As proteins are the ultimate bearers of organismal structure and function, it is now believed that the diversity of proteins as well as the interactions between the proteins correlates with the phenotypic complexity. The study of proteomics proceeds extensively after the genome projects. However, proteins are different from nucleic acids. Many proteins are subjected to a wide variety of chemical modifications after translation. A lot of these post-translational modifications, such as phosphorylation, ubiquitination, methylation, acetylation, glycosylation, oxidation, nitrosylation and protein splicing, are critical to the protein functions. The modified proteins display different physical and chemical properties and biological functions from the unmodified. If a modified protein can be seen as a new protein, then the size of the proteome would be much larger than the number of genes. The number of proteins in a living organism may never be accurately counted as the number of genes, because every modified protein can only be individually studied. That is technically much more difficult because different proteins have different properties. A proteomic study can become quite complex even if the object of the study is very restricted. Therefore, it seems difficult to calculate the phenotypic complexity of an organism at least at the present time.