I think you could very successfully argue that sample prep may be the aspect of proteomics where the most chaos is introduced. This is particularly true if you are accepting samples from multiple sources. Digestion is one of those steps. How much detergent (if any), urea (if any), reduction and alkylation techniques (and on and on) are all highly variable. I'm not sure I know two people who do this exactly the same way. And even when you do this the same way, there is still variability (see this very thorough analysis this year from Piehowski, et al., from May of this year).
Perfinity is a company in Indiana that wants to remove the variables from your protein digestion. They do this by employing a thermocycler and some very cool and very proprietary techniques to obtain reproducible and incredibly thorough digestion and peptide map coverage. The technique, called, flash digestion can digest up to 96 samples at once and has the potential for creating these digestions in as little as 4 minutes.
For more information, see the Perfinity website.
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