Problem with Immunoprecipitated samples - (Sep/14/2011 )

A protein that I immunoprecipitated from cell lysate, runs a little bit higher than the expected size. Has any one observed IP samples running at incorrect molecular weights on a 12% SDS-polyacrylamide gel?

Have you run this protein out on a gel before? If so, does it run at the expected size?

If not - have a look in the literature for your protein; some proteins do not run as their molecular mass would predict.

Exactly like Bob said, you should check the literature, since permanent PTMs like glycosylation can have a massive effect on the apparent molecular weight (see CD44 for a good example)