Proteomics

A proteome is the entire set of proteins coded and producible or produced (active proteome) by an organism or system.

Just like in a computer we have data separated by curly braces or indentation that define computer software functions, the DNA has start and stop codons, that codes genes, that code peptides or proteins. The proteins, when produced, are a bit like actively deployed instances of functions (they are like computer system processes).

So, imagine that a cell is a computer, and a set of proteins that instantiated in it are the processes of functions. A living cell is the computer that is able to sustain its internal state or homeostatic equilibrium, where the membrane proteins and internal processing proteins are together producing equilibria as their phase space portraits with "stable steady states".

How can we define a set of processes (proteins), that, when executed (instantiated and run) consistently (like instances of workers on a computer) create a useful system with an internal equilibrium?

How to reorganize, tweak existing living system that runs based on proteome?

Imagine that each protein behaves like a process or like an independent worker that listens only to its environmental factors like hormones, catalysts, etc., which you can think of as system parameters. Now, imagine that the cell is supposed to do something, like, e.g., a neuron to transduce electricity, or liver cell, to do blood filtering, as part of certain tissue. You need very specific external properties for that type of cell, and to diagnose, if that cell doesn't work well, then because of what specific breakdown of its set of proteins, or environmental factors. Sometimes it's easier to replace entire tissue, but sometimes, small intervention to change the "stable steady state" may be sufficient, which depends on the proteins expressed within the specific cell environment from the DNA that contains the library of all of the proteins that could be expressed.

Knowing the set of proteins (or "workers") that, when expressed, define healthy cells of specific type within each different tissue, is thus essential to answering these questions. For that, we need:

• Library of all tissue types (histology, or histomics?)
  • Library of all cell types for each different tissue.
    • Library of expressed part of proteome ("sub-proteome") for each cell type to maintain its function ( "stable steady states" of phase portrait ).
      • The cell and environment conditions (matrix) that induce the correct expression of each "sub-proteome".