ABSTRACT
The objective in many proteomics experiments is to identify proteins whose abundance differs across two or more related samples. For example, the proteome varies according to cell type, developmental stage and the cell state (e.g. stage of the cell cycle) and also responds to changes in the environment. There are also proteomic changes associated with disease, e.g. a comparison of normal skin and squamous cell carcinoma might reveal a set of proteins unique to the disease. Once identified, these proteins could be useful as disease markers and might even represent potential new therapeutic targets. Unfortunately, there are very few proteins that show such unambiguous on/off changes. More often, the difference between samples is one of degree. Therefore, the accurate quantitation of proteins is a vital component of proteomics.
