassie G250, your protein will run either down or up the gel depending on its overall charge, which means you will need to reverse the current if the protein wants to go up the gel so that it goes down instead. This is why you generally can't run mixtures of different proteins on the same gel with the old fashioned native gels. I have no experience with these native gels, but I guess you could try a little bit of your protein in one lane and see if it goes up or down. If it waft up, reverse the current (plug the red cable in the black socket and vice versa) and run the rest of the sample in another lane. Remember that native gels have to run for a long time, so you need to put the tank, the gel, the buffer, etc... in a cold room at 4oC and let them get down to that temperature. You then run the gel in the cold room as well to stop the gel from overheating during the lengthy run.

The pH of the buffer I used for BN-gels was 8.8, but I guess the pH needed for other native gels will be different.

I'm afraid this is all I know about this subject, LOL. I hope someone else chirps in and gives you better advice than me.