Protomatter is a substance developed by the Mi-Go,1 possibly on the basis of artifacts from the Elder Things.
Protomatter is genetically and physiologically polymorphic on the cellular level. It can mimic any terrestrial organic substance with ease and even improve on it; protomatter muscle tissue, for example, can be (if so desired by the Mi-Go) far stronger and more efficient than normal human muscle tissue. Although protomatter is proving to be useful, its implantation into humans is still problematic. Tissue rejection can occur, and the psychological repercussions of the experimental body alteration can be severe.
It has frequently been suggested on the DGML that protomatter is the same stuff from which shoggoths are made, suggesting some connection with Elder Things. It's also been suggested that perhaps both shoggoths and protomatter were derived from Ubbo-Sathla, Abhoth, or some other earthly manifestation of Shub-Niggurath.
Davide Mana has suggested that protomatter is a generic alternative to terrestrially evolved “bodies”, in the sense of Richard Dawkins' survival machine metaphor in The Selfish Gene. Protomatter gradually replaces everything except the DNA of experimental subjects, and perhaps recodes the contents of the DNA onto some other substrate. In this model, protomatter can build structures analogous (on a large scale) to those coded for in animal DNA, by actually interpreting it.