In the mid-1990s, as the Human Genome Project was in full swing, sci­en­tists started thinking about the pro­tein com­ple­ment of the genome, and proteomics—the iden­ti­fi­ca­tion and char­ac­ter­i­za­tion of all of an organism’s proteins—was born. Early pro­teomics methods used enzymes to digest pro­teins into pieces that could be easily ana­lyzed by mass spec­trom­etry. Those methods are now mature and rou­tinely detect pep­tides from thou­sands of pro­teins in a single run.

But the great strength of those methods is also their greatest weak­ness. What’s being ana­lyzed is no longer the actual bio­log­ical actors but the pieces left after they’ve been broken apart. Biol­o­gists and chemists are deprived of cru­cial infor­ma­tion such as the masses of intact pro­teins and the loca­tions of behavior-​​controlling mod­i­fi­ca­tions, such as the addi­tion of methyl groups, sugars, or phos­phate, that occur after a pro­tein leaves the ribo­some that cre­ated it.

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