Proper sample preparation is an empirical process involving the comparison of detergent extraction versus whole cell lysate, salt concentrations, buffer types, inhibitors (to prevent degradation and loss of post-translational events), reducing agents and heating times. While labs often have their own sample preparation methods, consider optimizing your own process. Bad protein samples due to improper or sub-optimal protein preparation can result in poor Western blots. Proper protein extraction and sample preparation is critical. While some of these mistakes are perplexing, others are just plain dumb but none of them have to happen to you.
Sadly this is usually due to mistakes on the experimenter’s part. As bitter experience has likely taught you, not all Western blots are pretty.
