Is protein denaturation the key to the serum proteomics?

Serum and plasma proteomics experiments suck.  They just do.  With modern instrumentation you can take a cell pellet from just about anything and knock out an easy 2,000 plus unique proteins.  But then someone brings you some plasma or serum.  You do a BCA assay and it's the highest protein concentration you've ever seen.  So you digest it exactly the same way, pop it onto the instrument and walk away with 300 or 400 proteins and see that less than 10% of your spectra matched anything in your database.

You have options to increase this coverage.  You can deplete with a fancy column or these sweet new spin cartridges I haven't had a chance to try yet, or you can go to 2- or 3- dimensional fractionation, but you never get to the number of proteins that you can find in any cell pellet.  There are lots of explanations for this; the dynamic range is terrible, 15 or so proteins make up >90% of plasma proteins, there are glycos and lipids everywhere, and on and on.  The worst part of all of this is that we know that plasma contains a wealth of information about the physiological condition of the animal it comes from.  But we have to go to herculean efforts to see anything in there.

What if there was a factor that we weren't considering?  Vincenzo Verdoliva thinks that there is a really simple one.  In this new paper at Plos One, Verdoliva et al., examine the effect that denaturation conditions affect our ability to see into the serum proteome.  They try nearly 70 different protocols to denature serum proteins and find that changing these conditions dramatically changes what we can find by LC-MS/MS analysis.  In an even simpler way, they find that these conditions even change how the plasma proteins look on an SDS-PAGE gel.

The researchers seem as surprised by these findings as I am.  Proteins just denature, right?  Why would wouldn't they do it the same way in serum as in everything else?  They do a pretty good job of leaving this story open-ended by stating that further study into denaturing proteins is obviously needed to see what effect this is really having on our ability to see what we want to.

If you are doing serum or plasma proteomics, you should give the aptly named "Differential Denaturation of Serum Proteome Reveals a Significant Amount of Hidden Information in Complex Mixtures of Proteins," a read.  It is definitely worth thinking about.