When we harvest out our proteins for shotgun proteomics one of the first things we do is mess them all up. The proteins that get to meet our trypsin are completely inactivated by reduction and alkylation and whatever other awful things we do to them. Is there a chance this is causing problems in re-assembling the original biological picture?
No, wait, maybe we will!
Avantika Dhabaria et al., may even have a mechanism for us to figure it out! In this new paper in JPR, they introduce us to: "A high-efficiency cellular extraction system for biological proteomics!" Wait...I added the exclamation point. Holy cow. There are exclamation points everywhere! Google's analytics engine just informed me that I use those more than periods...TIME FOR MORE ELLIPSES!...
Anyway, they used acoustic pulses and all sorts of other things and compare the samples. Is this better for us downstream? Who knows! But if you have a mechanism where you should be investigating functional proteins....then you have a protocol!!
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