Protein analytics is not trivial. This is due to the facts that
1) there are so many different proteins. While about 10.000 genes may be transcribed per cell, each single gene transcript may give rise to more than hundred different protein entities.
2) Proteins occur in very different abundances. Compared to e.g. cytoskeletal proteins, some signaling proteins may be million-fold or even less abundant. It is a hard analytical challenge, to identify and quantify them out of one complex protein mixture.
3) Not all proteins existing in a sample may be accessible for quantification. Proteins may occur in tight, large and dense complexes or polymers, which may be resistant to standard protein solving or proteolytic protocols. As a consequence, only solubilised proteins can be observed by analytical techniques, while larger complexes remain virtually invisible. Quite often this invisible part is simply ignored, which results in incorrect protein quantification data.
Currently there is no strategy available to overcome all these problems. The only way is to improve the protocols being aware of limitations, and to apply different strategies in order to reproduce the data in independent ways.
