What if I came to your lab and said that I needed to see every bit of every protein in a sample? I bet you'd 1) think I was crazy and 2) would have some pretty good ideas for finding peptides that you normally miss.
We compromise because we know we have to. Not everything sticks well to C-18. Good peptides are below and above the mass range of our instrument settings. Molecular weight cutoff filters like we use in FASP lose some cool small signaling molecules. Just a few examples. I'm sure you can come up with others.
But if you really had to do it, how low could you go? Great question, right? And that's why we have awesome projects like the C-HPP. A brand new chapter from this endeavor is in this month's JPR (here!)
In this study they do this...
Yeah....glad it was them and not me. That is a LOOOOONNNNGGGG day (semester?) of wet bench work, not to mention instrument run time.
How'd they do? ~9000 proteins. Not too shabby. But that's not even the goal. The goal was trying to hunt down missing proteins. Things that look like they should be expressed from what we know of the chromosome and exons/introns and what not. And they found at least 30 of them! One step closer to the complete proteome!
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