I've been using microBCA for protein concentration estimation for exosome samples. I used to get very consistent results with lysed exosome samples, however this is no longer the case and I am getting very low, and even negative protein concentrations calculated using this assay now.
I have thought it may have been something wrong with the lysis buffer, I normally used a 1% NP-40 lysis buffer, and have tried using RIPA buffer as well as a 0.1% SDS buffer. I've checked for incompatibilities with the reagents and have ruled these out.
I have also used a Bradford assay on the same samples, and instead of low and negative values, get uniformly high values, but when these samples are run on a gel, I see nothing appear using Ponceau-S or Coomassie staining suggesting there's nothing there.
I'm at a loss and any help or advice you could offer would be appreciated!